INFO 2017-03-18 22:07:32 Beginning InterMol conversion INFO 2017-03-18 22:07:32 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:07:32 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:07:32 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1017962.inpcrd INFO 2017-03-18 22:07:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1017962/mobley_1017962_converted.input INFO 2017-03-18 22:07:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1017962/mobley_1017962_converted.cms WARNING 2017-03-18 22:07:47 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:07:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1017962/mobley_1017962_converted.inp INFO 2017-03-18 22:07:47 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1017962/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1017962/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1017962/mobley_1017962_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1017962/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -44.50883195 -44.50883195 0.00000000 0.00000000 0.00000000 0.00000000 -62.77828408 -62.77828408 coulomb total -62.77171520 -62.77533578 -0.00362058 -62.77533436 -0.00361916 -62.77524101 -0.00352581 -62.77828408 -0.00656888 coulomb-14 -18.26274160 -18.26650383 -0.00376223 0.00000000 18.26274160 -18.26640214 -0.00366054 0.00000000 18.26274160 improper 0.00000000 0.00780066 0.00780066 0.00000000 0.00000000 0.00000000 0.00000000 0.00778224 0.00778224 proper 6.69774720 6.68975368 -0.00799352 6.69755306 -0.00019414 6.69758658 -0.00016062 6.68975576 -0.00799144 vdw (SR) 0.00000000 -3.25037769 -3.25037769 0.00000000 0.00000000 0.00000000 0.00000000 11.32156928 11.32156928 vdw total 11.32148560 11.32142122 -0.00006438 11.32142158 -0.00006402 11.32138467 -0.00010093 11.32156928 0.00008368 vdw-14 14.57203520 14.57179891 -0.00023629 0.00000000 -14.57203520 14.57175525 -0.00027995 0.00000000 -14.57203520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.07730800 4.07718181 -0.00012619 4.07718181 -0.00012619 4.07724039 -0.00006761 4.07718248 -0.00012552 bond 1.94137600 1.94134443 -0.00003157 1.94134441 -0.00003159 1.94168884 0.00031284 1.94133416 -0.00004184 bonded 12.71643120 12.71608056 -0.00035064 12.71607928 -0.00035192 12.71651580 0.00008460 12.71605464 -0.00037656 dihedral 6.69774720 6.69755433 -0.00019287 6.69755306 -0.00019414 6.69758658 -0.00016062 6.69753800 -0.00020920 nonbonded -51.45022960 -51.45391456 -0.00368496 -51.45391570 -0.00368610 -51.45385635 -0.00362675 -51.45671480 -0.00648520 potential -38.73379840 -38.73783399 -0.00403559 -38.73783429 -0.00403589 -38.73742756 -0.00362916 -38.74061832 -0.00681992 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -38.73379840 Difference in potential energy from amber=>gromacs conversion: -0.00403559 Difference in potential energy from amber=>lammps conversion: -0.00403589 Difference in potential energy from amber=>desmond conversion: -0.00362916 Difference in potential energy from amber=>charmm conversion: -0.00681992 ======================================================================= INFO 2017-03-18 22:07:47 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1017962.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1017962.inpcrd') INFO 2017-03-18 22:07:48 Beginning InterMol conversion INFO 2017-03-18 22:07:48 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:07:48 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:07:48 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1019269.inpcrd INFO 2017-03-18 22:07:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1019269/mobley_1019269_converted.input INFO 2017-03-18 22:07:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1019269/mobley_1019269_converted.cms WARNING 2017-03-18 22:08:03 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:08:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1019269/mobley_1019269_converted.inp INFO 2017-03-18 22:08:03 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1019269/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1019269/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1019269/mobley_1019269_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1019269/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 11.63631697 11.63631697 0.00000000 0.00000000 0.00000000 0.00000000 -6.56578384 -6.56578384 coulomb total -6.57641120 -6.56409796 0.01231324 -6.56409769 0.01231351 -6.56409179 0.01231941 -6.56578384 0.01062736 coulomb-14 -18.20416560 -18.20041493 0.00375067 0.00000000 18.20416560 -18.20036034 0.00380526 0.00000000 18.20416560 proper 4.93795680 4.93809918 0.00014238 4.93809906 0.00014226 4.93809274 0.00013594 4.93812416 0.00016736 vdw (SR) 0.00000000 -1.02237696 -1.02237696 0.00000000 0.00000000 0.00000000 0.00000000 2.69282240 2.69282240 vdw total 2.69282240 2.69274418 -0.00007822 2.69274424 -0.00007816 2.69272341 -0.00009899 2.69282240 0.00000000 vdw-14 3.71539200 3.71512114 -0.00027086 0.00000000 -3.71539200 3.71509557 -0.00029643 0.00000000 -3.71539200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.25729200 1.25730185 0.00000985 1.25730183 0.00000983 1.25738429 0.00009229 1.25725016 -0.00004184 bond 0.75019120 0.75034831 0.00015711 0.75034831 0.00015711 0.75016477 -0.00002643 0.75035856 0.00016736 bonded 6.94544000 6.94574935 0.00030935 6.94574920 0.00030920 6.94564179 0.00020179 6.94573288 0.00029288 dihedral 4.93795680 4.93809918 0.00014238 4.93809906 0.00014226 4.93809274 0.00013594 4.93812416 0.00016736 nonbonded -3.88358880 -3.87135377 0.01223503 -3.87135365 0.01223515 -3.87136838 0.01222042 -3.87296144 0.01062736 potential 3.06185120 3.07439557 0.01254437 3.07439567 0.01254447 3.07424776 0.01239656 3.07277144 0.01092024 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 3.06185120 Difference in potential energy from amber=>gromacs conversion: 0.01254437 Difference in potential energy from amber=>lammps conversion: 0.01254447 Difference in potential energy from amber=>desmond conversion: 0.01239656 Difference in potential energy from amber=>charmm conversion: 0.01092024 ======================================================================= INFO 2017-03-18 22:08:03 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1019269.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1019269.inpcrd') INFO 2017-03-18 22:08:04 Beginning InterMol conversion INFO 2017-03-18 22:08:04 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:08:04 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1034539.inpcrd INFO 2017-03-18 22:08:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1034539/mobley_1034539_converted.input INFO 2017-03-18 22:08:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1034539/mobley_1034539_converted.cms INFO 2017-03-18 22:08:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1034539/mobley_1034539_converted.rst7 WARNING 2017-03-18 22:08:20 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:08:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1034539/mobley_1034539_converted.inp INFO 2017-03-18 22:08:20 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1034539/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1034539/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1034539/mobley_1034539_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_1034539/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1034539/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -10.40994651 -10.40994651 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -4.26073456 -4.26073456 coulomb total -4.25805680 -4.25810190 -0.00004510 -4.25810199 -0.00004519 -4.25806634 -0.00000954 -4.25805680 0.00000000 -4.26073456 -0.00267776 coulomb-14 6.15173520 6.15184461 0.00010941 0.00000000 -6.15173520 6.15188771 0.00015251 6.15173520 0.00000000 0.00000000 -6.15173520 improper 0.00000000 0.00043658 0.00043658 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00041840 0.00041840 proper 33.47743920 33.47701936 -0.00041984 33.47745594 0.00001674 33.47743389 -0.00000531 33.47743920 0.00000000 33.47702080 -0.00041840 vdw (SR) 0.00000000 -13.12412068 -13.12412068 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 31.47794744 31.47794744 vdw total 31.47832400 31.47791680 -0.00040720 31.47791690 -0.00040710 31.47826793 -0.00005607 31.47790560 -0.00041840 31.47794744 -0.00037656 vdw-14 44.60227680 44.60203748 -0.00023932 0.00000000 -44.60227680 44.60239897 0.00012217 44.60185840 -0.00041840 0.00000000 -44.60227680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.45049680 5.45054545 0.00004865 5.45054533 0.00004853 5.45050391 0.00000711 5.45049680 0.00000000 5.45058048 0.00008368 bond 4.43545840 4.43531652 -0.00014188 4.43531656 -0.00014184 4.43405764 -0.00140076 4.43545840 0.00000000 4.43533288 -0.00012552 bonded 43.36339440 43.36331792 -0.00007648 43.36331783 -0.00007657 43.36199544 -0.00139896 43.36339440 0.00000000 43.36335256 -0.00004184 dihedral 33.47743920 33.47745594 0.00001674 33.47745594 0.00001674 33.47743389 -0.00000531 33.47743920 0.00000000 33.47743920 0.00000000 nonbonded 27.22026720 27.21981490 -0.00045230 27.21981491 -0.00045229 27.22020159 -0.00006561 27.21984880 -0.00041840 27.21721288 -0.00305432 potential 70.58366160 70.58313282 -0.00052878 70.58313442 -0.00052718 70.58191394 -0.00174766 70.58324320 -0.00041840 70.58056544 -0.00309616 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 70.58366160 Difference in potential energy from amber=>gromacs conversion: -0.00052878 Difference in potential energy from amber=>lammps conversion: -0.00052718 Difference in potential energy from amber=>desmond conversion: -0.00174766 Difference in potential energy from amber=>amber conversion: -0.00041840 Difference in potential energy from amber=>charmm conversion: -0.00309616 ======================================================================= INFO 2017-03-18 22:08:20 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1034539.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1034539.inpcrd') INFO 2017-03-18 22:08:20 Beginning InterMol conversion INFO 2017-03-18 22:08:20 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:08:20 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:08:20 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1036761.inpcrd INFO 2017-03-18 22:08:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1036761/mobley_1036761_converted.input INFO 2017-03-18 22:08:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1036761/mobley_1036761_converted.cms WARNING 2017-03-18 22:08:36 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:08:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1036761/mobley_1036761_converted.inp INFO 2017-03-18 22:08:36 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1036761/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1036761/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1036761/mobley_1036761_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1036761/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 19.00940919 19.00940919 0.00000000 0.00000000 0.00000000 0.00000000 -36.33632456 -36.33632456 coulomb total -36.32799840 -36.32113685 0.00686155 -36.32113664 0.00686176 -36.32113815 0.00686025 -36.33632456 -0.00832616 coulomb-14 -55.32545040 -55.33054603 -0.00509563 0.00000000 55.32545040 -55.33042559 -0.00497519 0.00000000 55.32545040 proper 16.73851040 16.73845876 -0.00005164 16.73845894 -0.00005146 16.73826166 -0.00024874 16.73851040 0.00000000 vdw (SR) 0.00000000 -3.16226087 -3.16226087 0.00000000 0.00000000 0.00000000 0.00000000 10.05335704 10.05335704 vdw total 10.05331520 10.05328594 -0.00002926 10.05328633 -0.00002887 10.05316435 -0.00015085 10.05335704 0.00004184 vdw-14 13.21558240 13.21554681 -0.00003559 0.00000000 -13.21558240 13.21542270 -0.00015970 0.00000000 -13.21558240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 22.13503360 22.13522027 0.00018667 22.13522021 0.00018661 22.13501912 -0.00001448 22.13532648 0.00029288 bond 2.44471120 2.44458745 -0.00012375 2.44458744 -0.00012376 2.44421680 -0.00049440 2.44458568 -0.00012552 bonded 41.31825520 41.31826648 0.00001128 41.31826658 0.00001138 41.31749759 -0.00075761 41.31842256 0.00016736 dihedral 16.73851040 16.73845876 -0.00005164 16.73845894 -0.00005146 16.73826166 -0.00024874 16.73851040 0.00000000 nonbonded -26.27468320 -26.26785091 0.00683229 -26.26785031 0.00683289 -26.26797380 0.00670940 -26.28296752 -0.00828432 potential 15.04357200 15.05041558 0.00684358 15.05041619 0.00684419 15.04946876 0.00589676 15.03541320 -0.00815880 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 15.04357200 Difference in potential energy from amber=>gromacs conversion: 0.00684358 Difference in potential energy from amber=>lammps conversion: 0.00684419 Difference in potential energy from amber=>desmond conversion: 0.00589676 Difference in potential energy from amber=>charmm conversion: -0.00815880 ======================================================================= INFO 2017-03-18 22:08:36 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1036761.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1036761.inpcrd') INFO 2017-03-18 22:08:36 Beginning InterMol conversion INFO 2017-03-18 22:08:36 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:08:36 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1046331.inpcrd INFO 2017-03-18 22:08:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1046331/mobley_1046331_converted.input INFO 2017-03-18 22:08:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1046331/mobley_1046331_converted.cms INFO 2017-03-18 22:08:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1046331/mobley_1046331_converted.rst7 WARNING 2017-03-18 22:08:52 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:08:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1046331/mobley_1046331_converted.inp INFO 2017-03-18 22:08:52 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1046331/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1046331/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1046331/mobley_1046331_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_1046331/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1046331/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 60.74080040 60.74080040 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -31.81438288 -31.81438288 coulomb total -31.80969680 -31.80586033 0.00383647 -31.80586007 0.00383673 -31.80588685 0.00380995 -31.80969680 0.00000000 -31.81438288 -0.00468608 coulomb-14 -92.54505920 -92.54666073 -0.00160153 0.00000000 92.54505920 -92.54664786 -0.00158866 -92.54505920 0.00000000 0.00000000 92.54505920 improper 0.00000000 0.00010332 0.00010332 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 15.06365520 15.06340685 -0.00024835 15.06351002 -0.00014518 15.06350738 -0.00014782 15.06365520 0.00000000 15.06340416 -0.00025104 vdw (SR) 0.00000000 -4.19561899 -4.19561899 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 17.73183384 17.73183384 vdw total 17.73179200 17.73184153 0.00004953 17.73184137 0.00004937 17.73206998 0.00027798 17.73179200 0.00000000 17.73183384 0.00004184 vdw-14 21.92750720 21.92746052 -0.00004668 0.00000000 -21.92750720 21.92767293 0.00016573 21.92750720 0.00000000 0.00000000 -21.92750720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.87266240 5.87278536 0.00012296 5.87278541 0.00012301 5.87249161 -0.00017079 5.87266240 0.00000000 5.87278792 0.00012552 bond 6.44084960 6.44065076 -0.00019884 6.44065086 -0.00019874 6.44040877 -0.00044083 6.44084960 0.00000000 6.44064040 -0.00020920 bonded 27.37716720 27.37694629 -0.00022091 27.37694628 -0.00022092 27.37640776 -0.00075944 27.37716720 0.00000000 27.37691616 -0.00025104 dihedral 15.06365520 15.06351018 -0.00014502 15.06351002 -0.00014518 15.06350738 -0.00014782 15.06365520 0.00000000 15.06348784 -0.00016736 nonbonded -14.07790480 -14.07401880 0.00388600 -14.07401828 0.00388652 -14.07381686 0.00408794 -14.07790480 0.00000000 -14.08254904 -0.00464424 potential 13.29926240 13.30292749 0.00366509 13.30292758 0.00366518 13.30253738 0.00327498 13.29926240 0.00000000 13.29440896 -0.00485344 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 13.29926240 Difference in potential energy from amber=>gromacs conversion: 0.00366509 Difference in potential energy from amber=>lammps conversion: 0.00366518 Difference in potential energy from amber=>desmond conversion: 0.00327498 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.00485344 ======================================================================= INFO 2017-03-18 22:08:52 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1046331.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1046331.inpcrd') INFO 2017-03-18 22:08:52 Beginning InterMol conversion INFO 2017-03-18 22:08:52 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:08:52 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:08:52 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1075836.inpcrd INFO 2017-03-18 22:08:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1075836/mobley_1075836_converted.input INFO 2017-03-18 22:08:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1075836/mobley_1075836_converted.cms WARNING 2017-03-18 22:09:08 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:09:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1075836/mobley_1075836_converted.inp INFO 2017-03-18 22:09:08 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1075836/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1075836/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1075836/mobley_1075836_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1075836/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -83.08258397 -83.08258397 0.00000000 0.00000000 0.00000000 0.00000000 -61.78977224 -61.78977224 coulomb total -61.74956400 -61.74893658 0.00062742 -61.74893640 0.00062760 -61.74882059 0.00074341 -61.78977224 -0.04020824 coulomb-14 21.33798160 21.33364739 -0.00433421 0.00000000 -21.33798160 21.33369543 -0.00428617 0.00000000 -21.33798160 improper 0.00000000 0.00000832 0.00000832 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 3.26895920 3.26903867 0.00007947 3.26904694 0.00008774 3.26907604 0.00011684 3.26904288 0.00008368 vdw (SR) 0.00000000 -1.04973359 -1.04973359 0.00000000 0.00000000 0.00000000 0.00000000 9.15693504 9.15693504 vdw total 9.15668400 9.15685374 0.00016974 9.15685387 0.00016987 9.15670723 0.00002323 9.15693504 0.00025104 vdw-14 10.20644960 10.20658733 0.00013773 0.00000000 -10.20644960 10.20644583 -0.00000377 0.00000000 -10.20644960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.62420480 2.62426955 0.00006475 2.62426957 0.00006477 2.62433988 0.00013508 2.62428848 0.00008368 bond 1.72380800 1.72385331 0.00004531 1.72385331 0.00004531 1.72376041 -0.00004759 1.72384984 0.00004184 bonded 7.61697200 7.61716984 0.00019784 7.61716982 0.00019782 7.61717633 0.00020433 7.61718120 0.00020920 dihedral 3.26895920 3.26904699 0.00008779 3.26904694 0.00008774 3.26907604 0.00011684 3.26904288 0.00008368 nonbonded -52.59288000 -52.59208284 0.00079716 -52.59208086 0.00079914 -52.59211335 0.00076665 -52.63283720 -0.03995720 potential -44.97590800 -44.97491300 0.00099500 -44.97491221 0.00099579 -44.97496869 0.00093931 -45.01565600 -0.03974800 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -44.97590800 Difference in potential energy from amber=>gromacs conversion: 0.00099500 Difference in potential energy from amber=>lammps conversion: 0.00099579 Difference in potential energy from amber=>desmond conversion: 0.00093931 Difference in potential energy from amber=>charmm conversion: -0.03974800 ======================================================================= INFO 2017-03-18 22:09:08 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1075836.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1075836.inpcrd') INFO 2017-03-18 22:09:08 Beginning InterMol conversion INFO 2017-03-18 22:09:08 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:09:08 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1079207.inpcrd INFO 2017-03-18 22:09:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1079207/mobley_1079207_converted.input INFO 2017-03-18 22:09:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1079207/mobley_1079207_converted.cms INFO 2017-03-18 22:09:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1079207/mobley_1079207_converted.rst7 WARNING 2017-03-18 22:09:24 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:09:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1079207/mobley_1079207_converted.inp INFO 2017-03-18 22:09:24 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1079207/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1079207/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1079207/mobley_1079207_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_1079207/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1079207/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 14.39061017 14.39061017 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -15.83146104 -15.83146104 coulomb total -15.84480800 -15.83437924 0.01042876 -15.83437896 0.01042904 -15.83435474 0.01045326 -15.84480800 0.00000000 -15.83146104 0.01334696 coulomb-14 -30.22772640 -30.22498940 0.00273700 0.00000000 30.22772640 -30.22496329 0.00276311 -30.22772640 0.00000000 0.00000000 30.22772640 improper 0.00000000 0.00001719 0.00001719 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00000000 0.00018401 0.00018401 0.00020119 0.00020119 0.00019851 0.00019851 0.00000000 0.00000000 0.00016736 0.00016736 vdw (SR) 0.00000000 -1.70129080 -1.70129080 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 14.01899408 14.01899408 vdw total 14.01891040 14.01899519 0.00008479 14.01899534 0.00008494 14.01903408 0.00012368 14.01891040 0.00000000 14.01899408 0.00008368 vdw-14 15.72012480 15.72028599 0.00016119 0.00000000 -15.72012480 15.72031856 0.00019376 15.72012480 0.00000000 0.00000000 -15.72012480 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.26526560 0.26525977 -0.00000583 0.26525977 -0.00000583 0.26534580 0.00008020 0.26526560 0.00000000 0.26526560 0.00000000 bond 0.89704960 0.89721179 0.00016219 0.89721177 0.00016217 0.89694849 -0.00010111 0.89704960 0.00000000 0.89721696 0.00016736 bonded 1.16231520 1.16267276 0.00035756 1.16267273 0.00035753 1.16249280 0.00017760 1.16231520 0.00000000 1.16264992 0.00033472 dihedral 0.00000000 0.00020121 0.00020121 0.00020119 0.00020119 0.00019851 0.00019851 0.00000000 0.00000000 0.00016736 0.00016736 nonbonded -1.82589760 -1.81538404 0.01051356 -1.81538388 0.01051372 -1.81532066 0.01057694 -1.82589760 0.00000000 -1.81246696 0.01343064 potential -0.66358240 -0.65271128 0.01087112 -0.65271111 0.01087129 -0.65288244 0.01069996 -0.66358240 0.00000000 -0.64981704 0.01376536 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -0.66358240 Difference in potential energy from amber=>gromacs conversion: 0.01087112 Difference in potential energy from amber=>lammps conversion: 0.01087129 Difference in potential energy from amber=>desmond conversion: 0.01069996 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.01376536 ======================================================================= INFO 2017-03-18 22:09:24 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1079207.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1079207.inpcrd') INFO 2017-03-18 22:09:24 Beginning InterMol conversion INFO 2017-03-18 22:09:24 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:09:24 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:09:24 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1107178.inpcrd INFO 2017-03-18 22:09:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1107178/mobley_1107178_converted.input INFO 2017-03-18 22:09:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1107178/mobley_1107178_converted.cms WARNING 2017-03-18 22:09:40 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:09:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1107178/mobley_1107178_converted.inp INFO 2017-03-18 22:09:40 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1107178/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1107178/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1107178/mobley_1107178_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1107178/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -3.47824288 -3.47824288 coulomb total -3.47899600 -3.47787843 0.00111757 -3.47787841 0.00111759 -3.47786962 0.00112638 -3.47824288 0.00075312 coulomb-14 -3.47899600 -3.47787843 0.00111757 0.00000000 3.47899600 -3.47786962 0.00112638 0.00000000 3.47899600 proper 0.01004160 0.00995365 -0.00008795 0.00995364 -0.00008796 0.00995660 -0.00008500 0.00995792 -0.00008368 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.06527040 0.06527040 vdw total 0.06527040 0.06524153 -0.00002887 0.06524153 -0.00002887 0.06525469 -0.00001571 0.06527040 0.00000000 vdw-14 0.06527040 0.06524153 -0.00002887 0.00000000 -0.06527040 0.06525469 -0.00001571 0.00000000 -0.06527040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.80495360 2.80487377 -0.00007983 2.80487377 -0.00007983 2.80511185 0.00015825 2.80491176 -0.00004184 bond 1.31252080 1.31254913 0.00002833 1.31254913 0.00002833 1.31236506 -0.00015574 1.31256264 0.00004184 bonded 4.12751600 4.12737655 -0.00013945 4.12737653 -0.00013947 4.12743352 -0.00008248 4.12743232 -0.00008368 dihedral 0.01004160 0.00995365 -0.00008795 0.00995364 -0.00008796 0.00995660 -0.00008500 0.00995792 -0.00008368 nonbonded -3.41372560 -3.41263691 0.00108869 -3.41263688 0.00108872 -3.41261493 0.00111067 -3.41297248 0.00075312 potential 0.71379040 0.71473964 0.00094924 0.71473967 0.00094927 0.71479590 0.00100550 0.71441800 0.00062760 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 0.71379040 Difference in potential energy from amber=>gromacs conversion: 0.00094924 Difference in potential energy from amber=>lammps conversion: 0.00094927 Difference in potential energy from amber=>desmond conversion: 0.00100550 Difference in potential energy from amber=>charmm conversion: 0.00062760 ======================================================================= INFO 2017-03-18 22:09:40 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1107178.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1107178.inpcrd') INFO 2017-03-18 22:09:40 Beginning InterMol conversion INFO 2017-03-18 22:09:40 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:09:40 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:09:40 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1139153.inpcrd INFO 2017-03-18 22:09:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1139153/mobley_1139153_converted.input INFO 2017-03-18 22:09:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1139153/mobley_1139153_converted.cms WARNING 2017-03-18 22:09:56 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:09:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1139153/mobley_1139153_converted.inp INFO 2017-03-18 22:09:56 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1139153/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1139153/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1139153/mobley_1139153_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1139153/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 21.98822857 21.98822857 0.00000000 0.00000000 0.00000000 0.00000000 -17.63313328 -17.63313328 coulomb total -17.62761040 -17.63278327 -0.00517287 -17.63278308 -0.00517268 -17.63345235 -0.00584195 -17.63313328 -0.00552288 coulomb-14 -39.62289840 -39.62101184 0.00188656 0.00000000 39.62289840 -39.62102204 0.00187636 0.00000000 39.62289840 proper 16.57115040 16.57116024 0.00000984 16.57116044 0.00001004 16.57116605 0.00001565 16.57115040 0.00000000 vdw (SR) 0.00000000 695.45018075 695.45018075 0.00000000 0.00000000 0.00000000 0.00000000 715.89767160 715.89767160 vdw total 715.89788080 715.89099232 -0.00688848 715.89101904 -0.00686176 715.88615828 -0.01172252 715.89767160 -0.00020920 vdw-14 20.44093200 20.44081157 -0.00012043 0.00000000 -20.44093200 20.44098325 0.00005125 0.00000000 -20.44093200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 9.22362800 9.22380581 0.00017781 9.22380582 0.00017782 9.22403778 0.00040978 9.22375352 0.00012552 bond 1.27151760 1.27153302 0.00001542 1.27153300 0.00001540 1.27169021 0.00017261 1.27151760 0.00000000 bonded 27.06629600 27.06649907 0.00020307 27.06649926 0.00020326 27.06689404 0.00059804 27.06642152 0.00012552 dihedral 16.57115040 16.57116024 0.00000984 16.57116044 0.00001004 16.57116605 0.00001565 16.57115040 0.00000000 nonbonded 698.27027040 698.25820905 -0.01206135 698.25822048 -0.01204992 698.25270593 -0.01756447 698.26453832 -0.00573208 potential 725.33656640 725.32470812 -0.01185828 725.32472568 -0.01184072 725.31952497 -0.01704143 725.33100168 -0.00556472 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 725.33656640 Difference in potential energy from amber=>gromacs conversion: -0.01185828 Difference in potential energy from amber=>lammps conversion: -0.01184072 Difference in potential energy from amber=>desmond conversion: -0.01704143 Difference in potential energy from amber=>charmm conversion: -0.00556472 ======================================================================= INFO 2017-03-18 22:09:56 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1139153.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1139153.inpcrd') INFO 2017-03-18 22:09:56 Beginning InterMol conversion INFO 2017-03-18 22:09:56 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:09:56 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:09:56 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1144156.inpcrd INFO 2017-03-18 22:09:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1144156/mobley_1144156_converted.input INFO 2017-03-18 22:09:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1144156/mobley_1144156_converted.cms WARNING 2017-03-18 22:10:12 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:10:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1144156/mobley_1144156_converted.inp INFO 2017-03-18 22:10:12 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1144156/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1144156/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1144156/mobley_1144156_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1144156/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 13.72408051 13.72408051 0.00000000 0.00000000 0.00000000 0.00000000 -29.92007688 -29.92007688 coulomb total -29.91936560 -29.91785581 0.00150979 -29.91785559 0.00151001 -29.91786856 0.00149704 -29.92007688 -0.00071128 coulomb-14 -43.63870160 -43.64193633 -0.00323473 0.00000000 43.63870160 -43.64194169 -0.00324009 0.00000000 43.63870160 proper 6.34294400 6.34310969 0.00016569 6.34310969 0.00016569 6.34310822 0.00016422 6.34311136 0.00016736 vdw (SR) 0.00000000 -1.28714076 -1.28714076 0.00000000 0.00000000 0.00000000 0.00000000 2.68524936 2.68524936 vdw total 2.68529120 2.68518047 -0.00011073 2.68518049 -0.00011071 2.68519021 -0.00010099 2.68524936 -0.00004184 vdw-14 3.97228960 3.97232123 0.00003163 0.00000000 -3.97228960 3.97232556 0.00003596 0.00000000 -3.97228960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.63638640 0.63626841 -0.00011799 0.63626841 -0.00011799 0.63622567 -0.00016073 0.63630272 -0.00008368 bond 2.07902960 2.07908988 0.00006028 2.07908989 0.00006029 2.07859293 -0.00043667 2.07907144 0.00004184 bonded 9.05836000 9.05846797 0.00010797 9.05846799 0.00010799 9.05792682 -0.00043318 9.05848552 0.00012552 dihedral 6.34294400 6.34310969 0.00016569 6.34310969 0.00016569 6.34310822 0.00016422 6.34311136 0.00016736 nonbonded -27.23407440 -27.23267534 0.00139906 -27.23267485 0.00139955 -27.23267836 0.00139604 -27.23482752 -0.00075312 potential -18.17571440 -18.17420737 0.00150703 -18.17420690 0.00150750 -18.17477635 0.00093805 -18.17630016 -0.00058576 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -18.17571440 Difference in potential energy from amber=>gromacs conversion: 0.00150703 Difference in potential energy from amber=>lammps conversion: 0.00150750 Difference in potential energy from amber=>desmond conversion: 0.00093805 Difference in potential energy from amber=>charmm conversion: -0.00058576 ======================================================================= INFO 2017-03-18 22:10:12 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1144156.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1144156.inpcrd') INFO 2017-03-18 22:10:12 Beginning InterMol conversion INFO 2017-03-18 22:10:12 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:10:13 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:10:13 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1160109.inpcrd INFO 2017-03-18 22:10:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1160109/mobley_1160109_converted.input INFO 2017-03-18 22:10:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1160109/mobley_1160109_converted.cms WARNING 2017-03-18 22:10:28 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:10:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1160109/mobley_1160109_converted.inp INFO 2017-03-18 22:10:28 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1160109/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1160109/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1160109/mobley_1160109_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1160109/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -32.51489988 -32.51489988 0.00000000 0.00000000 0.00000000 0.00000000 -35.80914056 -35.80914056 coulomb total -35.81294800 -35.82004462 -0.00709662 -35.82004406 -0.00709606 -35.82001345 -0.00706545 -35.80914056 0.00380744 coulomb-14 -3.30577840 -3.30514474 0.00063366 0.00000000 3.30577840 -3.30507420 0.00070420 0.00000000 3.30577840 improper 0.00000000 0.57741872 0.57741872 0.00000000 0.00000000 0.00000000 0.00000000 0.57743384 0.57743384 proper 40.50488560 39.92747071 -0.57741489 40.50490694 0.00002134 40.50499530 0.00010970 39.92753544 -0.57735016 vdw (SR) 0.00000000 -4.60679872 -4.60679872 0.00000000 0.00000000 0.00000000 0.00000000 20.11658832 20.11658832 vdw total 20.11667200 20.11643494 -0.00023706 20.11643519 -0.00023681 20.11643728 -0.00023472 20.11658832 -0.00008368 vdw-14 24.72325600 24.72323366 -0.00002234 0.00000000 -24.72325600 24.72319947 -0.00005653 0.00000000 -24.72325600 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.97438160 3.97446088 0.00007928 3.97446089 0.00007929 3.97444432 0.00006272 3.97433976 -0.00004184 bond 2.66897360 2.66878663 -0.00018697 2.66878662 -0.00018698 2.66911145 0.00013785 2.66880624 -0.00016736 bonded 47.14824080 47.14813694 -0.00010386 47.14815444 -0.00008636 47.14855107 0.00031027 47.14811528 -0.00012552 dihedral 40.50488560 40.50488943 0.00000383 40.50490694 0.00002134 40.50499530 0.00010970 40.50496928 0.00008368 nonbonded -15.69627600 -15.70360968 -0.00733368 -15.70360888 -0.00733288 -15.70357617 -0.00730017 -15.69255224 0.00372376 potential 31.45196480 31.44452726 -0.00743754 31.44454531 -0.00741949 31.44486459 -0.00710021 31.45552120 0.00355640 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 31.45196480 Difference in potential energy from amber=>gromacs conversion: -0.00743754 Difference in potential energy from amber=>lammps conversion: -0.00741949 Difference in potential energy from amber=>desmond conversion: -0.00710021 Difference in potential energy from amber=>charmm conversion: 0.00355640 ======================================================================= INFO 2017-03-18 22:10:28 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1160109.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1160109.inpcrd') INFO 2017-03-18 22:10:29 Beginning InterMol conversion INFO 2017-03-18 22:10:29 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:10:29 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1178614.inpcrd INFO 2017-03-18 22:10:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1178614/mobley_1178614_converted.input INFO 2017-03-18 22:10:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1178614/mobley_1178614_converted.cms INFO 2017-03-18 22:10:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1178614/mobley_1178614_converted.rst7 WARNING 2017-03-18 22:10:44 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:10:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1178614/mobley_1178614_converted.inp INFO 2017-03-18 22:10:44 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1178614/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1178614/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1178614/mobley_1178614_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_1178614/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1178614/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -27.96914241 -27.96914241 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -41.24754560 -41.24754560 coulomb total -41.27348640 -41.25982516 0.01366124 -41.25982480 0.01366160 -41.25961657 0.01386983 -41.27348640 0.00000000 -41.24754560 0.02594080 coulomb-14 -13.28880240 -13.29068275 -0.00188035 0.00000000 13.28880240 -13.29057734 -0.00177494 -13.28880240 0.00000000 0.00000000 13.28880240 improper 0.00000000 0.00001457 0.00001457 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00000000 0.00017717 0.00017717 0.00019170 0.00019170 0.00018804 0.00018804 0.00000000 0.00000000 0.00016736 0.00016736 vdw (SR) 0.00000000 -1.48976154 -1.48976154 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 15.98689664 15.98689664 vdw total 15.98664560 15.98686014 0.00021454 15.98686024 0.00021464 15.98695182 0.00030622 15.98664560 0.00000000 15.98689664 0.00025104 vdw-14 17.47656800 17.47662168 0.00005368 0.00000000 -17.47656800 17.47671206 0.00014406 17.47656800 0.00000000 0.00000000 -17.47656800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.61672160 0.61656480 -0.00015680 0.61656478 -0.00015682 0.61662875 -0.00009285 0.61672160 0.00000000 0.61659608 -0.00012552 bond 0.78282640 0.78286345 0.00003705 0.78286343 0.00003703 0.78269169 -0.00013471 0.78282640 0.00000000 0.78286824 0.00004184 bonded 1.39954800 1.39961999 0.00007199 1.39961991 0.00007191 1.39950848 -0.00003952 1.39954800 0.00000000 1.39963168 0.00008368 dihedral 0.00000000 0.00019175 0.00019175 0.00019170 0.00019170 0.00018804 0.00018804 0.00000000 0.00000000 0.00016736 0.00016736 nonbonded -25.28684080 -25.27296502 0.01387578 -25.27296456 0.01387624 -25.27266475 0.01417605 -25.28684080 0.00000000 -25.26064896 0.02619184 potential -23.88729280 -23.87334503 0.01394777 -23.87334460 0.01394820 -23.87320456 0.01408824 -23.88729280 0.00000000 -23.86101728 0.02627552 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -23.88729280 Difference in potential energy from amber=>gromacs conversion: 0.01394777 Difference in potential energy from amber=>lammps conversion: 0.01394820 Difference in potential energy from amber=>desmond conversion: 0.01408824 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.02627552 ======================================================================= INFO 2017-03-18 22:10:44 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1178614.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1178614.inpcrd') INFO 2017-03-18 22:10:45 Beginning InterMol conversion INFO 2017-03-18 22:10:45 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:10:45 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:10:45 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1189457.inpcrd INFO 2017-03-18 22:10:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1189457/mobley_1189457_converted.input INFO 2017-03-18 22:10:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1189457/mobley_1189457_converted.cms WARNING 2017-03-18 22:11:00 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:11:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1189457/mobley_1189457_converted.inp INFO 2017-03-18 22:11:00 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1189457/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1189457/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1189457/mobley_1189457_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1189457/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -6.26412994 -6.26412994 0.00000000 0.00000000 0.00000000 0.00000000 -8.48381312 -8.48381312 coulomb total -8.49770400 -8.48401386 0.01369014 -8.48401395 0.01369005 -8.48407281 0.01363119 -8.48381312 0.01389088 coulomb-14 -2.22086720 -2.21988393 0.00098327 0.00000000 2.22086720 -2.21992190 0.00094530 0.00000000 2.22086720 improper 0.00000000 0.00019393 0.00019393 0.00000000 0.00000000 0.00000000 0.00000000 0.00020920 0.00020920 proper 5.01661600 5.01638510 -0.00023090 5.01658295 -0.00003305 5.01656002 -0.00005598 5.01640680 -0.00020920 vdw (SR) 0.00000000 -2.25378280 -2.25378280 0.00000000 0.00000000 0.00000000 0.00000000 13.56984168 13.56984168 vdw total 13.56954880 13.56983021 0.00028141 13.56983038 0.00028158 13.56989838 0.00034958 13.56984168 0.00029288 vdw-14 15.82346960 15.82361301 0.00014341 0.00000000 -15.82346960 15.82368499 0.00021539 0.00000000 -15.82346960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.70249360 0.70265661 0.00016301 0.70265661 0.00016301 0.70259662 0.00010302 0.70266096 0.00016736 bond 1.06440960 1.06458878 0.00017918 1.06458876 0.00017916 1.06449189 0.00008229 1.06457696 0.00016736 bonded 6.78351920 6.78382441 0.00030521 6.78382831 0.00030911 6.78364853 0.00012933 6.78385392 0.00033472 dihedral 5.01661600 5.01657902 -0.00003698 5.01658295 -0.00003305 5.01656002 -0.00005598 5.01661600 -0.00000000 nonbonded 5.07184480 5.08581634 0.01397154 5.08581643 0.01397163 5.08582557 0.01398077 5.08602856 0.01418376 potential 11.85536400 11.86964076 0.01427676 11.86964483 0.01428083 11.86941806 0.01405406 11.86979880 0.01443480 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 11.85536400 Difference in potential energy from amber=>gromacs conversion: 0.01427676 Difference in potential energy from amber=>lammps conversion: 0.01428083 Difference in potential energy from amber=>desmond conversion: 0.01405406 Difference in potential energy from amber=>charmm conversion: 0.01443480 ======================================================================= INFO 2017-03-18 22:11:00 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1189457.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1189457.inpcrd') INFO 2017-03-18 22:11:01 Beginning InterMol conversion INFO 2017-03-18 22:11:01 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:11:01 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:11:01 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1199854.inpcrd INFO 2017-03-18 22:11:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1199854/mobley_1199854_converted.input INFO 2017-03-18 22:11:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1199854/mobley_1199854_converted.cms WARNING 2017-03-18 22:11:16 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:11:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1199854/mobley_1199854_converted.inp INFO 2017-03-18 22:11:17 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1199854/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1199854/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1199854/mobley_1199854_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1199854/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -0.85810048 -0.85810048 0.00000000 0.00000000 0.00000000 0.00000000 4.30106832 4.30106832 coulomb total 4.30031520 4.30047575 0.00016055 4.30047587 0.00016067 4.30046712 0.00015192 4.30106832 0.00075312 coulomb-14 5.15845360 5.15857622 0.00012262 0.00000000 -5.15845360 5.15858581 0.00013221 0.00000000 -5.15845360 proper 0.02845120 0.02848369 0.00003249 0.02848368 0.00003248 0.02848061 0.00002941 0.02849304 0.00004184 vdw (SR) 0.00000000 -0.50962838 -0.50962838 0.00000000 0.00000000 0.00000000 0.00000000 0.76102776 0.76102776 vdw total 0.76106960 0.76099818 -0.00007142 0.76099818 -0.00007142 0.76101616 -0.00005344 0.76102776 -0.00004184 vdw-14 1.27068080 1.27062656 -0.00005424 0.00000000 -1.27068080 1.27064675 -0.00003405 0.00000000 -1.27068080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.45935520 2.45918377 -0.00017143 2.45918378 -0.00017142 2.45920912 -0.00014608 2.45922968 -0.00012552 bond 0.97403520 0.97395269 -0.00008251 0.97395269 -0.00008251 0.97399317 -0.00004203 0.97395152 -0.00008368 bonded 3.46184160 3.46162016 -0.00022144 3.46162016 -0.00022144 3.46168289 -0.00015871 3.46167424 -0.00016736 dihedral 0.02845120 0.02848369 0.00003249 0.02848368 0.00003248 0.02848061 0.00002941 0.02849304 0.00004184 nonbonded 5.06138480 5.06147393 0.00008913 5.06147392 0.00008912 5.06148328 0.00009848 5.06209608 0.00071128 potential 8.52322640 8.52309409 -0.00013231 8.52309419 -0.00013221 8.52313059 -0.00009581 8.52377032 0.00054392 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 8.52322640 Difference in potential energy from amber=>gromacs conversion: -0.00013231 Difference in potential energy from amber=>lammps conversion: -0.00013221 Difference in potential energy from amber=>desmond conversion: -0.00009581 Difference in potential energy from amber=>charmm conversion: 0.00054392 ======================================================================= INFO 2017-03-18 22:11:17 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1199854.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1199854.inpcrd') INFO 2017-03-18 22:11:17 Beginning InterMol conversion INFO 2017-03-18 22:11:17 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:11:17 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:11:17 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1231151.inpcrd INFO 2017-03-18 22:11:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1231151/mobley_1231151_converted.input INFO 2017-03-18 22:11:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1231151/mobley_1231151_converted.cms WARNING 2017-03-18 22:11:32 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:11:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1231151/mobley_1231151_converted.inp INFO 2017-03-18 22:11:33 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1231151/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1231151/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1231151/mobley_1231151_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1231151/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 8.77142552 8.77142552 0.00000000 0.00000000 0.00000000 0.00000000 -17.00001040 -17.00001040 coulomb total -17.00419440 -17.00157913 0.00261527 -17.00157898 0.00261542 -17.00158953 0.00260487 -17.00001040 0.00418400 coulomb-14 -25.76883760 -25.77300466 -0.00416706 0.00000000 25.76883760 -25.77301252 -0.00417492 0.00000000 25.76883760 proper 6.26470320 6.26473725 0.00003405 6.26473709 0.00003389 6.26473881 0.00003561 6.26474504 0.00004184 vdw (SR) 0.00000000 -0.16534044 -0.16534044 0.00000000 0.00000000 0.00000000 0.00000000 1.93731752 1.93731752 vdw total 1.93719200 1.93727790 0.00008590 1.93727794 0.00008594 1.93728736 0.00009536 1.93731752 0.00012552 vdw-14 2.10246000 2.10261833 0.00015833 0.00000000 -2.10246000 2.10261761 0.00015761 0.00000000 -2.10246000 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.76650880 0.76665293 0.00014413 0.76665294 0.00014414 0.76650857 -0.00000023 0.76667616 0.00016736 bond 0.55270640 0.55280136 0.00009496 0.55280138 0.00009498 0.55255674 -0.00014966 0.55279008 0.00008368 bonded 7.58391840 7.58419154 0.00027314 7.58419141 0.00027301 7.58380412 -0.00011428 7.58421128 0.00029288 dihedral 6.26470320 6.26473725 0.00003405 6.26473709 0.00003389 6.26473881 0.00003561 6.26474504 0.00004184 nonbonded -15.06700240 -15.06430124 0.00270116 -15.06430121 0.00270119 -15.06430217 0.00270023 -15.06269288 0.00430952 potential -7.48308400 -7.48010969 0.00297431 -7.48010959 0.00297441 -7.48052067 0.00256333 -7.47848160 0.00460240 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -7.48308400 Difference in potential energy from amber=>gromacs conversion: 0.00297431 Difference in potential energy from amber=>lammps conversion: 0.00297441 Difference in potential energy from amber=>desmond conversion: 0.00256333 Difference in potential energy from amber=>charmm conversion: 0.00460240 ======================================================================= INFO 2017-03-18 22:11:33 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1231151.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1231151.inpcrd') INFO 2017-03-18 22:11:33 Beginning InterMol conversion INFO 2017-03-18 22:11:33 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:11:33 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:11:33 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1235151.inpcrd INFO 2017-03-18 22:11:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1235151/mobley_1235151_converted.input INFO 2017-03-18 22:11:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1235151/mobley_1235151_converted.cms WARNING 2017-03-18 22:11:49 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:11:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1235151/mobley_1235151_converted.inp INFO 2017-03-18 22:11:49 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1235151/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1235151/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1235151/mobley_1235151_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1235151/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -5.12059976 -5.12059976 0.00000000 0.00000000 0.00000000 0.00000000 -12.14029440 -12.14029440 coulomb total -12.14071280 -12.14564417 -0.00493137 -12.14564406 -0.00493126 -12.14570565 -0.00499285 -12.14029440 0.00041840 coulomb-14 -7.02242560 -7.02504441 -0.00261881 0.00000000 7.02242560 -7.02503043 -0.00260483 0.00000000 7.02242560 proper 3.42460400 3.42468955 0.00008555 3.42468956 0.00008556 3.42469975 0.00009575 3.42468768 0.00008368 vdw (SR) 0.00000000 -3.38519797 -3.38519797 0.00000000 0.00000000 0.00000000 0.00000000 3.93467544 3.93467544 vdw total 3.93463360 3.93455654 -0.00007706 3.93455657 -0.00007703 3.93461225 -0.00002135 3.93467544 0.00004184 vdw-14 7.31990800 7.31975451 -0.00015349 0.00000000 -7.31990800 7.31981403 -0.00009397 0.00000000 -7.31990800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.03844480 2.03847603 0.00003123 2.03847601 0.00003121 2.03869220 0.00024740 2.03852848 0.00008368 bond 10.71982640 10.71995664 0.00013024 10.71995652 0.00013012 10.71945055 -0.00037585 10.71995192 0.00012552 bonded 16.18287520 16.18312222 0.00024702 16.18312210 0.00024690 16.18284250 -0.00003270 16.18316808 0.00029288 dihedral 3.42460400 3.42468955 0.00008555 3.42468956 0.00008556 3.42469975 0.00009575 3.42468768 0.00008368 nonbonded -8.20607920 -8.21108762 -0.00500842 -8.21108745 -0.00500825 -8.21109340 -0.00501420 -8.20561896 0.00046024 potential 7.97679600 7.97203460 -0.00476140 7.97203461 -0.00476139 7.97168156 -0.00511444 7.97754912 0.00075312 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 7.97679600 Difference in potential energy from amber=>gromacs conversion: -0.00476140 Difference in potential energy from amber=>lammps conversion: -0.00476139 Difference in potential energy from amber=>desmond conversion: -0.00511444 Difference in potential energy from amber=>charmm conversion: 0.00075312 ======================================================================= INFO 2017-03-18 22:11:49 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1235151.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1235151.inpcrd') INFO 2017-03-18 22:11:49 Beginning InterMol conversion INFO 2017-03-18 22:11:49 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:11:49 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:11:49 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1244778.inpcrd INFO 2017-03-18 22:11:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1244778/mobley_1244778_converted.input INFO 2017-03-18 22:11:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1244778/mobley_1244778_converted.cms WARNING 2017-03-18 22:12:05 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:12:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1244778/mobley_1244778_converted.inp INFO 2017-03-18 22:12:05 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1244778/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1244778/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1244778/mobley_1244778_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1244778/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 18.42931811 18.42931811 0.00000000 0.00000000 0.00000000 0.00000000 -29.91543264 -29.91543264 coulomb total -29.82899120 -29.84322848 -0.01423728 -29.84322810 -0.01423690 -29.84331056 -0.01431936 -29.91543264 -0.08644144 coulomb-14 -48.27415520 -48.27254659 0.00160861 0.00000000 48.27415520 -48.27259248 0.00156272 0.00000000 48.27415520 proper 39.20491680 39.20480987 -0.00010693 39.20480676 -0.00011004 39.20480668 -0.00011012 39.20495864 0.00004184 vdw (SR) 0.00000000 -3.36162742 -3.36162742 0.00000000 0.00000000 0.00000000 0.00000000 11.37600312 11.37600312 vdw total 11.37629600 11.37585145 -0.00044455 11.37585166 -0.00044434 11.37584832 -0.00044768 11.37600312 -0.00029288 vdw-14 14.73772160 14.73747887 -0.00024273 0.00000000 -14.73772160 14.73746843 -0.00025317 0.00000000 -14.73772160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 18.95979600 18.95981479 0.00001879 18.95981483 0.00001883 18.95960826 -0.00018774 18.95975416 -0.00004184 bond 1.34975840 1.34956588 -0.00019252 1.34956589 -0.00019251 1.34956421 -0.00019419 1.34954920 -0.00020920 bonded 59.51447120 59.51419054 -0.00028066 59.51418748 -0.00028372 59.51397915 -0.00049205 59.51426200 -0.00020920 dihedral 39.20491680 39.20480987 -0.00010693 39.20480676 -0.00011004 39.20480668 -0.00011012 39.20495864 0.00004184 nonbonded -18.45269520 -18.46737703 -0.01468183 -18.46737644 -0.01468124 -18.46746224 -0.01476704 -18.53942952 -0.08673432 potential 41.06177600 41.04681351 -0.01496249 41.04681109 -0.01496491 41.04644833 -0.01532767 40.97483248 -0.08694352 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 41.06177600 Difference in potential energy from amber=>gromacs conversion: -0.01496249 Difference in potential energy from amber=>lammps conversion: -0.01496491 Difference in potential energy from amber=>desmond conversion: -0.01532767 Difference in potential energy from amber=>charmm conversion: -0.08694352 ======================================================================= INFO 2017-03-18 22:12:05 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1244778.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1244778.inpcrd') INFO 2017-03-18 22:12:05 Beginning InterMol conversion INFO 2017-03-18 22:12:05 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:12:05 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:12:05 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1261349.inpcrd INFO 2017-03-18 22:12:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1261349/mobley_1261349_converted.input INFO 2017-03-18 22:12:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1261349/mobley_1261349_converted.cms WARNING 2017-03-18 22:12:21 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:12:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1261349/mobley_1261349_converted.inp INFO 2017-03-18 22:12:21 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1261349/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1261349/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1261349/mobley_1261349_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1261349/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 25.07559741 25.07559741 0.00000000 0.00000000 0.00000000 0.00000000 -14.67475240 -14.67475240 coulomb total -14.69169760 -14.67358108 0.01811652 -14.67358088 0.01811672 -14.67362611 0.01807149 -14.67475240 0.01694520 coulomb-14 -39.73084560 -39.74917849 -0.01833289 0.00000000 39.73084560 -39.74917361 -0.01832801 0.00000000 39.73084560 proper 0.00000000 0.00002601 0.00002601 0.00002601 0.00002601 0.00002594 0.00002594 0.00004184 0.00004184 vdw (SR) 0.00000000 -0.64801445 -0.64801445 0.00000000 0.00000000 0.00000000 0.00000000 8.71895392 8.71895392 vdw total 8.71903760 8.71884674 -0.00019086 8.71884681 -0.00019079 8.71881194 -0.00022566 8.71895392 -0.00008368 vdw-14 9.36713920 9.36686119 -0.00027801 0.00000000 -9.36713920 9.36683586 -0.00030334 0.00000000 -9.36713920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.80246720 1.80260320 0.00013600 1.80260322 0.00013602 1.80274836 0.00028116 1.80259272 0.00012552 bond 0.24183520 0.24201198 0.00017678 0.24201198 0.00017678 0.24217947 0.00034427 0.24200256 0.00016736 bonded 2.04430240 2.04464119 0.00033879 2.04464121 0.00033881 2.04495377 0.00065137 2.04463712 0.00033472 dihedral 0.00000000 0.00002601 0.00002601 0.00002601 0.00002601 0.00002594 0.00002594 0.00004184 0.00004184 nonbonded -5.97266000 -5.95473434 0.01792566 -5.95473407 0.01792593 -5.95481417 0.01784583 -5.95579848 0.01686152 potential -3.92835760 -3.91009315 0.01826445 -3.91009277 0.01826483 -3.90989442 0.01846318 -3.91116136 0.01719624 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -3.92835760 Difference in potential energy from amber=>gromacs conversion: 0.01826445 Difference in potential energy from amber=>lammps conversion: 0.01826483 Difference in potential energy from amber=>desmond conversion: 0.01846318 Difference in potential energy from amber=>charmm conversion: 0.01719624 ======================================================================= INFO 2017-03-18 22:12:21 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1261349.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1261349.inpcrd') INFO 2017-03-18 22:12:21 Beginning InterMol conversion INFO 2017-03-18 22:12:21 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:12:21 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:12:21 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1278715.inpcrd INFO 2017-03-18 22:12:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1278715/mobley_1278715_converted.input INFO 2017-03-18 22:12:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1278715/mobley_1278715_converted.cms WARNING 2017-03-18 22:12:37 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:12:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1278715/mobley_1278715_converted.inp INFO 2017-03-18 22:12:37 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1278715/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1278715/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1278715/mobley_1278715_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1278715/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 15.68920504 15.68920504 coulomb total 15.64983360 15.66102606 0.01119246 15.66102580 0.01119220 15.66104417 0.01121057 15.68920504 0.03937144 coulomb-14 15.64983360 15.66102606 0.01119246 0.00000000 -15.64983360 15.66104417 0.01121057 0.00000000 -15.64983360 proper 16.94520000 16.94519999 -0.00000001 16.94520000 0.00000000 16.94519946 -0.00000054 16.94520000 0.00000000 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 2.87896856 2.87896856 vdw total 2.87901040 2.87890009 -0.00011031 2.87890011 -0.00011029 2.87906930 0.00005890 2.87896856 -0.00004184 vdw-14 2.87901040 2.87890009 -0.00011031 0.00000000 -2.87901040 2.87906930 0.00005890 0.00000000 -2.87901040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 7.72199040 7.72210738 0.00011698 7.72210755 0.00011715 7.72227596 0.00028556 7.72199040 0.00000000 bond 3.12168240 3.12166598 -0.00001642 3.12166600 -0.00001640 3.12119682 -0.00048558 3.12168240 0.00000000 bonded 27.78887280 27.78897335 0.00010055 27.78897355 0.00010075 27.78867223 -0.00020057 27.78887280 0.00000000 dihedral 16.94520000 16.94519999 -0.00000001 16.94520000 0.00000000 16.94519946 -0.00000054 16.94520000 0.00000000 nonbonded 18.52884400 18.53992614 0.01108214 18.53992616 0.01108216 18.54011347 0.01126947 18.56817360 0.03932960 potential 46.31771680 46.32889949 0.01118269 46.32890063 0.01118383 46.32869520 0.01097840 46.35700456 0.03928776 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 46.31771680 Difference in potential energy from amber=>gromacs conversion: 0.01118269 Difference in potential energy from amber=>lammps conversion: 0.01118383 Difference in potential energy from amber=>desmond conversion: 0.01097840 Difference in potential energy from amber=>charmm conversion: 0.03928776 ======================================================================= INFO 2017-03-18 22:12:37 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1278715.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1278715.inpcrd') INFO 2017-03-18 22:12:37 Beginning InterMol conversion INFO 2017-03-18 22:12:37 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:12:37 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:12:37 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_129464.inpcrd INFO 2017-03-18 22:12:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_129464/mobley_129464_converted.input INFO 2017-03-18 22:12:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_129464/mobley_129464_converted.cms WARNING 2017-03-18 22:12:53 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:12:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_129464/mobley_129464_converted.inp INFO 2017-03-18 22:12:53 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_129464/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_129464/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_129464/mobley_129464_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_129464/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 11.19486731 11.19486731 0.00000000 0.00000000 0.00000000 0.00000000 -8.92518328 -8.92518328 coulomb total -8.90899120 -8.92766560 -0.01867440 -8.92766565 -0.01867445 -8.92770970 -0.01871850 -8.92518328 -0.01619208 coulomb-14 -20.11709040 -20.12253291 -0.00544251 0.00000000 20.11709040 -20.12253441 -0.00544401 0.00000000 20.11709040 proper 9.88595520 9.88586921 -0.00008599 9.88586901 -0.00008619 9.88583361 -0.00012159 9.88587152 -0.00008368 vdw (SR) 0.00000000 -4.11961028 -4.11961028 0.00000000 0.00000000 0.00000000 0.00000000 5.77986128 5.77986128 vdw total 5.77977760 5.77971251 -0.00006509 5.77971275 -0.00006485 5.77976803 -0.00000957 5.77986128 0.00008368 vdw-14 9.89934400 9.89932279 -0.00002121 0.00000000 -9.89934400 9.89937990 0.00003590 0.00000000 -9.89934400 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.94304960 1.94302425 -0.00002535 1.94302424 -0.00002536 1.94262129 -0.00042831 1.94300776 -0.00004184 bond 2.33927440 2.33915222 -0.00012218 2.33915223 -0.00012217 2.33802317 -0.00125123 2.33914888 -0.00012552 bonded 14.16827920 14.16804568 -0.00023352 14.16804548 -0.00023372 14.16647808 -0.00180112 14.16802816 -0.00025104 dihedral 9.88595520 9.88586921 -0.00008599 9.88586901 -0.00008619 9.88583361 -0.00012159 9.88587152 -0.00008368 nonbonded -3.12921360 -3.14795309 -0.01873949 -3.14795290 -0.01873930 -3.14794168 -0.01872808 -3.14532200 -0.01610840 potential 11.03906560 11.02009260 -0.01897300 11.02009283 -0.01897277 11.01844530 -0.02062030 11.02274800 -0.01631760 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 11.03906560 Difference in potential energy from amber=>gromacs conversion: -0.01897300 Difference in potential energy from amber=>lammps conversion: -0.01897277 Difference in potential energy from amber=>desmond conversion: -0.02062030 Difference in potential energy from amber=>charmm conversion: -0.01631760 ======================================================================= INFO 2017-03-18 22:12:53 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_129464.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_129464.inpcrd') INFO 2017-03-18 22:12:53 Beginning InterMol conversion INFO 2017-03-18 22:12:53 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:12:53 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:12:53 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1323538.inpcrd INFO 2017-03-18 22:12:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1323538/mobley_1323538_converted.input INFO 2017-03-18 22:12:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1323538/mobley_1323538_converted.cms WARNING 2017-03-18 22:13:09 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:13:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1323538/mobley_1323538_converted.inp INFO 2017-03-18 22:13:09 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1323538/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1323538/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1323538/mobley_1323538_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1323538/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 32.26171677 32.26171677 0.00000000 0.00000000 0.00000000 0.00000000 -361.03493328 -361.03493328 coulomb total -361.01183760 -361.01805963 -0.00622203 -361.01805502 -0.00621742 -361.01786536 -0.00602776 -361.03493328 -0.02309568 coulomb-14 -393.34118720 -393.27977639 0.06141081 0.00000000 393.34118720 -393.27980666 0.06138054 0.00000000 393.34118720 proper 50.25444240 50.25460198 0.00015958 50.25460139 0.00015899 50.25462399 0.00018159 50.25460976 0.00016736 vdw (SR) 0.00000000 -9.67774645 -9.67774645 0.00000000 0.00000000 0.00000000 0.00000000 -5.00937768 -5.00937768 vdw total -5.00908480 -5.00955054 -0.00046574 -5.00955090 -0.00046610 -5.00944906 -0.00036426 -5.00937768 -0.00029288 vdw-14 4.66850720 4.66819592 -0.00031128 0.00000000 -4.66850720 4.66827972 -0.00022748 0.00000000 -4.66850720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.70119040 2.70132981 0.00013941 2.70132981 0.00013941 2.70111971 -0.00007069 2.70139960 0.00020920 bond 5.85048720 5.85048602 -0.00000118 5.85048594 -0.00000126 5.85048691 -0.00000029 5.85048720 0.00000000 bonded 58.80612000 58.80641780 0.00029780 58.80641715 0.00029715 58.80623060 0.00011060 58.80649656 0.00037656 dihedral 50.25444240 50.25460198 0.00015958 50.25460139 0.00015899 50.25462399 0.00018159 50.25460976 0.00016736 nonbonded -366.02092240 -366.02761016 -0.00668776 -366.02760425 -0.00668185 -366.02731442 -0.00639202 -366.04431096 -0.02338856 potential -307.21480240 -307.22119236 -0.00638996 -307.22118718 -0.00638478 -307.22120518 -0.00640278 -307.23781440 -0.02301200 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -307.21480240 Difference in potential energy from amber=>gromacs conversion: -0.00638996 Difference in potential energy from amber=>lammps conversion: -0.00638478 Difference in potential energy from amber=>desmond conversion: -0.00640278 Difference in potential energy from amber=>charmm conversion: -0.02301200 ======================================================================= INFO 2017-03-18 22:13:09 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1323538.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1323538.inpcrd') INFO 2017-03-18 22:13:09 Beginning InterMol conversion INFO 2017-03-18 22:13:09 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:13:09 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:13:09 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1328465.inpcrd INFO 2017-03-18 22:13:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1328465/mobley_1328465_converted.input INFO 2017-03-18 22:13:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1328465/mobley_1328465_converted.cms WARNING 2017-03-18 22:13:25 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:13:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1328465/mobley_1328465_converted.inp INFO 2017-03-18 22:13:25 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1328465/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1328465/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1328465/mobley_1328465_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1328465/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.56521656 0.56521656 coulomb total 0.57613680 0.57608533 -0.00005147 0.57608534 -0.00005146 0.57608851 -0.00004829 0.56521656 -0.01092024 coulomb-14 0.57613680 0.57608533 -0.00005147 0.00000000 -0.57613680 0.57608851 -0.00004829 0.00000000 -0.57613680 proper 5.20949840 5.20961475 0.00011635 5.20961472 0.00011632 5.20961948 0.00012108 5.20962392 0.00012552 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.86884944 0.86884944 vdw total 0.86901680 0.86881281 -0.00020399 0.86881283 -0.00020397 0.86889584 -0.00012096 0.86884944 -0.00016736 vdw-14 0.86901680 0.86881281 -0.00020399 0.00000000 -0.86901680 0.86889584 -0.00012096 0.00000000 -0.86901680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.93510000 1.93500445 -0.00009555 1.93500444 -0.00009556 1.93486779 -0.00023221 1.93501632 -0.00008368 bond 0.22426240 0.22427307 0.00001067 0.22427307 0.00001067 0.22445120 0.00018880 0.22426240 0.00000000 bonded 7.36886080 7.36889228 0.00003148 7.36889223 0.00003143 7.36893848 0.00007768 7.36890264 0.00004184 dihedral 5.20949840 5.20961475 0.00011635 5.20961472 0.00011632 5.20961948 0.00012108 5.20962392 0.00012552 nonbonded 1.44515360 1.44489814 -0.00025546 1.44489812 -0.00025548 1.44498435 -0.00016925 1.43406600 -0.01108760 potential 8.81401440 8.81379042 -0.00022398 8.81379014 -0.00022426 8.81388888 -0.00012552 8.80301048 -0.01100392 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 8.81401440 Difference in potential energy from amber=>gromacs conversion: -0.00022398 Difference in potential energy from amber=>lammps conversion: -0.00022426 Difference in potential energy from amber=>desmond conversion: -0.00012552 Difference in potential energy from amber=>charmm conversion: -0.01100392 ======================================================================= INFO 2017-03-18 22:13:25 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1328465.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1328465.inpcrd') INFO 2017-03-18 22:13:25 Beginning InterMol conversion INFO 2017-03-18 22:13:25 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:13:25 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:13:25 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1328936.inpcrd INFO 2017-03-18 22:13:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1328936/mobley_1328936_converted.input INFO 2017-03-18 22:13:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1328936/mobley_1328936_converted.cms WARNING 2017-03-18 22:13:41 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:13:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1328936/mobley_1328936_converted.inp INFO 2017-03-18 22:13:41 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1328936/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1328936/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1328936/mobley_1328936_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1328936/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -169.77098139 -169.77098139 0.00000000 0.00000000 0.00000000 0.00000000 10.97463200 10.97463200 coulomb total 10.99346000 10.99595698 0.00249698 10.99595701 0.00249701 10.99643231 0.00297231 10.97463200 -0.01882800 coulomb-14 180.75423920 180.76693837 0.01269917 0.00000000 -180.75423920 180.76686442 0.01262522 0.00000000 -180.75423920 improper 0.00000000 0.00005728 0.00005728 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 8.36925520 8.36910633 -0.00014887 8.36914349 -0.00011171 8.36913177 -0.00012343 8.36908784 -0.00016736 vdw (SR) 0.00000000 1.66273051 1.66273051 0.00000000 0.00000000 0.00000000 0.00000000 38.26929072 38.26929072 vdw total 38.26937440 38.26912074 -0.00025366 38.26912085 -0.00025355 38.26938825 0.00001385 38.26929072 -0.00008368 vdw-14 36.60665280 36.60639024 -0.00026256 0.00000000 -36.60665280 36.60663920 -0.00001360 0.00000000 -36.60665280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.64256640 4.64274058 0.00017418 4.64274045 0.00017405 4.64234498 -0.00022142 4.64273376 0.00016736 bond 13.78837200 13.78850791 0.00013591 13.78850798 0.00013598 13.78706630 -0.00130570 13.78849752 0.00012552 bonded 26.80019360 26.80041210 0.00021850 26.80039192 0.00019832 26.79854305 -0.00165055 26.80036096 0.00016736 dihedral 8.36925520 8.36916361 -0.00009159 8.36914349 -0.00011171 8.36913177 -0.00012343 8.36912968 -0.00012552 nonbonded 49.26283440 49.26507773 0.00224333 49.26507702 0.00224262 49.26582057 0.00298617 49.24392272 -0.01891168 potential 76.06302800 76.06548983 0.00246183 76.06547146 0.00244346 76.06425600 0.00122800 76.04428368 -0.01874432 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 76.06302800 Difference in potential energy from amber=>gromacs conversion: 0.00246183 Difference in potential energy from amber=>lammps conversion: 0.00244346 Difference in potential energy from amber=>desmond conversion: 0.00122800 Difference in potential energy from amber=>charmm conversion: -0.01874432 ======================================================================= INFO 2017-03-18 22:13:41 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1328936.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1328936.inpcrd') INFO 2017-03-18 22:13:41 Beginning InterMol conversion INFO 2017-03-18 22:13:41 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:13:42 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:13:42 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1352110.inpcrd INFO 2017-03-18 22:13:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1352110/mobley_1352110_converted.input INFO 2017-03-18 22:13:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1352110/mobley_1352110_converted.cms WARNING 2017-03-18 22:13:57 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:13:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1352110/mobley_1352110_converted.inp INFO 2017-03-18 22:13:57 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1352110/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1352110/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1352110/mobley_1352110_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1352110/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -39.27193986 -39.27193986 0.00000000 0.00000000 0.00000000 0.00000000 -91.59424520 -91.59424520 coulomb total -91.60575120 -91.60178744 0.00396376 -91.60178477 0.00396643 -91.60144373 0.00430747 -91.59424520 0.01150600 coulomb-14 -52.33807440 -52.32984758 0.00822682 0.00000000 52.33807440 -52.32967795 0.00839645 0.00000000 52.33807440 improper 0.00000000 0.00298172 0.00298172 0.00000000 0.00000000 0.00000000 0.00000000 0.00297064 0.00297064 proper 7.52910800 7.52593195 -0.00317605 7.52891679 -0.00019121 7.52892725 -0.00018075 7.52597000 -0.00313800 vdw (SR) 0.00000000 -0.31362240 -0.31362240 0.00000000 0.00000000 0.00000000 0.00000000 21.24283744 21.24283744 vdw total 21.24300480 21.24240026 -0.00060454 21.24240063 -0.00060417 21.24164890 -0.00135590 21.24283744 -0.00016736 vdw-14 21.55638640 21.55602266 -0.00036374 0.00000000 -21.55638640 21.55573449 -0.00065191 0.00000000 -21.55638640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 12.89048560 12.89052516 0.00003956 12.89052535 0.00003975 12.89099274 0.00050714 12.89048560 0.00000000 bond 18.50917920 18.50899201 -0.00018719 18.50899218 -0.00018702 18.51113911 0.00195991 18.50901184 -0.00016736 bonded 38.92877280 38.92843084 -0.00034196 38.92843431 -0.00033849 38.93105910 0.00228630 38.92843808 -0.00033472 dihedral 7.52910800 7.52891368 -0.00019432 7.52891679 -0.00019121 7.52892725 -0.00018075 7.52894064 -0.00016736 nonbonded -70.36274640 -70.35938718 0.00335922 -70.35938665 0.00335975 -70.35979483 0.00295157 -70.35140776 0.01133864 potential -31.43397360 -31.43095634 0.00301726 -31.43095192 0.00302168 -31.42895293 0.00502067 -31.42296968 0.01100392 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -31.43397360 Difference in potential energy from amber=>gromacs conversion: 0.00301726 Difference in potential energy from amber=>lammps conversion: 0.00302168 Difference in potential energy from amber=>desmond conversion: 0.00502067 Difference in potential energy from amber=>charmm conversion: 0.01100392 ======================================================================= INFO 2017-03-18 22:13:57 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1352110.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1352110.inpcrd') INFO 2017-03-18 22:13:58 Beginning InterMol conversion INFO 2017-03-18 22:13:58 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:13:58 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:13:58 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1363784.inpcrd INFO 2017-03-18 22:13:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1363784/mobley_1363784_converted.input INFO 2017-03-18 22:13:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1363784/mobley_1363784_converted.cms WARNING 2017-03-18 22:14:13 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:14:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1363784/mobley_1363784_converted.inp INFO 2017-03-18 22:14:13 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1363784/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1363784/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1363784/mobley_1363784_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1363784/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -68.60865371 -68.60865371 0.00000000 0.00000000 0.00000000 0.00000000 -11.67110064 -11.67110064 coulomb total -11.70683200 -11.68216324 0.02466876 -11.68216314 0.02466886 -11.68225937 0.02457263 -11.67110064 0.03573136 coulomb-14 56.90574720 56.92649048 0.02074328 0.00000000 -56.90574720 56.92641239 0.02066519 0.00000000 -56.90574720 improper 0.00000000 0.00014569 0.00014569 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00125520 0.00123200 -0.00002320 0.00137768 0.00012248 0.00138160 0.00012640 0.00121336 -0.00004184 vdw (SR) 0.00000000 -2.48121404 -2.48121404 0.00000000 0.00000000 0.00000000 0.00000000 20.25453480 20.25453480 vdw total 20.25474400 20.25452551 -0.00021849 20.25452560 -0.00021840 20.25490784 0.00016384 20.25453480 -0.00020920 vdw-14 22.73585600 22.73573955 -0.00011645 0.00000000 -22.73585600 22.73612332 0.00026732 0.00000000 -22.73585600 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.86941120 1.86920279 -0.00020841 1.86920279 -0.00020841 1.86915459 -0.00025661 1.86920200 -0.00020920 bond 2.54554560 2.54569827 0.00015267 2.54569827 0.00015267 2.54547496 -0.00007064 2.54571296 0.00016736 bonded 4.41621200 4.41627874 0.00006674 4.41627874 0.00006674 4.41601115 -0.00020085 4.41625384 0.00004184 dihedral 0.00125520 0.00137768 0.00012248 0.00137768 0.00012248 0.00138160 0.00012640 0.00133888 0.00008368 nonbonded 8.54791200 8.57236227 0.02445027 8.57236246 0.02445046 8.57264847 0.02473647 8.58343416 0.03552216 potential 12.96412400 12.98864101 0.02451701 12.98864098 0.02451698 12.98860270 0.02447870 12.99972984 0.03560584 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 12.96412400 Difference in potential energy from amber=>gromacs conversion: 0.02451701 Difference in potential energy from amber=>lammps conversion: 0.02451698 Difference in potential energy from amber=>desmond conversion: 0.02447870 Difference in potential energy from amber=>charmm conversion: 0.03560584 ======================================================================= INFO 2017-03-18 22:14:13 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1363784.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1363784.inpcrd') INFO 2017-03-18 22:14:14 Beginning InterMol conversion INFO 2017-03-18 22:14:14 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:14:14 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1396156.inpcrd INFO 2017-03-18 22:14:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1396156/mobley_1396156_converted.input INFO 2017-03-18 22:14:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1396156/mobley_1396156_converted.cms INFO 2017-03-18 22:14:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1396156/mobley_1396156_converted.rst7 WARNING 2017-03-18 22:14:29 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:14:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1396156/mobley_1396156_converted.inp INFO 2017-03-18 22:14:29 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1396156/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1396156/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1396156/mobley_1396156_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_1396156/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1396156/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -2.75320488 -2.75320488 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -20.99673456 -20.99673456 coulomb total -20.99238320 -20.99596291 -0.00357971 -20.99596261 -0.00357941 -20.99597693 -0.00359373 -20.99238320 0.00000000 -20.99673456 -0.00435136 coulomb-14 -18.24642400 -18.24275802 0.00366598 0.00000000 18.24642400 -18.24277446 0.00364954 -18.24642400 0.00000000 0.00000000 18.24642400 improper 0.00000000 0.00002629 0.00002629 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00032493 -0.00009347 0.00035115 -0.00006725 0.00034715 -0.00007125 0.00041840 0.00000000 0.00033472 -0.00008368 vdw (SR) 0.00000000 166.75790176 166.75790176 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 208.03065568 208.03065568 vdw total 208.03057200 208.02937470 -0.00119730 208.02937538 -0.00119662 208.03131073 0.00073873 208.02931680 -0.00125520 208.03065568 0.00008368 vdw-14 41.27139440 41.27147295 0.00007855 0.00000000 -41.27139440 41.27165699 0.00026259 41.27139440 0.00000000 0.00000000 -41.27139440 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.02256960 1.02239375 -0.00017585 1.02239375 -0.00017585 1.02243021 -0.00013939 1.02256960 0.00000000 1.02244408 -0.00012552 bond 10.18678480 10.18669060 -0.00009420 10.18669066 -0.00009414 10.18635983 -0.00042497 10.18678480 0.00000000 10.18670112 -0.00008368 bonded 11.20977280 11.20943557 -0.00033723 11.20943556 -0.00033724 11.20913719 -0.00063561 11.20977280 0.00000000 11.20952176 -0.00025104 dihedral 0.00041840 0.00035122 -0.00006718 0.00035115 -0.00006725 0.00034715 -0.00007125 0.00041840 0.00000000 0.00037656 -0.00004184 nonbonded 187.03818880 187.03341180 -0.00477700 187.03341067 -0.00477813 187.03533379 -0.00285501 187.03693360 -0.00125520 187.03392112 -0.00426768 potential 198.24796160 198.24284736 -0.00511424 198.24284875 -0.00511285 198.24430102 -0.00366058 198.24670640 -0.00125520 198.24340104 -0.00456056 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 198.24796160 Difference in potential energy from amber=>gromacs conversion: -0.00511424 Difference in potential energy from amber=>lammps conversion: -0.00511285 Difference in potential energy from amber=>desmond conversion: -0.00366058 Difference in potential energy from amber=>amber conversion: -0.00125520 Difference in potential energy from amber=>charmm conversion: -0.00456056 ======================================================================= INFO 2017-03-18 22:14:29 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1396156.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1396156.inpcrd') INFO 2017-03-18 22:14:30 Beginning InterMol conversion INFO 2017-03-18 22:14:30 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:14:30 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:14:30 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1417007.inpcrd INFO 2017-03-18 22:14:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1417007/mobley_1417007_converted.input INFO 2017-03-18 22:14:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1417007/mobley_1417007_converted.cms WARNING 2017-03-18 22:14:46 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:14:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1417007/mobley_1417007_converted.inp INFO 2017-03-18 22:14:46 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1417007/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1417007/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1417007/mobley_1417007_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1417007/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -55.09484596 -55.09484596 0.00000000 0.00000000 0.00000000 0.00000000 -154.33713264 -154.33713264 coulomb total -154.35236240 -154.35750520 -0.00514280 -154.35750454 -0.00514214 -154.35776311 -0.00540071 -154.33713264 0.01522976 coulomb-14 -99.25494000 -99.26265924 -0.00771924 0.00000000 99.25494000 -99.26295822 -0.00801822 0.00000000 99.25494000 improper 0.00000000 0.83546792 0.83546792 0.00000000 0.00000000 0.00000000 0.00000000 0.83550296 0.83550296 proper 33.75442000 32.91885674 -0.83556326 33.75432042 -0.00009958 33.75409720 -0.00032280 32.91971200 -0.83470800 vdw (SR) 0.00000000 -12.57826651 -12.57826651 0.00000000 0.00000000 0.00000000 0.00000000 4.69181208 4.69181208 vdw total 4.69151920 4.69169613 0.00017693 4.69169618 0.00017698 4.69177204 0.00025284 4.69181208 0.00029288 vdw-14 17.26987840 17.26996264 0.00008424 0.00000000 -17.26987840 17.27007819 0.00019979 0.00000000 -17.26987840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 80.72107520 80.72118392 0.00010872 80.72118398 0.00010878 80.72155510 0.00047990 80.72086600 -0.00020920 bond 12.60471840 12.60467319 -0.00004521 12.60467321 -0.00004519 12.60488459 0.00016619 12.60467656 -0.00004184 bonded 127.08021360 127.08018177 -0.00003183 127.08017762 -0.00003598 127.08053690 0.00032330 127.08075752 0.00054392 dihedral 33.75442000 33.75432466 -0.00009534 33.75432042 -0.00009958 33.75409720 -0.00032280 33.75521496 0.00079496 nonbonded -149.66084320 -149.66580907 -0.00496587 -149.66580542 -0.00496222 -149.66599107 -0.00514787 -149.64532056 0.01552264 potential -22.58062960 -22.58562731 -0.00499771 -22.58562948 -0.00499988 -22.58569220 -0.00506260 -22.56460488 0.01602472 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -22.58062960 Difference in potential energy from amber=>gromacs conversion: -0.00499771 Difference in potential energy from amber=>lammps conversion: -0.00499988 Difference in potential energy from amber=>desmond conversion: -0.00506260 Difference in potential energy from amber=>charmm conversion: 0.01602472 ======================================================================= INFO 2017-03-18 22:14:46 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1417007.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1417007.inpcrd') INFO 2017-03-18 22:14:46 Beginning InterMol conversion INFO 2017-03-18 22:14:46 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:14:46 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:14:46 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1424265.inpcrd INFO 2017-03-18 22:14:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1424265/mobley_1424265_converted.input INFO 2017-03-18 22:14:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1424265/mobley_1424265_converted.cms WARNING 2017-03-18 22:15:02 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:15:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1424265/mobley_1424265_converted.inp INFO 2017-03-18 22:15:02 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1424265/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1424265/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1424265/mobley_1424265_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1424265/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 22.09620949 22.09620949 0.00000000 0.00000000 0.00000000 0.00000000 -21.48718304 -21.48718304 coulomb total -21.48818720 -21.48872067 -0.00053347 -21.48872024 -0.00053304 -21.48874861 -0.00056141 -21.48718304 0.00100416 coulomb-14 -43.58347280 -43.58493016 -0.00145736 0.00000000 43.58347280 -43.58492925 -0.00145645 0.00000000 43.58347280 improper 0.00000000 0.00019574 0.00019574 0.00000000 0.00000000 0.00000000 0.00000000 0.00020920 0.00020920 proper 0.00209200 0.00182811 -0.00026389 0.00202375 -0.00006825 0.00202402 -0.00006798 0.00184096 -0.00025104 vdw (SR) 0.00000000 -2.24674917 -2.24674917 0.00000000 0.00000000 0.00000000 0.00000000 17.53832384 17.53832384 vdw total 17.53807280 17.53831015 0.00023735 17.53831003 0.00023723 17.53835971 0.00028691 17.53832384 0.00025104 vdw-14 19.78488080 19.78505932 0.00017852 0.00000000 -19.78488080 19.78511038 0.00022958 0.00000000 -19.78488080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.63220240 0.63202346 -0.00017894 0.63202345 -0.00017895 0.63204297 -0.00015943 0.63203504 -0.00016736 bond 2.08865280 2.08851275 -0.00014005 2.08851276 -0.00014004 2.08857597 -0.00007683 2.08852728 -0.00012552 bonded 2.72294720 2.72256006 -0.00038714 2.72255996 -0.00038724 2.72264296 -0.00030424 2.72261248 -0.00033472 dihedral 0.00209200 0.00202385 -0.00006815 0.00202375 -0.00006825 0.00202402 -0.00006798 0.00205016 -0.00004184 nonbonded -3.95011440 -3.95041052 -0.00029612 -3.95041025 -0.00029585 -3.95038890 -0.00027450 -3.94885920 0.00125520 potential -1.22716720 -1.22785046 -0.00068326 -1.22785032 -0.00068312 -1.22779706 -0.00062986 -1.22633040 0.00083680 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -1.22716720 Difference in potential energy from amber=>gromacs conversion: -0.00068326 Difference in potential energy from amber=>lammps conversion: -0.00068312 Difference in potential energy from amber=>desmond conversion: -0.00062986 Difference in potential energy from amber=>charmm conversion: 0.00083680 ======================================================================= INFO 2017-03-18 22:15:02 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1424265.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1424265.inpcrd') INFO 2017-03-18 22:15:02 Beginning InterMol conversion INFO 2017-03-18 22:15:02 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:15:02 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:15:02 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1449384.inpcrd INFO 2017-03-18 22:15:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1449384/mobley_1449384_converted.input INFO 2017-03-18 22:15:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1449384/mobley_1449384_converted.cms WARNING 2017-03-18 22:15:18 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:15:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1449384/mobley_1449384_converted.inp INFO 2017-03-18 22:15:18 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1449384/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1449384/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1449384/mobley_1449384_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1449384/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -3.71310878 -3.71310878 0.00000000 0.00000000 0.00000000 0.00000000 -22.91309024 -22.91309024 coulomb total -22.90698160 -22.90791524 -0.00093364 -22.90791505 -0.00093345 -22.90796379 -0.00098219 -22.91309024 -0.00610864 coulomb-14 -19.19410000 -19.19480645 -0.00070645 0.00000000 19.19410000 -19.19478216 -0.00068216 0.00000000 19.19410000 improper 0.00000000 0.00006772 0.00006772 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.19664800 0.19661004 -0.00003796 0.19667780 0.00002980 0.19667571 0.00002771 0.19660616 -0.00004184 vdw (SR) 0.00000000 -3.37104942 -3.37104942 0.00000000 0.00000000 0.00000000 0.00000000 20.90431000 20.90431000 vdw total 20.90410080 20.90424045 0.00013965 20.90424055 0.00013975 20.90431636 0.00021556 20.90431000 0.00020920 vdw-14 24.27514960 24.27528987 0.00014027 0.00000000 -24.27514960 24.27537344 0.00022384 0.00000000 -24.27514960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.17356400 3.17345799 -0.00010601 3.17345798 -0.00010602 3.17349855 -0.00006545 3.17339664 -0.00016736 bond 2.49868480 2.49864528 -0.00003952 2.49864530 -0.00003950 2.49831151 -0.00037329 2.49864296 -0.00004184 bonded 5.86889680 5.86878103 -0.00011577 5.86878108 -0.00011572 5.86848577 -0.00041103 5.86872944 -0.00016736 dihedral 0.19664800 0.19667776 0.00002976 0.19667780 0.00002980 0.19667571 0.00002771 0.19668984 0.00004184 nonbonded -2.00288080 -2.00367478 -0.00079398 -2.00367446 -0.00079366 -2.00364743 -0.00076663 -2.00878024 -0.00589944 potential 3.86601600 3.86510625 -0.00090975 3.86510661 -0.00090939 3.86474852 -0.00126748 3.85999104 -0.00602496 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 3.86601600 Difference in potential energy from amber=>gromacs conversion: -0.00090975 Difference in potential energy from amber=>lammps conversion: -0.00090939 Difference in potential energy from amber=>desmond conversion: -0.00126748 Difference in potential energy from amber=>charmm conversion: -0.00602496 ======================================================================= INFO 2017-03-18 22:15:18 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1449384.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1449384.inpcrd') INFO 2017-03-18 22:15:18 Beginning InterMol conversion INFO 2017-03-18 22:15:18 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:15:18 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1469079.inpcrd INFO 2017-03-18 22:15:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1469079/mobley_1469079_converted.input INFO 2017-03-18 22:15:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1469079/mobley_1469079_converted.cms INFO 2017-03-18 22:15:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1469079/mobley_1469079_converted.rst7 WARNING 2017-03-18 22:15:34 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:15:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1469079/mobley_1469079_converted.inp INFO 2017-03-18 22:15:34 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1469079/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1469079/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1469079/mobley_1469079_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_1469079/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1469079/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -32.20926679 -32.20926679 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -9.16559592 -9.16559592 coulomb total -9.23827200 -9.23537901 0.00289299 -9.23537876 0.00289324 -9.23539077 0.00288123 -9.23869040 -0.00041840 -9.16559592 0.07267608 coulomb-14 22.97392560 22.97388778 -0.00003782 0.00000000 -22.97392560 22.97385895 -0.00006665 22.97350720 -0.00041840 0.00000000 -22.97392560 improper 0.00000000 0.00015661 0.00015661 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00016736 0.00016736 proper 0.00167360 0.00133660 -0.00033700 0.00149320 -0.00018040 0.00149432 -0.00017928 0.00167360 0.00000000 0.00133888 -0.00033472 vdw (SR) 0.00000000 -8.36283303 -8.36283303 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 40.59199648 40.59199648 vdw total 40.59191280 40.59201241 0.00009961 40.59201238 0.00009958 40.59207330 0.00016050 40.59191280 0.00000000 40.59199648 0.00008368 vdw-14 48.95489200 48.95484543 -0.00004657 0.00000000 -48.95489200 48.95491710 0.00002510 48.95489200 0.00000000 0.00000000 -48.95489200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 8.43159680 8.43150438 -0.00009242 8.43150433 -0.00009247 8.43223327 0.00063647 8.43159680 0.00000000 8.43151312 -0.00008368 bond 1.51335280 1.51350073 0.00014793 1.51350075 0.00014795 1.51372696 0.00037416 1.51335280 0.00000000 1.51352016 0.00016736 bonded 9.94662320 9.94649831 -0.00012489 9.94649828 -0.00012492 9.94745455 0.00083135 9.94662320 0.00000000 9.94653952 -0.00008368 dihedral 0.00167360 0.00149321 -0.00018039 0.00149320 -0.00018040 0.00149432 -0.00017928 0.00167360 0.00000000 0.00150624 -0.00016736 nonbonded 31.35364080 31.35663340 0.00299260 31.35663362 0.00299282 31.35668253 0.00304173 31.35322240 -0.00041840 31.42640056 0.07275976 potential 41.30026400 41.30313171 0.00286771 41.30313171 0.00286771 41.30396199 0.00369799 41.29984560 -0.00041840 41.37285640 0.07259240 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 41.30026400 Difference in potential energy from amber=>gromacs conversion: 0.00286771 Difference in potential energy from amber=>lammps conversion: 0.00286771 Difference in potential energy from amber=>desmond conversion: 0.00369799 Difference in potential energy from amber=>amber conversion: -0.00041840 Difference in potential energy from amber=>charmm conversion: 0.07259240 ======================================================================= INFO 2017-03-18 22:15:34 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1469079.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1469079.inpcrd') INFO 2017-03-18 22:15:34 Beginning InterMol conversion INFO 2017-03-18 22:15:34 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:15:34 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:15:34 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1502181.inpcrd INFO 2017-03-18 22:15:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1502181/mobley_1502181_converted.input INFO 2017-03-18 22:15:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1502181/mobley_1502181_converted.cms WARNING 2017-03-18 22:15:50 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:15:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1502181/mobley_1502181_converted.inp INFO 2017-03-18 22:15:50 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1502181/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1502181/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1502181/mobley_1502181_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1502181/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -2.93363757 -2.93363757 0.00000000 0.00000000 0.00000000 0.00000000 -60.21545856 -60.21545856 coulomb total -60.14207120 -60.14296092 -0.00088972 -60.14295821 -0.00088701 -60.14289346 -0.00082226 -60.21545856 -0.07338736 coulomb-14 -57.20532160 -57.20932335 -0.00400175 0.00000000 57.20532160 -57.20934870 -0.00402710 0.00000000 57.20532160 improper 0.00000000 0.00129835 0.00129835 0.00000000 0.00000000 0.00000000 0.00000000 0.00129704 0.00129704 proper 21.03715200 21.03584462 -0.00130738 21.03714447 -0.00000753 21.03713907 -0.00001293 21.03585496 -0.00129704 vdw (SR) 0.00000000 -3.63973719 -3.63973719 0.00000000 0.00000000 0.00000000 0.00000000 10.27209656 10.27209656 vdw total 10.27213840 10.27190237 -0.00023603 10.27190242 -0.00023598 10.27181336 -0.00032504 10.27209656 -0.00004184 vdw-14 13.91180000 13.91163955 -0.00016045 0.00000000 -13.91180000 13.91158666 -0.00021334 0.00000000 -13.91180000 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.43422720 3.43439605 0.00016885 3.43439607 0.00016887 3.43472482 0.00049762 3.43435272 0.00012552 bond 1.71251120 1.71243804 -0.00007316 1.71243802 -0.00007318 1.71296678 0.00045558 1.71242752 -0.00008368 bonded 26.18389040 26.18397706 0.00008666 26.18397856 0.00008816 26.18483067 0.00094027 26.18393224 0.00004184 dihedral 21.03715200 21.03714297 -0.00000903 21.03714447 -0.00000753 21.03713907 -0.00001293 21.03715200 0.00000000 nonbonded -49.86993280 -49.87105855 -0.00112575 -49.87105830 -0.00112550 -49.87108011 -0.00114731 -49.94336200 -0.07342920 potential -23.68604240 -23.68708150 -0.00103910 -23.68707920 -0.00103680 -23.68634687 -0.00030447 -23.75942976 -0.07338736 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -23.68604240 Difference in potential energy from amber=>gromacs conversion: -0.00103910 Difference in potential energy from amber=>lammps conversion: -0.00103680 Difference in potential energy from amber=>desmond conversion: -0.00030447 Difference in potential energy from amber=>charmm conversion: -0.07338736 ======================================================================= INFO 2017-03-18 22:15:50 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1502181.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1502181.inpcrd') INFO 2017-03-18 22:15:51 Beginning InterMol conversion INFO 2017-03-18 22:15:51 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:15:51 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:15:51 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1520842.inpcrd INFO 2017-03-18 22:15:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1520842/mobley_1520842_converted.input INFO 2017-03-18 22:15:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1520842/mobley_1520842_converted.cms WARNING 2017-03-18 22:16:06 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:16:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1520842/mobley_1520842_converted.inp INFO 2017-03-18 22:16:06 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1520842/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1520842/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1520842/mobley_1520842_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1520842/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 89.46305506 89.46305506 0.00000000 0.00000000 0.00000000 0.00000000 -116.57234864 -116.57234864 coulomb total -116.49427520 -116.49252397 0.00175123 -116.49252210 0.00175310 -116.49264888 0.00162632 -116.57234864 -0.07807344 coulomb-14 -205.94610320 -205.95557904 -0.00947584 0.00000000 205.94610320 -205.95567368 -0.00957048 0.00000000 205.94610320 improper 0.00000000 0.00013684 0.00013684 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00125520 0.00097323 -0.00028197 0.00111016 -0.00014504 0.00111276 -0.00014244 0.00096232 -0.00029288 vdw (SR) 0.00000000 -1.40558315 -1.40558315 0.00000000 0.00000000 0.00000000 0.00000000 19.94713632 19.94713632 vdw total 19.94722000 19.94715999 -0.00006001 19.94716017 -0.00005983 19.94748468 0.00026468 19.94713632 -0.00008368 vdw-14 21.35262560 21.35274314 0.00011754 0.00000000 -21.35262560 21.35307467 0.00044907 0.00000000 -21.35262560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.69075440 1.69082877 0.00007437 1.69082875 0.00007435 1.69079709 0.00004269 1.69083808 0.00008368 bond 1.25729200 1.25728496 -0.00000704 1.25728497 -0.00000703 1.25699635 -0.00029565 1.25729200 0.00000000 bonded 2.94930160 2.94922379 -0.00007781 2.94922388 -0.00007772 2.94890619 -0.00039541 2.94921792 -0.00008368 dihedral 0.00125520 0.00111007 -0.00014513 0.00111016 -0.00014504 0.00111276 -0.00014244 0.00108784 -0.00016736 nonbonded -96.54705520 -96.54536398 0.00169122 -96.54536068 0.00169452 -96.54516420 0.00189100 -96.62521232 -0.07815712 potential -93.59775360 -93.59614019 0.00161341 -93.59613858 0.00161502 -93.59628962 0.00146398 -93.67599440 -0.07824080 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -93.59775360 Difference in potential energy from amber=>gromacs conversion: 0.00161341 Difference in potential energy from amber=>lammps conversion: 0.00161502 Difference in potential energy from amber=>desmond conversion: 0.00146398 Difference in potential energy from amber=>charmm conversion: -0.07824080 ======================================================================= INFO 2017-03-18 22:16:06 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1520842.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1520842.inpcrd') INFO 2017-03-18 22:16:07 Beginning InterMol conversion INFO 2017-03-18 22:16:07 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:16:07 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:16:07 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1527293.inpcrd INFO 2017-03-18 22:16:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1527293/mobley_1527293_converted.input INFO 2017-03-18 22:16:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1527293/mobley_1527293_converted.cms WARNING 2017-03-18 22:16:22 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:16:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1527293/mobley_1527293_converted.inp INFO 2017-03-18 22:16:23 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1527293/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1527293/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1527293/mobley_1527293_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1527293/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 35.16212015 35.16212015 0.00000000 0.00000000 0.00000000 0.00000000 -88.10483104 -88.10483104 coulomb total -88.04893280 -88.05196019 -0.00302739 -88.05195783 -0.00302503 -88.05202854 -0.00309574 -88.10483104 -0.05589824 coulomb-14 -123.21001360 -123.21408033 -0.00406673 0.00000000 123.21001360 -123.21413442 -0.00412082 0.00000000 123.21001360 improper 0.00000000 0.00015078 0.00015078 0.00000000 0.00000000 0.00000000 0.00000000 0.00016736 0.00016736 proper 25.99142640 25.99112724 -0.00029916 25.99129753 -0.00012887 25.99130887 -0.00011753 25.99117536 -0.00025104 vdw (SR) 0.00000000 -10.49501784 -10.49501784 0.00000000 0.00000000 0.00000000 0.00000000 34.76636224 34.76636224 vdw total 34.76611120 34.76636258 0.00025138 34.76636266 0.00025146 34.76671960 0.00060840 34.76636224 0.00025104 vdw-14 45.26125680 45.26138042 0.00012362 0.00000000 -45.26125680 45.26173587 0.00047907 0.00000000 -45.26125680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 7.98139840 7.98147583 0.00007743 7.98147580 0.00007740 7.98167300 0.00027460 7.98152392 0.00012552 bond 10.55999760 10.55997810 -0.00001950 10.55997794 -0.00001966 10.56026128 0.00026368 10.55999760 0.00000000 bonded 44.53282240 44.53273195 -0.00009045 44.53275127 -0.00007113 44.53324314 0.00042074 44.53286424 0.00004184 dihedral 25.99142640 25.99127802 -0.00014838 25.99129753 -0.00012887 25.99130887 -0.00011753 25.99134272 -0.00008368 nonbonded -53.28282160 -53.28559760 -0.00277600 -53.28559559 -0.00277399 -53.28530895 -0.00248735 -53.33846880 -0.05564720 potential -8.74999920 -8.75286565 -0.00286645 -8.75284474 -0.00284554 -8.75226994 -0.00227074 -8.80564640 -0.05564720 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -8.74999920 Difference in potential energy from amber=>gromacs conversion: -0.00286645 Difference in potential energy from amber=>lammps conversion: -0.00284554 Difference in potential energy from amber=>desmond conversion: -0.00227074 Difference in potential energy from amber=>charmm conversion: -0.05564720 ======================================================================= INFO 2017-03-18 22:16:23 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1527293.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1527293.inpcrd') INFO 2017-03-18 22:16:23 Beginning InterMol conversion INFO 2017-03-18 22:16:23 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:16:23 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:16:23 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1563176.inpcrd INFO 2017-03-18 22:16:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1563176/mobley_1563176_converted.input INFO 2017-03-18 22:16:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1563176/mobley_1563176_converted.cms WARNING 2017-03-18 22:16:39 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:16:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1563176/mobley_1563176_converted.inp INFO 2017-03-18 22:16:39 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1563176/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1563176/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1563176/mobley_1563176_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1563176/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 10.22978214 10.22978214 0.00000000 0.00000000 0.00000000 0.00000000 9.90361168 9.90361168 coulomb total 9.89892560 9.89935909 0.00043349 9.89935906 0.00043346 9.89932149 0.00039589 9.90361168 0.00468608 coulomb-14 -0.33053600 -0.33042305 0.00011295 0.00000000 0.33053600 -0.33042249 0.00011351 0.00000000 0.33053600 proper 1.82087680 1.82083645 -0.00004035 1.82083642 -0.00004038 1.82085319 -0.00002361 1.82087680 0.00000000 vdw (SR) 0.00000000 -1.11140103 -1.11140103 0.00000000 0.00000000 0.00000000 0.00000000 1.67841160 1.67841160 vdw total 1.67862080 1.67834498 -0.00027582 1.67834499 -0.00027581 1.67831483 -0.00030597 1.67841160 -0.00020920 vdw-14 2.78989120 2.78974600 -0.00014520 0.00000000 -2.78989120 2.78972119 -0.00017001 0.00000000 -2.78989120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.26145200 2.26126163 -0.00019037 2.26126163 -0.00019037 2.26165085 0.00019885 2.26124280 -0.00020920 bond 0.51797920 0.51789605 -0.00008315 0.51789606 -0.00008314 0.51820506 0.00022586 0.51789552 -0.00008368 bonded 4.60030800 4.59999413 -0.00031387 4.59999412 -0.00031388 4.60070910 0.00040110 4.60001512 -0.00029288 dihedral 1.82087680 1.82083645 -0.00004035 1.82083642 -0.00004038 1.82085319 -0.00002361 1.82087680 0.00000000 nonbonded 11.57754640 11.57770407 0.00015767 11.57770414 0.00015774 11.57763632 0.00008992 11.58202328 0.00447688 potential 16.17785440 16.17769820 -0.00015620 16.17769792 -0.00015648 16.17831192 0.00045752 16.18199656 0.00414216 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 16.17785440 Difference in potential energy from amber=>gromacs conversion: -0.00015620 Difference in potential energy from amber=>lammps conversion: -0.00015648 Difference in potential energy from amber=>desmond conversion: 0.00045752 Difference in potential energy from amber=>charmm conversion: 0.00414216 ======================================================================= INFO 2017-03-18 22:16:39 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1563176.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1563176.inpcrd') INFO 2017-03-18 22:16:39 Beginning InterMol conversion INFO 2017-03-18 22:16:39 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:16:39 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:16:39 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1571523.inpcrd INFO 2017-03-18 22:16:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1571523/mobley_1571523_converted.input INFO 2017-03-18 22:16:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1571523/mobley_1571523_converted.cms WARNING 2017-03-18 22:16:55 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:16:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1571523/mobley_1571523_converted.inp INFO 2017-03-18 22:16:55 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1571523/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1571523/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1571523/mobley_1571523_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1571523/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -1.36237854 -1.36237854 0.00000000 0.00000000 0.00000000 0.00000000 -70.66876416 -70.66876416 coulomb total -70.67278080 -70.68061216 -0.00783136 -70.68061325 -0.00783245 -70.68141539 -0.00863459 -70.66876416 0.00401664 coulomb-14 -69.31883840 -69.31823362 0.00060478 0.00000000 69.31883840 -69.31823339 0.00060501 0.00000000 69.31883840 improper 0.00000000 0.00010045 0.00010045 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00125520 0.00128231 0.00002711 0.00138270 0.00012750 0.00137686 0.00012166 0.00129704 0.00004184 vdw (SR) 0.00000000 30.17833434 30.17833434 0.00000000 0.00000000 0.00000000 0.00000000 55.19198080 55.19198080 vdw total 55.19198080 55.19155861 -0.00042219 55.19155822 -0.00042258 55.19023954 -0.00174126 55.19198080 0.00000000 vdw-14 25.01320720 25.01322427 0.00001707 0.00000000 -25.01320720 25.01323193 0.00002473 0.00000000 -25.01320720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.94432880 0.94437563 0.00004683 0.94437562 0.00004682 0.94457794 0.00024914 0.94437064 0.00004184 bond 1.77987360 1.77980322 -0.00007038 1.77980323 -0.00007037 1.77961752 -0.00025608 1.77978992 -0.00008368 bonded 2.72545760 2.72556161 0.00010401 2.72556155 0.00010395 2.72557233 0.00011473 2.72554128 0.00008368 dihedral 0.00125520 0.00138275 0.00012755 0.00138270 0.00012750 0.00137686 0.00012166 0.00138072 0.00012552 nonbonded -15.48080000 -15.48905355 -0.00825355 -15.48905252 -0.00825252 -15.49117584 -0.01037584 -15.47678336 0.00401664 potential -12.75534240 -12.76349194 -0.00814954 -12.76349074 -0.00814834 -12.76567086 -0.01032846 -12.75120024 0.00414216 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -12.75534240 Difference in potential energy from amber=>gromacs conversion: -0.00814954 Difference in potential energy from amber=>lammps conversion: -0.00814834 Difference in potential energy from amber=>desmond conversion: -0.01032846 Difference in potential energy from amber=>charmm conversion: 0.00414216 ======================================================================= INFO 2017-03-18 22:16:55 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1571523.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1571523.inpcrd') INFO 2017-03-18 22:16:55 Beginning InterMol conversion INFO 2017-03-18 22:16:55 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:16:55 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:16:55 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1592519.inpcrd INFO 2017-03-18 22:16:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1592519/mobley_1592519_converted.input INFO 2017-03-18 22:16:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1592519/mobley_1592519_converted.cms WARNING 2017-03-18 22:17:11 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:17:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1592519/mobley_1592519_converted.inp INFO 2017-03-18 22:17:11 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1592519/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1592519/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1592519/mobley_1592519_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1592519/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -10.64178429 -10.64178429 0.00000000 0.00000000 0.00000000 0.00000000 -82.62224296 -82.62224296 coulomb total -82.58881280 -82.59374683 -0.00493403 -82.59374574 -0.00493294 -82.59370674 -0.00489394 -82.62224296 -0.03343016 coulomb-14 -71.94639040 -71.95196255 -0.00557215 0.00000000 71.94639040 -71.95191705 -0.00552665 0.00000000 71.94639040 improper 0.00000000 0.00780066 0.00780066 0.00000000 0.00000000 0.00000000 0.00000000 0.00778224 0.00778224 proper 16.56069040 16.55276157 -0.00792883 16.56056111 -0.00012929 16.56059454 -0.00009586 16.55278264 -0.00790776 vdw (SR) 0.00000000 -4.35149202 -4.35149202 0.00000000 0.00000000 0.00000000 0.00000000 10.67451368 10.67451368 vdw total 10.67463920 10.67432201 -0.00031719 10.67432205 -0.00031715 10.67430230 -0.00033690 10.67451368 -0.00012552 vdw-14 15.02599920 15.02581403 -0.00018517 0.00000000 -15.02599920 15.02578510 -0.00021410 0.00000000 -15.02599920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.30198880 4.30215319 0.00016439 4.30215323 0.00016443 4.30238055 0.00039175 4.30215616 0.00016736 bond 2.64261440 2.64245324 -0.00016116 2.64245323 -0.00016117 2.64278916 0.00017476 2.64244704 -0.00016736 bonded 23.50529360 23.50516865 -0.00012495 23.50516758 -0.00012602 23.50576425 0.00047065 23.50516808 -0.00012552 dihedral 16.56069040 16.56056222 -0.00012818 16.56056111 -0.00012929 16.56059454 -0.00009586 16.56056488 -0.00012552 nonbonded -71.91417360 -71.91942482 -0.00525122 -71.91942452 -0.00525092 -71.91940444 -0.00523084 -71.94772928 -0.03355568 potential -48.40888000 -48.41425617 -0.00537617 -48.41425644 -0.00537644 -48.41373470 -0.00485470 -48.44256120 -0.03368120 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -48.40888000 Difference in potential energy from amber=>gromacs conversion: -0.00537617 Difference in potential energy from amber=>lammps conversion: -0.00537644 Difference in potential energy from amber=>desmond conversion: -0.00485470 Difference in potential energy from amber=>charmm conversion: -0.03368120 ======================================================================= INFO 2017-03-18 22:17:11 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1592519.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1592519.inpcrd') INFO 2017-03-18 22:17:11 Beginning InterMol conversion INFO 2017-03-18 22:17:11 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:17:11 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:17:11 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1615431.inpcrd INFO 2017-03-18 22:17:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1615431/mobley_1615431_converted.input INFO 2017-03-18 22:17:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1615431/mobley_1615431_converted.cms WARNING 2017-03-18 22:17:27 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:17:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1615431/mobley_1615431_converted.inp INFO 2017-03-18 22:17:27 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1615431/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1615431/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1615431/mobley_1615431_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1615431/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 40.51179459 40.51179459 0.00000000 0.00000000 0.00000000 0.00000000 -74.02173808 -74.02173808 coulomb total -74.01872560 -74.02003201 -0.00130641 -74.02003101 -0.00130541 -74.02009812 -0.00137252 -74.02173808 -0.00301248 coulomb-14 -114.52068240 -114.53182660 -0.01114420 0.00000000 114.52068240 -114.53181937 -0.01113697 0.00000000 114.52068240 proper 24.40778240 24.40772743 -0.00005497 24.40772633 -0.00005607 24.40775935 -0.00002305 24.40744768 -0.00033472 vdw (SR) 0.00000000 -0.95822784 -0.95822784 0.00000000 0.00000000 0.00000000 0.00000000 11.69440552 11.69440552 vdw total 11.69428000 11.69421661 -0.00006339 11.69421682 -0.00006318 11.69405818 -0.00022182 11.69440552 0.00012552 vdw-14 12.65241600 12.65244445 0.00002845 0.00000000 -12.65241600 12.65229613 -0.00011987 0.00000000 -12.65241600 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.14513680 2.14533560 0.00019880 2.14533558 0.00019878 2.14554867 0.00041187 2.14538784 0.00025104 bond 1.78656800 1.78656916 0.00000116 1.78656917 0.00000117 1.78702480 0.00045680 1.78656800 0.00000000 bonded 28.33948720 28.33963219 0.00014499 28.33963109 0.00014389 28.34033281 0.00084561 28.33940352 -0.00008368 dihedral 24.40778240 24.40772743 -0.00005497 24.40772633 -0.00005607 24.40775935 -0.00002305 24.40744768 -0.00033472 nonbonded -62.32444560 -62.32581540 -0.00136980 -62.32581377 -0.00136817 -62.32603994 -0.00159434 -62.32733256 -0.00288696 potential -33.98495840 -33.98618321 -0.00122481 -33.98618306 -0.00122466 -33.98577185 -0.00081345 -33.98792904 -0.00297064 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -33.98495840 Difference in potential energy from amber=>gromacs conversion: -0.00122481 Difference in potential energy from amber=>lammps conversion: -0.00122466 Difference in potential energy from amber=>desmond conversion: -0.00081345 Difference in potential energy from amber=>charmm conversion: -0.00297064 ======================================================================= INFO 2017-03-18 22:17:27 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1615431.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1615431.inpcrd') INFO 2017-03-18 22:17:27 Beginning InterMol conversion INFO 2017-03-18 22:17:27 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:17:27 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:17:27 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1636752.inpcrd INFO 2017-03-18 22:17:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1636752/mobley_1636752_converted.input INFO 2017-03-18 22:17:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1636752/mobley_1636752_converted.cms WARNING 2017-03-18 22:17:43 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:17:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1636752/mobley_1636752_converted.inp INFO 2017-03-18 22:17:43 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1636752/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1636752/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1636752/mobley_1636752_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1636752/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 16.05974008 16.05974008 coulomb total 16.04731360 16.05789569 0.01058209 16.05789535 0.01058175 16.05789648 0.01058288 16.05974008 0.01242648 coulomb-14 16.04731360 16.05789569 0.01058209 0.00000000 -16.04731360 16.05789648 0.01058288 0.00000000 -16.04731360 proper 0.00083680 0.00079715 -0.00003965 0.00079715 -0.00003965 0.00079673 -0.00004007 0.00079496 -0.00004184 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.15815520 0.15805081 -0.00010439 0.15805081 -0.00010439 0.15798667 -0.00016853 0.15802968 -0.00012552 bond 0.14769520 0.14763044 -0.00006476 0.14763044 -0.00006476 0.14774870 0.00005350 0.14761152 -0.00008368 bonded 0.30668720 0.30647840 -0.00020880 0.30647840 -0.00020880 0.30653210 -0.00015510 0.30643616 -0.00025104 dihedral 0.00083680 0.00079715 -0.00003965 0.00079715 -0.00003965 0.00079673 -0.00004007 0.00079496 -0.00004184 nonbonded 16.04731360 16.05789569 0.01058209 16.05789535 0.01058175 16.05789648 0.01058288 16.05974008 0.01242648 potential 16.35400080 16.36437409 0.01037329 16.36437377 0.01037297 16.36442461 0.01042381 16.36617624 0.01217544 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 16.35400080 Difference in potential energy from amber=>gromacs conversion: 0.01037329 Difference in potential energy from amber=>lammps conversion: 0.01037297 Difference in potential energy from amber=>desmond conversion: 0.01042381 Difference in potential energy from amber=>charmm conversion: 0.01217544 ======================================================================= INFO 2017-03-18 22:17:43 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1636752.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1636752.inpcrd') INFO 2017-03-18 22:17:43 Beginning InterMol conversion INFO 2017-03-18 22:17:43 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:17:43 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:17:43 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1650157.inpcrd INFO 2017-03-18 22:17:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1650157/mobley_1650157_converted.input INFO 2017-03-18 22:17:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1650157/mobley_1650157_converted.cms WARNING 2017-03-18 22:17:59 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:17:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1650157/mobley_1650157_converted.inp INFO 2017-03-18 22:17:59 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1650157/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1650157/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1650157/mobley_1650157_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1650157/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 88.62200571 88.62200571 0.00000000 0.00000000 0.00000000 0.00000000 -92.02067848 -92.02067848 coulomb total -92.00574160 -92.00487712 0.00086448 -92.00487551 0.00086609 -92.00503952 0.00070208 -92.02067848 -0.01493688 coulomb-14 -180.60654400 -180.62688283 -0.02033883 0.00000000 180.60654400 -180.62669582 -0.02015182 0.00000000 180.60654400 proper 12.63609840 12.63594671 -0.00015169 12.63594652 -0.00015188 12.63594644 -0.00015196 12.63593104 -0.00016736 vdw (SR) 0.00000000 -0.40206476 -0.40206476 0.00000000 0.00000000 0.00000000 0.00000000 5.86140744 5.86140744 vdw total 5.86136560 5.86129564 -0.00006996 5.86129573 -0.00006987 5.86114516 -0.00022044 5.86140744 0.00004184 vdw-14 6.26344800 6.26336040 -0.00008760 0.00000000 -6.26344800 6.26323466 -0.00021334 0.00000000 -6.26344800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.89953600 1.89940177 -0.00013423 1.89940178 -0.00013422 1.89940657 -0.00012943 1.89941048 -0.00012552 bond 0.39413280 0.39428234 0.00014954 0.39428234 0.00014954 0.39407894 -0.00005386 0.39430016 0.00016736 bonded 14.92976720 14.92963082 -0.00013638 14.92963063 -0.00013657 14.92943195 -0.00033525 14.92964168 -0.00012552 dihedral 12.63609840 12.63594671 -0.00015169 12.63594652 -0.00015188 12.63594644 -0.00015196 12.63593104 -0.00016736 nonbonded -86.14437600 -86.14358148 0.00079452 -86.14358104 0.00079496 -86.14389437 0.00048163 -86.15927104 -0.01489504 potential -71.21460880 -71.21395067 0.00065813 -71.21394773 0.00066107 -71.21449583 0.00011297 -71.22962936 -0.01502056 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -71.21460880 Difference in potential energy from amber=>gromacs conversion: 0.00065813 Difference in potential energy from amber=>lammps conversion: 0.00066107 Difference in potential energy from amber=>desmond conversion: 0.00011297 Difference in potential energy from amber=>charmm conversion: -0.01502056 ======================================================================= INFO 2017-03-18 22:17:59 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1650157.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1650157.inpcrd') INFO 2017-03-18 22:17:59 Beginning InterMol conversion INFO 2017-03-18 22:17:59 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:17:59 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:17:59 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1659169.inpcrd INFO 2017-03-18 22:17:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1659169/mobley_1659169_converted.input INFO 2017-03-18 22:17:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1659169/mobley_1659169_converted.cms WARNING 2017-03-18 22:18:15 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:18:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1659169/mobley_1659169_converted.inp INFO 2017-03-18 22:18:15 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1659169/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1659169/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1659169/mobley_1659169_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1659169/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 2.58962144 2.58962144 0.00000000 0.00000000 0.00000000 0.00000000 145.96750088 145.96750088 coulomb total 145.97055520 145.95404293 -0.01651227 145.95404095 -0.01651425 145.95413834 -0.01641686 145.96750088 -0.00305432 coulomb-14 143.35890240 143.36442149 0.00551909 0.00000000 -143.35890240 143.36453448 0.00563208 0.00000000 -143.35890240 proper 10.40895520 10.40879507 -0.00016013 10.40879495 -0.00016025 10.40879353 -0.00016167 10.40882968 -0.00012552 vdw (SR) 0.00000000 -1.37741856 -1.37741856 0.00000000 0.00000000 0.00000000 0.00000000 13.25758976 13.25758976 vdw total 13.25742240 13.25757477 0.00015237 13.25757512 0.00015272 13.25751423 0.00009183 13.25758976 0.00016736 vdw-14 14.63479520 14.63499333 0.00019813 0.00000000 -14.63479520 14.63492921 0.00013401 0.00000000 -14.63479520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.25392080 2.25384076 -0.00008004 2.25384076 -0.00008004 2.25367410 -0.00024670 2.25379528 -0.00012552 bond 0.69663600 0.69648397 -0.00015203 0.69648395 -0.00015205 0.69648879 -0.00014721 0.69646864 -0.00016736 bonded 13.35951200 13.35911980 -0.00039220 13.35911967 -0.00039233 13.35895642 -0.00055558 13.35909360 -0.00041840 dihedral 10.40895520 10.40879507 -0.00016013 10.40879495 -0.00016025 10.40879353 -0.00016167 10.40882968 -0.00012552 nonbonded 159.22797760 159.21161770 -0.01635990 159.21161816 -0.01635944 159.21165257 -0.01632503 159.22509064 -0.00288696 potential 172.58748960 172.57073750 -0.01675210 172.57073686 -0.01675274 172.57059293 -0.01689667 172.58422608 -0.00326352 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 172.58748960 Difference in potential energy from amber=>gromacs conversion: -0.01675210 Difference in potential energy from amber=>lammps conversion: -0.01675274 Difference in potential energy from amber=>desmond conversion: -0.01689667 Difference in potential energy from amber=>charmm conversion: -0.00326352 ======================================================================= INFO 2017-03-18 22:18:15 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1659169.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1659169.inpcrd') INFO 2017-03-18 22:18:15 Beginning InterMol conversion INFO 2017-03-18 22:18:15 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:18:15 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:18:15 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1662128.inpcrd INFO 2017-03-18 22:18:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1662128/mobley_1662128_converted.input INFO 2017-03-18 22:18:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1662128/mobley_1662128_converted.cms WARNING 2017-03-18 22:18:31 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:18:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1662128/mobley_1662128_converted.inp INFO 2017-03-18 22:18:31 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1662128/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1662128/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1662128/mobley_1662128_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1662128/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 4.60044472 4.60044472 0.00000000 0.00000000 0.00000000 0.00000000 8.30549104 8.30549104 coulomb total 8.29310640 8.29950228 0.00639588 8.29950206 0.00639566 8.29949438 0.00638798 8.30549104 0.01238464 coulomb-14 3.69740080 3.69905756 0.00165676 0.00000000 -3.69740080 3.69907249 0.00167169 0.00000000 -3.69740080 improper 0.00000000 0.00123551 0.00123551 0.00000000 0.00000000 0.00000000 0.00000000 0.00125520 0.00125520 proper 12.89801680 12.89676111 -0.00125569 12.89799923 -0.00001757 12.89799521 -0.00002159 12.89676160 -0.00125520 vdw (SR) 0.00000000 -0.79521709 -0.79521709 0.00000000 0.00000000 0.00000000 0.00000000 1.23796192 1.23796192 vdw total 1.23762720 1.23792998 0.00030278 1.23793000 0.00030280 1.23790559 0.00027839 1.23796192 0.00033472 vdw-14 2.03300560 2.03314706 0.00014146 0.00000000 -2.03300560 2.03312977 0.00012417 0.00000000 -2.03300560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.95980960 0.95992539 0.00011579 0.95992541 0.00011581 0.96029993 0.00049033 0.95989328 0.00008368 bond 0.92173520 0.92185658 0.00012138 0.92185658 0.00012138 0.92205501 0.00031981 0.92186072 0.00012552 bonded 14.77956160 14.77977859 0.00021699 14.77978122 0.00021962 14.78035015 0.00078855 14.77977080 0.00020920 dihedral 12.89801680 12.89799662 -0.00002018 12.89799923 -0.00001757 12.89799521 -0.00002159 12.89801680 -0.00000000 nonbonded 9.53073360 9.53743225 0.00669865 9.53743218 0.00669858 9.53739997 0.00666637 9.54345296 0.01271936 potential 24.31029520 24.31721084 0.00691564 24.31721344 0.00691824 24.31773234 0.00743714 24.32322376 0.01292856 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 24.31029520 Difference in potential energy from amber=>gromacs conversion: 0.00691564 Difference in potential energy from amber=>lammps conversion: 0.00691824 Difference in potential energy from amber=>desmond conversion: 0.00743714 Difference in potential energy from amber=>charmm conversion: 0.01292856 ======================================================================= INFO 2017-03-18 22:18:31 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1662128.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1662128.inpcrd') INFO 2017-03-18 22:18:31 Beginning InterMol conversion INFO 2017-03-18 22:18:31 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:18:31 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:18:31 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1674094.inpcrd INFO 2017-03-18 22:18:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1674094/mobley_1674094_converted.input INFO 2017-03-18 22:18:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1674094/mobley_1674094_converted.cms WARNING 2017-03-18 22:18:47 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:18:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1674094/mobley_1674094_converted.inp INFO 2017-03-18 22:18:47 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1674094/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1674094/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1674094/mobley_1674094_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1674094/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 6.40003060 6.40003060 0.00000000 0.00000000 0.00000000 0.00000000 1.79589832 1.79589832 coulomb total 1.78573120 1.79460928 0.00887808 1.79460927 0.00887807 1.79458647 0.00885527 1.79589832 0.01016712 coulomb-14 -4.60742080 -4.60542132 0.00199948 0.00000000 4.60742080 -4.60542394 0.00199686 0.00000000 4.60742080 proper 1.72715520 1.72733049 0.00017529 1.72733047 0.00017527 1.72733469 0.00017949 1.72732256 0.00016736 vdw (SR) 0.00000000 -1.94851242 -1.94851242 0.00000000 0.00000000 0.00000000 0.00000000 2.55240736 2.55240736 vdw total 2.55224000 2.55234705 0.00010705 2.55234711 0.00010711 2.55243534 0.00019534 2.55240736 0.00016736 vdw-14 4.50072880 4.50085947 0.00013067 0.00000000 -4.50072880 4.50095189 0.00022309 0.00000000 -4.50072880 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.80249120 0.95616108 0.15366988 0.95616107 0.15366987 0.95626005 0.15376885 0.95616952 0.15367832 bond 2.21082560 2.21083409 0.00000849 2.21083409 0.00000849 2.21165273 0.00082713 2.21082560 0.00000000 bonded 4.74047200 4.89432566 0.15385366 4.89432563 0.15385363 4.89524746 0.15477546 4.89431768 0.15384568 dihedral 1.72715520 1.72733049 0.00017529 1.72733047 0.00017527 1.72733469 0.00017949 1.72732256 0.00016736 nonbonded 4.33797120 4.34695633 0.00898513 4.34695634 0.00898514 4.34702181 0.00905061 4.34830568 0.01033448 potential 9.07844320 9.24128199 0.16283879 9.24128197 0.16283877 9.24222220 0.16377900 9.24266520 0.16422200 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 9.07844320 Difference in potential energy from amber=>gromacs conversion: 0.16283879 Difference in potential energy from amber=>lammps conversion: 0.16283877 Difference in potential energy from amber=>desmond conversion: 0.16377900 Difference in potential energy from amber=>charmm conversion: 0.16422200 ======================================================================= INFO 2017-03-18 22:18:47 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1674094.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1674094.inpcrd') INFO 2017-03-18 22:18:47 Beginning InterMol conversion INFO 2017-03-18 22:18:47 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:18:47 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:18:47 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1708457.inpcrd INFO 2017-03-18 22:18:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1708457/mobley_1708457_converted.input INFO 2017-03-18 22:18:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1708457/mobley_1708457_converted.cms WARNING 2017-03-18 22:19:03 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:19:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1708457/mobley_1708457_converted.inp INFO 2017-03-18 22:19:03 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1708457/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1708457/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1708457/mobley_1708457_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1708457/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 48.97451122 48.97451122 0.00000000 0.00000000 0.00000000 0.00000000 -393.04445792 -393.04445792 coulomb total -393.36754640 -393.36124337 0.00630303 -393.36123693 0.00630947 -393.36132354 0.00622286 -393.04445792 0.32308848 coulomb-14 -442.34796080 -442.33575459 0.01220621 0.00000000 442.34796080 -442.33573934 0.01222146 0.00000000 442.34796080 proper 0.64057040 0.64057654 0.00000614 0.64057655 0.00000615 0.64060393 0.00003353 0.64036120 -0.00020920 vdw (SR) 0.00000000 -0.27134552 -0.27134552 0.00000000 0.00000000 0.00000000 0.00000000 -1.34745720 -1.34745720 vdw total -1.34766640 -1.34748845 0.00017795 -1.34748845 0.00017795 -1.34749140 0.00017500 -1.34745720 0.00020920 vdw-14 -1.07612480 -1.07614292 -0.00001812 0.00000000 1.07612480 -1.07614638 -0.00002158 0.00000000 1.07612480 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.93679760 0.93691809 0.00012049 0.93691810 0.00012050 0.93711112 0.00031352 0.93696496 0.00016736 bond 1.09955520 1.09973037 0.00017517 1.09973038 0.00017518 1.09977894 0.00022374 1.09972256 0.00016736 bonded 2.67692320 2.67722501 0.00030181 2.67722503 0.00030183 2.67749399 0.00057079 2.67704872 0.00012552 dihedral 0.64057040 0.64057654 0.00000614 0.64057655 0.00000615 0.64060393 0.00003353 0.64036120 -0.00020920 nonbonded -394.71521280 -394.70873182 0.00648098 -394.70872760 0.00648520 -394.70881494 0.00639786 -394.39191512 0.32329768 potential -392.03828960 -392.03150681 0.00678279 -392.03150315 0.00678645 -392.03133454 0.00695506 -391.71490824 0.32338136 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -392.03828960 Difference in potential energy from amber=>gromacs conversion: 0.00678279 Difference in potential energy from amber=>lammps conversion: 0.00678645 Difference in potential energy from amber=>desmond conversion: 0.00695506 Difference in potential energy from amber=>charmm conversion: 0.32338136 ======================================================================= INFO 2017-03-18 22:19:03 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1708457.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1708457.inpcrd') INFO 2017-03-18 22:19:03 Beginning InterMol conversion INFO 2017-03-18 22:19:03 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:19:03 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:19:03 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1717215.inpcrd INFO 2017-03-18 22:19:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1717215/mobley_1717215_converted.input INFO 2017-03-18 22:19:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1717215/mobley_1717215_converted.cms WARNING 2017-03-18 22:19:19 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:19:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1717215/mobley_1717215_converted.inp INFO 2017-03-18 22:19:19 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1717215/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1717215/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1717215/mobley_1717215_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1717215/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -34.03719087 -34.03719087 0.00000000 0.00000000 0.00000000 0.00000000 -18.65687440 -18.65687440 coulomb total -18.62005520 -18.62303961 -0.00298441 -18.62303923 -0.00298403 -18.62305868 -0.00300348 -18.65687440 -0.03681920 coulomb-14 15.42264240 15.41415126 -0.00849114 0.00000000 -15.42264240 15.41411369 -0.00852871 0.00000000 -15.42264240 improper 0.00000000 0.00000009 0.00000009 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00167360 0.00156690 -0.00010670 0.00156692 -0.00010668 0.00156926 -0.00010434 0.00154808 -0.00012552 vdw (SR) 0.00000000 -0.12133498 -0.12133498 0.00000000 0.00000000 0.00000000 0.00000000 5.43911632 5.43911632 vdw total 5.43920000 5.43906424 -0.00013576 5.43906444 -0.00013556 5.43929671 0.00009671 5.43911632 -0.00008368 vdw-14 5.56053600 5.56039922 -0.00013678 0.00000000 -5.56053600 5.56061286 0.00007686 0.00000000 -5.56053600 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.10706240 2.10692713 -0.00013527 2.10692713 -0.00013527 2.10680211 -0.00026029 2.10697872 -0.00008368 bond 0.64517280 0.64532541 0.00015261 0.64532539 0.00015259 0.64533855 0.00016575 0.64534016 0.00016736 bonded 2.75390880 2.75381952 -0.00008928 2.75381944 -0.00008936 2.75370992 -0.00019888 2.75386696 -0.00004184 dihedral 0.00167360 0.00156699 -0.00010661 0.00156692 -0.00010668 0.00156926 -0.00010434 0.00154808 -0.00012552 nonbonded -13.18085520 -13.18397537 -0.00312017 -13.18397521 -0.00312001 -13.18376198 -0.00290678 -13.21775808 -0.03690288 potential -10.42694640 -10.43015585 -0.00320945 -10.43015553 -0.00320913 -10.43006478 -0.00311838 -10.46389112 -0.03694472 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -10.42694640 Difference in potential energy from amber=>gromacs conversion: -0.00320945 Difference in potential energy from amber=>lammps conversion: -0.00320913 Difference in potential energy from amber=>desmond conversion: -0.00311838 Difference in potential energy from amber=>charmm conversion: -0.03694472 ======================================================================= INFO 2017-03-18 22:19:19 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1717215.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1717215.inpcrd') INFO 2017-03-18 22:19:19 Beginning InterMol conversion INFO 2017-03-18 22:19:19 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:19:20 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:19:20 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1722522.inpcrd INFO 2017-03-18 22:19:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1722522/mobley_1722522_converted.input INFO 2017-03-18 22:19:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1722522/mobley_1722522_converted.cms WARNING 2017-03-18 22:19:35 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:19:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1722522/mobley_1722522_converted.inp INFO 2017-03-18 22:19:35 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1722522/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1722522/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1722522/mobley_1722522_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1722522/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -8.32256188 -8.32256188 0.00000000 0.00000000 0.00000000 0.00000000 -81.05010496 -81.05010496 coulomb total -80.99094320 -80.99481756 -0.00387436 -80.99481758 -0.00387438 -80.99475516 -0.00381196 -81.05010496 -0.05916176 coulomb-14 -72.67147760 -72.67225568 -0.00077808 0.00000000 72.67147760 -72.67229641 -0.00081881 0.00000000 72.67147760 improper 0.00000000 0.00003243 0.00003243 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 13.13273920 13.13280203 0.00006283 13.13283460 0.00009540 13.13280924 0.00007004 13.13282288 0.00008368 vdw (SR) 0.00000000 -2.84907602 -2.84907602 0.00000000 0.00000000 0.00000000 0.00000000 9.45420824 9.45420824 vdw total 9.45458480 9.45408470 -0.00050010 9.45408481 -0.00049999 9.45410094 -0.00048386 9.45420824 -0.00037656 vdw-14 12.30347040 12.30316073 -0.00030967 0.00000000 -12.30347040 12.30320585 -0.00026455 0.00000000 -12.30347040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.08444480 3.08447180 0.00002700 3.08447179 0.00002699 3.08453991 0.00009511 3.08448664 0.00004184 bond 2.62002080 2.62003855 0.00001775 2.62003854 0.00001774 2.61925410 -0.00076670 2.62002080 0.00000000 bonded 18.83720480 18.83734482 0.00014002 18.83734492 0.00014012 18.83660325 -0.00060155 18.83737216 0.00016736 dihedral 13.13273920 13.13283446 0.00009526 13.13283460 0.00009540 13.13280924 0.00007004 13.13286472 0.00012552 nonbonded -71.53635840 -71.54073286 -0.00437446 -71.54073068 -0.00437228 -71.54065422 -0.00429582 -71.59589672 -0.05953832 potential -52.69915360 -52.70338804 -0.00423444 -52.70338781 -0.00423421 -52.70410620 -0.00495260 -52.75852456 -0.05937096 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -52.69915360 Difference in potential energy from amber=>gromacs conversion: -0.00423444 Difference in potential energy from amber=>lammps conversion: -0.00423421 Difference in potential energy from amber=>desmond conversion: -0.00495260 Difference in potential energy from amber=>charmm conversion: -0.05937096 ======================================================================= INFO 2017-03-18 22:19:35 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1722522.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1722522.inpcrd') INFO 2017-03-18 22:19:36 Beginning InterMol conversion INFO 2017-03-18 22:19:36 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:19:36 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:19:36 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1723043.inpcrd INFO 2017-03-18 22:19:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1723043/mobley_1723043_converted.input INFO 2017-03-18 22:19:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1723043/mobley_1723043_converted.cms WARNING 2017-03-18 22:19:51 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:19:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1723043/mobley_1723043_converted.inp INFO 2017-03-18 22:19:51 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1723043/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1723043/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1723043/mobley_1723043_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1723043/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 85.51311310 85.51311310 0.00000000 0.00000000 0.00000000 0.00000000 87.32865720 87.32865720 coulomb total 87.30376240 87.30688167 0.00311927 87.30687948 0.00311708 87.30701564 0.00325324 87.32865720 0.02489480 coulomb-14 1.79368080 1.79376857 0.00008777 0.00000000 -1.79368080 1.79392407 0.00024327 0.00000000 -1.79368080 proper 30.86494960 30.86473926 -0.00021034 30.86473914 -0.00021046 30.86477082 -0.00017878 30.87377784 0.00882824 vdw (SR) 0.00000000 -0.45955165 -0.45955165 0.00000000 0.00000000 0.00000000 0.00000000 12.92881104 12.92881104 vdw total 12.92897840 12.92913544 0.00015704 12.92913530 0.00015690 12.92919149 0.00021309 12.92881104 -0.00016736 vdw-14 13.38838160 13.38868709 0.00030549 0.00000000 -13.38838160 13.38874113 0.00035953 0.00000000 -13.38838160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 9.00606000 9.00595303 -0.00010697 9.00595289 -0.00010711 9.00541269 -0.00064731 9.00626920 0.00020920 bond 0.24727440 0.24725497 -0.00001943 0.24725497 -0.00001943 0.24702156 -0.00025284 0.24727440 0.00000000 bonded 40.11828400 40.11794726 -0.00033674 40.11794700 -0.00033700 40.11720507 -0.00107893 40.12732144 0.00903744 dihedral 30.86494960 30.86473926 -0.00021034 30.86473914 -0.00021046 30.86477082 -0.00017878 30.87377784 0.00882824 nonbonded 100.23274080 100.23601711 0.00327631 100.23601687 0.00327607 100.23620713 0.00346633 100.25746824 0.02472744 potential 140.35102480 140.35396437 0.00293957 140.35396197 0.00293717 140.35337495 0.00235015 140.38478968 0.03376488 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 140.35102480 Difference in potential energy from amber=>gromacs conversion: 0.00293957 Difference in potential energy from amber=>lammps conversion: 0.00293717 Difference in potential energy from amber=>desmond conversion: 0.00235015 Difference in potential energy from amber=>charmm conversion: 0.03376488 ======================================================================= INFO 2017-03-18 22:19:51 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1723043.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1723043.inpcrd') INFO 2017-03-18 22:19:52 Beginning InterMol conversion INFO 2017-03-18 22:19:52 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:19:52 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:19:52 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1728386.inpcrd INFO 2017-03-18 22:19:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1728386/mobley_1728386_converted.input INFO 2017-03-18 22:19:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1728386/mobley_1728386_converted.cms WARNING 2017-03-18 22:20:07 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:20:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1728386/mobley_1728386_converted.inp INFO 2017-03-18 22:20:07 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1728386/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1728386/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1728386/mobley_1728386_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1728386/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -57.67516029 -57.67516029 0.00000000 0.00000000 0.00000000 0.00000000 -142.22566600 -142.22566600 coulomb total -142.20579200 -142.21469709 -0.00890509 -142.21469555 -0.00890355 -142.21854065 -0.01274865 -142.22566600 -0.01987400 coulomb-14 -84.53562800 -84.53953680 -0.00390880 0.00000000 84.53562800 -84.53958439 -0.00395639 0.00000000 84.53562800 improper 0.00000000 0.03134035 0.03134035 0.00000000 0.00000000 0.00000000 0.00000000 0.03133816 0.03133816 proper 16.81675120 16.78529314 -0.03145806 16.81663070 -0.00012050 16.81661125 -0.00013995 16.78528752 -0.03146368 vdw (SR) 0.00000000 3.28487595 3.28487595 0.00000000 0.00000000 0.00000000 0.00000000 26.63354488 26.63354488 vdw total 26.63367040 26.63356514 -0.00010526 26.63356496 -0.00010544 26.63340952 -0.00026088 26.63354488 -0.00012552 vdw-14 23.34881200 23.34868918 -0.00012282 0.00000000 -23.34881200 23.34869330 -0.00011870 0.00000000 -23.34881200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.03925760 3.03907569 -0.00018191 3.03907568 -0.00018192 3.03926679 0.00000919 3.03909024 -0.00016736 bond 9.07718800 9.07700403 -0.00018397 9.07700390 -0.00018410 9.07638907 -0.00079893 9.07702064 -0.00016736 bonded 28.93319680 28.93271321 -0.00048359 28.93271028 -0.00048652 28.93226710 -0.00092970 28.93273656 -0.00046024 dihedral 16.81675120 16.81663349 -0.00011771 16.81663070 -0.00012050 16.81661125 -0.00013995 16.81662568 -0.00012552 nonbonded -115.57212160 -115.58113196 -0.00901036 -115.58112975 -0.00900815 -115.58513113 -0.01300953 -115.59212112 -0.01999952 potential -86.63892480 -86.64841875 -0.00949395 -86.64841830 -0.00949350 -86.65290480 -0.01398000 -86.65934272 -0.02041792 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -86.63892480 Difference in potential energy from amber=>gromacs conversion: -0.00949395 Difference in potential energy from amber=>lammps conversion: -0.00949350 Difference in potential energy from amber=>desmond conversion: -0.01398000 Difference in potential energy from amber=>charmm conversion: -0.02041792 ======================================================================= INFO 2017-03-18 22:20:07 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1728386.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1728386.inpcrd') INFO 2017-03-18 22:20:08 Beginning InterMol conversion INFO 2017-03-18 22:20:08 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:20:08 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_172879.inpcrd INFO 2017-03-18 22:20:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_172879/mobley_172879_converted.input INFO 2017-03-18 22:20:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_172879/mobley_172879_converted.cms INFO 2017-03-18 22:20:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_172879/mobley_172879_converted.rst7 WARNING 2017-03-18 22:20:23 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:20:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_172879/mobley_172879_converted.inp INFO 2017-03-18 22:20:24 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_172879/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_172879/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_172879/mobley_172879_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_172879/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_172879/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -32.51924893 -32.51924893 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 21.92800928 21.92800928 coulomb total 21.85554240 21.85620254 0.00066014 21.85620222 0.00065982 21.85619464 0.00065224 21.85554240 0.00000000 21.92800928 0.07246688 coulomb-14 54.37359040 54.37545147 0.00186107 0.00000000 -54.37359040 54.37542216 0.00183176 54.37359040 0.00000000 0.00000000 -54.37359040 improper 0.00000000 0.00010898 0.00010898 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00125520 0.00105477 -0.00020043 0.00116370 -0.00009150 0.00115665 -0.00009855 0.00125520 0.00000000 0.00104600 -0.00020920 vdw (SR) 0.00000000 -6.85572908 -6.85572908 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 40.35861296 40.35861296 vdw total 40.35844560 40.35865808 0.00021248 40.35865815 0.00021255 40.35869777 0.00025217 40.35844560 0.00000000 40.35861296 0.00016736 vdw-14 47.21434800 47.21438716 0.00003916 0.00000000 -47.21434800 47.21443461 0.00008661 47.21434800 0.00000000 0.00000000 -47.21434800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 6.92828560 6.92841134 0.00012574 6.92841154 0.00012594 6.92918227 0.00089667 6.92828560 0.00000000 6.92841112 0.00012552 bond 1.51418960 1.51423898 0.00004938 1.51423897 0.00004937 1.51445157 0.00026197 1.51418960 0.00000000 1.51423144 0.00004184 bonded 8.44373040 8.44381406 0.00008366 8.44381421 0.00008381 8.44479049 0.00106009 8.44373040 0.00000000 8.44381408 0.00008368 dihedral 0.00125520 0.00116375 -0.00009145 0.00116370 -0.00009150 0.00115665 -0.00009855 0.00125520 0.00000000 0.00117152 -0.00008368 nonbonded 62.21398800 62.21486062 0.00087262 62.21486246 0.00087446 62.21489241 0.00090441 62.21398800 0.00000000 62.28662224 0.07263424 potential 70.65771840 70.65867469 0.00095629 70.65867235 0.00095395 70.65955936 0.00184096 70.65771840 0.00000000 70.73043632 0.07271792 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 70.65771840 Difference in potential energy from amber=>gromacs conversion: 0.00095629 Difference in potential energy from amber=>lammps conversion: 0.00095395 Difference in potential energy from amber=>desmond conversion: 0.00184096 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.07271792 ======================================================================= INFO 2017-03-18 22:20:24 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_172879.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_172879.inpcrd') INFO 2017-03-18 22:20:24 Beginning InterMol conversion INFO 2017-03-18 22:20:24 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:20:24 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1733799.inpcrd INFO 2017-03-18 22:20:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1733799/mobley_1733799_converted.input INFO 2017-03-18 22:20:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1733799/mobley_1733799_converted.cms INFO 2017-03-18 22:20:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1733799/mobley_1733799_converted.rst7 WARNING 2017-03-18 22:20:40 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:20:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1733799/mobley_1733799_converted.inp INFO 2017-03-18 22:20:40 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1733799/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1733799/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1733799/mobley_1733799_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_1733799/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1733799/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 28.03517016 28.03517016 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -74.13633784 -74.13633784 coulomb total -74.13294880 -74.12743235 0.00551645 -74.12743010 0.00551870 -74.12794264 0.00500616 -74.13294880 0.00000000 -74.13633784 -0.00338904 coulomb-14 -102.15779920 -102.16260251 -0.00480331 0.00000000 102.15779920 -102.16257607 -0.00477687 -102.15779920 0.00000000 0.00000000 102.15779920 improper 0.00000000 0.00004666 0.00004666 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00038095 -0.00003745 0.00042761 0.00000921 0.00041822 -0.00000018 0.00041840 0.00000000 0.00037656 -0.00004184 vdw (SR) 0.00000000 -1.67216056 -1.67216056 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 13.90832728 13.90832728 vdw total 13.90803440 13.90833145 0.00029705 13.90833146 0.00029706 13.90839087 0.00035647 13.90803440 0.00000000 13.90832728 0.00029288 vdw-14 15.58037920 15.58049202 0.00011282 0.00000000 -15.58037920 15.58055371 0.00017451 15.58037920 0.00000000 0.00000000 -15.58037920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.83889200 0.83878893 -0.00010307 0.83878895 -0.00010305 0.83880850 -0.00008350 0.83889200 0.00000000 0.83880832 -0.00008368 bond 0.81211440 0.81217090 0.00005650 0.81217088 0.00005648 0.81214426 0.00002986 0.81211440 0.00000000 0.81215624 0.00004184 bonded 1.65142480 1.65138743 -0.00003737 1.65138744 -0.00003736 1.65137098 -0.00005382 1.65142480 0.00000000 1.65138296 -0.00004184 dihedral 0.00041840 0.00042760 0.00000920 0.00042761 0.00000921 0.00041822 -0.00000018 0.00041840 0.00000000 0.00041840 0.00000000 nonbonded -60.22491440 -60.21910090 0.00581350 -60.21909864 0.00581576 -60.21955177 0.00536263 -60.22491440 0.00000000 -60.22801056 -0.00309616 potential -58.57348960 -58.56771347 0.00577613 -58.56771150 0.00577810 -58.56823575 0.00525385 -58.57348960 0.00000000 -58.57658576 -0.00309616 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -58.57348960 Difference in potential energy from amber=>gromacs conversion: 0.00577613 Difference in potential energy from amber=>lammps conversion: 0.00577810 Difference in potential energy from amber=>desmond conversion: 0.00525385 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.00309616 ======================================================================= INFO 2017-03-18 22:20:40 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1733799.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1733799.inpcrd') INFO 2017-03-18 22:20:40 Beginning InterMol conversion INFO 2017-03-18 22:20:40 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:20:40 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:20:40 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1735893.inpcrd INFO 2017-03-18 22:20:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1735893/mobley_1735893_converted.input INFO 2017-03-18 22:20:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1735893/mobley_1735893_converted.cms WARNING 2017-03-18 22:20:56 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:20:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1735893/mobley_1735893_converted.inp INFO 2017-03-18 22:20:56 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1735893/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1735893/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1735893/mobley_1735893_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1735893/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 8.70363733 8.70363733 0.00000000 0.00000000 0.00000000 0.00000000 -116.98920056 -116.98920056 coulomb total -117.01476480 -117.01862769 -0.00386289 -117.01862663 -0.00386183 -117.01877751 -0.00401271 -116.98920056 0.02556424 coulomb-14 -125.71790320 -125.72226503 -0.00436183 0.00000000 125.71790320 -125.72223448 -0.00433128 0.00000000 125.71790320 improper 0.00000000 0.00035654 0.00035654 0.00000000 0.00000000 0.00000000 0.00000000 0.00037656 0.00037656 proper 6.80192880 6.80168781 -0.00024099 6.80204428 0.00011548 6.80202156 0.00009276 6.80167776 -0.00025104 vdw (SR) 0.00000000 -2.45024352 -2.45024352 0.00000000 0.00000000 0.00000000 0.00000000 5.40183688 5.40183688 vdw total 5.40196240 5.40170403 -0.00025837 5.40170425 -0.00025815 5.40162043 -0.00034197 5.40183688 -0.00012552 vdw-14 7.85211280 7.85194756 -0.00016524 0.00000000 -7.85211280 7.85188034 -0.00023246 0.00000000 -7.85211280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 10.43782480 10.43778120 -0.00004360 10.43778129 -0.00004351 10.43698721 -0.00083759 10.43782480 0.00000000 bond 6.43080800 6.43101475 0.00020675 6.43101469 0.00020669 6.43185789 0.00104989 6.43101720 0.00020920 bonded 23.67056160 23.67084030 0.00027870 23.67084025 0.00027865 23.67086666 0.00030506 23.67089632 0.00033472 dihedral 6.80192880 6.80204435 0.00011555 6.80204428 0.00011548 6.80202156 0.00009276 6.80205432 0.00012552 nonbonded -111.61280240 -111.61692366 -0.00412126 -111.61692364 -0.00412124 -111.61715708 -0.00435468 -111.58736368 0.02543872 potential -87.94224080 -87.94608336 -0.00384256 -87.94608171 -0.00384091 -87.94635284 -0.00411204 -87.91646736 0.02577344 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -87.94224080 Difference in potential energy from amber=>gromacs conversion: -0.00384256 Difference in potential energy from amber=>lammps conversion: -0.00384091 Difference in potential energy from amber=>desmond conversion: -0.00411204 Difference in potential energy from amber=>charmm conversion: 0.02577344 ======================================================================= INFO 2017-03-18 22:20:56 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1735893.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1735893.inpcrd') INFO 2017-03-18 22:20:56 Beginning InterMol conversion INFO 2017-03-18 22:20:56 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:20:56 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:20:56 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1743409.inpcrd INFO 2017-03-18 22:20:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1743409/mobley_1743409_converted.input INFO 2017-03-18 22:20:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1743409/mobley_1743409_converted.cms WARNING 2017-03-18 22:21:12 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:21:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1743409/mobley_1743409_converted.inp INFO 2017-03-18 22:21:12 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1743409/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1743409/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1743409/mobley_1743409_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1743409/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -277.83821980 -277.83821980 0.00000000 0.00000000 0.00000000 0.00000000 -202.08427120 -202.08427120 coulomb total -202.12150880 -202.12426022 -0.00275142 -202.12425769 -0.00274889 -202.12434179 -0.00283299 -202.08427120 0.03723760 coulomb-14 75.71324560 75.71395959 0.00071399 0.00000000 -75.71324560 75.71391588 0.00067028 0.00000000 -75.71324560 improper 0.00000000 0.00162997 0.00162997 0.00000000 0.00000000 0.00000000 0.00000000 0.00163176 0.00163176 proper 26.24748720 26.24598231 -0.00150489 26.24761272 0.00012552 26.24759506 0.00010786 26.24598096 -0.00150624 vdw (SR) 0.00000000 -5.66082612 -5.66082612 0.00000000 0.00000000 0.00000000 0.00000000 14.51454704 14.51454704 vdw total 14.51429600 14.51434341 0.00004741 14.51434370 0.00004770 14.51426680 -0.00002920 14.51454704 0.00025104 vdw-14 20.17524800 20.17516953 -0.00007847 0.00000000 -20.17524800 20.17509888 -0.00014912 0.00000000 -20.17524800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 6.76929360 6.76926321 -0.00003039 6.76926306 -0.00003054 6.76906854 -0.00022506 6.76933544 0.00004184 bond 4.27772160 4.27769178 -0.00002982 4.27769189 -0.00002971 4.27736638 -0.00035522 4.27767976 -0.00004184 bonded 37.29450240 37.29456727 0.00006487 37.29456767 0.00006527 37.29402998 -0.00047242 37.29462792 0.00012552 dihedral 26.24748720 26.24761227 0.00012507 26.24761272 0.00012552 26.24759506 0.00010786 26.24761272 0.00012552 nonbonded -187.60721280 -187.60991681 -0.00270401 -187.60991566 -0.00270286 -187.61007499 -0.00286219 -187.56972416 0.03748864 potential -150.31271040 -150.31534955 -0.00263915 -150.31534632 -0.00263592 -150.31615634 -0.00344594 -150.27509624 0.03761416 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -150.31271040 Difference in potential energy from amber=>gromacs conversion: -0.00263915 Difference in potential energy from amber=>lammps conversion: -0.00263592 Difference in potential energy from amber=>desmond conversion: -0.00344594 Difference in potential energy from amber=>charmm conversion: 0.03761416 ======================================================================= INFO 2017-03-18 22:21:12 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1743409.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1743409.inpcrd') INFO 2017-03-18 22:21:12 Beginning InterMol conversion INFO 2017-03-18 22:21:12 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:21:12 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:21:12 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1755375.inpcrd INFO 2017-03-18 22:21:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1755375/mobley_1755375_converted.input INFO 2017-03-18 22:21:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1755375/mobley_1755375_converted.cms WARNING 2017-03-18 22:21:28 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:21:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1755375/mobley_1755375_converted.inp INFO 2017-03-18 22:21:28 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1755375/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1755375/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1755375/mobley_1755375_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1755375/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -65.41963215 -65.41963215 0.00000000 0.00000000 0.00000000 0.00000000 -42.07857168 -42.07857168 coulomb total -42.06342560 -42.07179257 -0.00836697 -42.07179360 -0.00836800 -42.07357372 -0.01014812 -42.07857168 -0.01514608 coulomb-14 23.34588320 23.34783958 0.00195638 0.00000000 -23.34588320 23.34782098 0.00193778 0.00000000 -23.34588320 improper 0.00000000 0.00008958 0.00008958 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00083680 0.00086339 0.00002659 0.00095299 0.00011619 0.00095365 0.00011685 0.00087864 0.00004184 vdw (SR) 0.00000000 1.52464952 1.52464952 0.00000000 0.00000000 0.00000000 0.00000000 26.32351048 26.32351048 vdw total 26.32321760 26.32335943 0.00014183 26.32335986 0.00014226 26.32331994 0.00010234 26.32351048 0.00029288 vdw-14 24.79856800 24.79870991 0.00014191 0.00000000 -24.79856800 24.79864101 0.00007301 0.00000000 -24.79856800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.84433120 0.84417959 -0.00015161 0.84417957 -0.00015163 0.84419015 -0.00014105 0.84416384 -0.00016736 bond 1.89451520 1.89455970 0.00004450 1.89455972 0.00004452 1.89417763 -0.00033757 1.89455704 0.00004184 bonded 2.73968320 2.73969225 0.00000905 2.73969228 0.00000908 2.73932144 -0.00036176 2.73968320 0.00000000 dihedral 0.00083680 0.00095297 0.00011617 0.00095299 0.00011619 0.00095365 0.00011685 0.00096232 0.00012552 nonbonded -15.74020800 -15.74843314 -0.00822514 -15.74843249 -0.00822449 -15.75025379 -0.01004579 -15.75506120 -0.01485320 potential -13.00052480 -13.00874088 -0.00821608 -13.00874008 -0.00821528 -13.01099438 -0.01046958 -13.01537800 -0.01485320 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -13.00052480 Difference in potential energy from amber=>gromacs conversion: -0.00821608 Difference in potential energy from amber=>lammps conversion: -0.00821528 Difference in potential energy from amber=>desmond conversion: -0.01046958 Difference in potential energy from amber=>charmm conversion: -0.01485320 ======================================================================= INFO 2017-03-18 22:21:28 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1755375.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1755375.inpcrd') INFO 2017-03-18 22:21:28 Beginning InterMol conversion INFO 2017-03-18 22:21:28 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:21:28 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:21:28 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1760914.inpcrd INFO 2017-03-18 22:21:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1760914/mobley_1760914_converted.input INFO 2017-03-18 22:21:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1760914/mobley_1760914_converted.cms WARNING 2017-03-18 22:21:44 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:21:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1760914/mobley_1760914_converted.inp INFO 2017-03-18 22:21:44 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1760914/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1760914/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1760914/mobley_1760914_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1760914/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -6.63560944 -6.63560944 0.00000000 0.00000000 0.00000000 0.00000000 -1.58029680 -1.58029680 coulomb total -1.57485760 -1.57509536 -0.00023776 -1.57509533 -0.00023773 -1.57512387 -0.00026627 -1.58029680 -0.00543920 coulomb-14 5.06054800 5.06051408 -0.00003392 0.00000000 -5.06054800 5.06052143 -0.00002657 0.00000000 -5.06054800 improper 0.00000000 0.00034359 0.00034359 0.00000000 0.00000000 0.00000000 0.00000000 0.00033472 0.00033472 proper 0.00292880 0.00275996 -0.00016884 0.00310340 0.00017460 0.00310136 0.00017256 0.00276144 -0.00016736 vdw (SR) 0.00000000 1.30223158 1.30223158 0.00000000 0.00000000 0.00000000 0.00000000 20.96200736 20.96200736 vdw total 20.96225840 20.96195787 -0.00030053 20.96195799 -0.00030041 20.96202347 -0.00023493 20.96200736 -0.00025104 vdw-14 19.65977920 19.65972630 -0.00005290 0.00000000 -19.65977920 19.65971313 -0.00006607 0.00000000 -19.65977920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.15185520 1.15166563 -0.00018957 1.15166562 -0.00018958 1.15170522 -0.00014998 1.15168784 -0.00016736 bond 1.19620560 1.19616610 -0.00003950 1.19616610 -0.00003950 1.19601868 -0.00018692 1.19616376 -0.00004184 bonded 2.35098960 2.35093528 -0.00005432 2.35093513 -0.00005447 2.35082526 -0.00016434 2.35094776 -0.00004184 dihedral 0.00292880 0.00310355 0.00017475 0.00310340 0.00017460 0.00310136 0.00017256 0.00309616 0.00016736 nonbonded 19.38740080 19.38686251 -0.00053829 19.38686274 -0.00053806 19.38689960 -0.00050120 19.38171056 -0.00569024 potential 21.73839040 21.73779779 -0.00059261 21.73779753 -0.00059287 21.73766925 -0.00072115 21.73265832 -0.00573208 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 21.73839040 Difference in potential energy from amber=>gromacs conversion: -0.00059261 Difference in potential energy from amber=>lammps conversion: -0.00059287 Difference in potential energy from amber=>desmond conversion: -0.00072115 Difference in potential energy from amber=>charmm conversion: -0.00573208 ======================================================================= INFO 2017-03-18 22:21:44 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1760914.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1760914.inpcrd') INFO 2017-03-18 22:21:44 Beginning InterMol conversion INFO 2017-03-18 22:21:44 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:21:44 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:21:44 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1770205.inpcrd INFO 2017-03-18 22:21:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1770205/mobley_1770205_converted.input INFO 2017-03-18 22:21:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1770205/mobley_1770205_converted.cms WARNING 2017-03-18 22:22:00 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:22:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1770205/mobley_1770205_converted.inp INFO 2017-03-18 22:22:00 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1770205/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1770205/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1770205/mobley_1770205_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1770205/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 12.15118861 12.15118861 0.00000000 0.00000000 0.00000000 0.00000000 -363.64587480 -363.64587480 coulomb total -363.61763280 -363.62809375 -0.01046095 -363.62808862 -0.01045582 -363.62769842 -0.01006562 -363.64587480 -0.02824200 coulomb-14 -375.77675520 -375.77928236 -0.00252716 0.00000000 375.77675520 -375.77920451 -0.00244931 0.00000000 375.77675520 improper 0.00000000 0.00012730 0.00012730 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 64.56288560 64.56277231 -0.00011329 64.56290234 0.00001674 64.56312995 0.00024435 64.56276008 -0.00012552 vdw (SR) 0.00000000 -14.72206629 -14.72206629 0.00000000 0.00000000 0.00000000 0.00000000 25.83030056 25.83030056 vdw total 25.83034240 25.83028686 -0.00005554 25.83028675 -0.00005565 25.83070570 0.00036330 25.83030056 -0.00004184 vdw-14 40.55216480 40.55235315 0.00018835 0.00000000 -40.55216480 40.55270428 0.00053948 0.00000000 -40.55216480 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 61.36923840 61.36914123 -0.00009717 61.36914217 -0.00009623 61.36890619 -0.00033221 61.36928024 0.00004184 bond 34.96694320 34.96710552 0.00016232 34.96710554 0.00016234 34.96741160 0.00046840 34.96711056 0.00016736 bonded 160.89906720 160.89914636 0.00007916 160.89915004 0.00008284 160.89944773 0.00038053 160.89927640 0.00020920 dihedral 64.56288560 64.56289961 0.00001401 64.56290234 0.00001674 64.56312995 0.00024435 64.56288560 0.00000000 nonbonded -337.78729040 -337.79780689 -0.01051649 -337.79780479 -0.01051439 -337.79699272 -0.00970232 -337.81557424 -0.02828384 potential -176.88822320 -176.89866053 -0.01043733 -176.89865391 -0.01043071 -176.89786899 -0.00964579 -176.91625600 -0.02803280 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -176.88822320 Difference in potential energy from amber=>gromacs conversion: -0.01043733 Difference in potential energy from amber=>lammps conversion: -0.01043071 Difference in potential energy from amber=>desmond conversion: -0.00964579 Difference in potential energy from amber=>charmm conversion: -0.02803280 ======================================================================= INFO 2017-03-18 22:22:00 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1770205.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1770205.inpcrd') INFO 2017-03-18 22:22:00 Beginning InterMol conversion INFO 2017-03-18 22:22:00 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:22:01 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:22:01 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1781152.inpcrd INFO 2017-03-18 22:22:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1781152/mobley_1781152_converted.input INFO 2017-03-18 22:22:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1781152/mobley_1781152_converted.cms WARNING 2017-03-18 22:22:16 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:22:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1781152/mobley_1781152_converted.inp INFO 2017-03-18 22:22:16 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1781152/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1781152/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1781152/mobley_1781152_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1781152/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -171.58413582 -171.58413582 0.00000000 0.00000000 0.00000000 0.00000000 6.27093736 6.27093736 coulomb total 6.31407440 6.31299757 -0.00107683 6.31299744 -0.00107696 6.31308990 -0.00098450 6.27093736 -0.04313704 coulomb-14 177.88359680 177.89713339 0.01353659 0.00000000 -177.88359680 177.89710526 0.01350846 0.00000000 -177.88359680 improper 0.00000000 0.00002626 0.00002626 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00669440 0.00657903 -0.00011537 0.00660530 -0.00008910 0.00660816 -0.00008624 0.00656888 -0.00012552 vdw (SR) 0.00000000 -1.52516177 -1.52516177 0.00000000 0.00000000 0.00000000 0.00000000 18.07341560 18.07341560 vdw total 18.07362480 18.07322677 -0.00039803 18.07322690 -0.00039790 18.07349261 -0.00013219 18.07341560 -0.00020920 vdw-14 19.59869280 19.59838855 -0.00030425 0.00000000 -19.59869280 19.59855816 -0.00013464 0.00000000 -19.59869280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.63759360 2.63747207 -0.00012153 2.63747205 -0.00012155 2.63735422 -0.00023938 2.63746808 -0.00012552 bond 2.55391360 2.55393062 0.00001702 2.55393063 0.00001703 2.55371463 -0.00019897 2.55391360 0.00000000 bonded 5.19820160 5.19800799 -0.00019361 5.19800799 -0.00019361 5.19767701 -0.00052459 5.19799240 -0.00020920 dihedral 0.00669440 0.00660529 -0.00008911 0.00660530 -0.00008910 0.00660816 -0.00008624 0.00661072 -0.00008368 nonbonded 24.38769920 24.38622434 -0.00147486 24.38622476 -0.00147444 24.38658251 -0.00111669 24.34435296 -0.04334624 potential 29.58590080 29.58423233 -0.00166847 29.58423264 -0.00166816 29.58420030 -0.00170050 29.54234536 -0.04355544 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 29.58590080 Difference in potential energy from amber=>gromacs conversion: -0.00166847 Difference in potential energy from amber=>lammps conversion: -0.00166816 Difference in potential energy from amber=>desmond conversion: -0.00170050 Difference in potential energy from amber=>charmm conversion: -0.04355544 ======================================================================= INFO 2017-03-18 22:22:16 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1781152.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1781152.inpcrd') INFO 2017-03-18 22:22:17 Beginning InterMol conversion INFO 2017-03-18 22:22:17 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:22:17 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:22:17 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1792062.inpcrd INFO 2017-03-18 22:22:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1792062/mobley_1792062_converted.input INFO 2017-03-18 22:22:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1792062/mobley_1792062_converted.cms WARNING 2017-03-18 22:22:32 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:22:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1792062/mobley_1792062_converted.inp INFO 2017-03-18 22:22:32 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1792062/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1792062/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1792062/mobley_1792062_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1792062/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -2.21555352 -2.21555352 coulomb total -2.22044880 -2.21809209 0.00235671 -2.21809208 0.00235672 -2.21809546 0.00235334 -2.21555352 0.00489528 coulomb-14 -2.22044880 -2.21809209 0.00235671 0.00000000 2.22044880 -2.21809546 0.00235334 0.00000000 2.22044880 proper 13.58712160 13.58723986 0.00011826 13.58724001 0.00011841 13.58724248 0.00012088 13.58724712 0.00012552 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.73144688 -0.73144688 vdw total -0.73136320 -0.73146543 -0.00010223 -0.73146542 -0.00010222 -0.73148986 -0.00012666 -0.73144688 -0.00008368 vdw-14 -0.73136320 -0.73146543 -0.00010223 0.00000000 0.73136320 -0.73148986 -0.00012666 0.00000000 0.73136320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.11538240 4.11523248 -0.00014992 4.11523249 -0.00014991 4.11531000 -0.00007240 4.11534056 -0.00004184 bond 1.61837120 1.61841022 0.00003902 1.61841024 0.00003904 1.61802679 -0.00034441 1.61841304 0.00004184 bonded 19.32087520 19.32088256 0.00000736 19.32088273 0.00000753 19.32057927 -0.00029593 19.32100072 0.00012552 dihedral 13.58712160 13.58723986 0.00011826 13.58724001 0.00011841 13.58724248 0.00012088 13.58724712 0.00012552 nonbonded -2.95181200 -2.94955752 0.00225448 -2.94955749 0.00225451 -2.94958533 0.00222667 -2.94700040 0.00481160 potential 16.36906320 16.37132505 0.00226185 16.37132507 0.00226187 16.37095989 0.00189669 16.37400032 0.00493712 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 16.36906320 Difference in potential energy from amber=>gromacs conversion: 0.00226185 Difference in potential energy from amber=>lammps conversion: 0.00226187 Difference in potential energy from amber=>desmond conversion: 0.00189669 Difference in potential energy from amber=>charmm conversion: 0.00493712 ======================================================================= INFO 2017-03-18 22:22:32 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1792062.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1792062.inpcrd') INFO 2017-03-18 22:22:33 Beginning InterMol conversion INFO 2017-03-18 22:22:33 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:22:33 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:22:33 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1800170.inpcrd INFO 2017-03-18 22:22:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1800170/mobley_1800170_converted.input INFO 2017-03-18 22:22:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1800170/mobley_1800170_converted.cms WARNING 2017-03-18 22:22:48 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:22:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1800170/mobley_1800170_converted.inp INFO 2017-03-18 22:22:48 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1800170/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1800170/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1800170/mobley_1800170_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1800170/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 11.62058189 11.62058189 0.00000000 0.00000000 0.00000000 0.00000000 4.97260032 4.97260032 coulomb total 4.97184720 4.97213615 0.00028895 4.97213590 0.00028870 4.97212196 0.00027476 4.97260032 0.00075312 coulomb-14 -6.64837600 -6.64844574 -0.00006974 0.00000000 6.64837600 -6.64842395 -0.00004795 0.00000000 6.64837600 proper 0.01338880 0.01335246 -0.00003634 0.01335245 -0.00003635 0.01334981 -0.00003899 0.01334696 -0.00004184 vdw (SR) 0.00000000 -0.04774904 -0.04774904 0.00000000 0.00000000 0.00000000 0.00000000 0.35718808 0.35718808 vdw total 0.35731360 0.35718451 -0.00012909 0.35718451 -0.00012909 0.35716753 -0.00014607 0.35718808 -0.00012552 vdw-14 0.40501120 0.40493355 -0.00007765 0.00000000 -0.40501120 0.40491598 -0.00009522 0.00000000 -0.40501120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.93345040 0.93338908 -0.00006132 0.93338906 -0.00006134 0.93337978 -0.00007062 0.93336672 -0.00008368 bond 0.52676560 0.52685661 0.00009101 0.52685660 0.00009100 0.52653601 -0.00022959 0.52684928 0.00008368 bonded 1.47360480 1.47359815 -0.00000665 1.47359811 -0.00000669 1.47326560 -0.00033920 1.47356296 -0.00004184 dihedral 0.01338880 0.01335246 -0.00003634 0.01335245 -0.00003635 0.01334981 -0.00003899 0.01334696 -0.00004184 nonbonded 5.32916080 5.32932066 0.00015986 5.32932063 0.00015983 5.32928950 0.00012870 5.32978840 0.00062760 potential 6.80276560 6.80291881 0.00015321 6.80291873 0.00015313 6.80253983 -0.00022577 6.80339320 0.00062760 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 6.80276560 Difference in potential energy from amber=>gromacs conversion: 0.00015321 Difference in potential energy from amber=>lammps conversion: 0.00015313 Difference in potential energy from amber=>desmond conversion: -0.00022577 Difference in potential energy from amber=>charmm conversion: 0.00062760 ======================================================================= INFO 2017-03-18 22:22:48 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1800170.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1800170.inpcrd') INFO 2017-03-18 22:22:48 Beginning InterMol conversion INFO 2017-03-18 22:22:48 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:22:49 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:22:49 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1803862.inpcrd INFO 2017-03-18 22:22:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1803862/mobley_1803862_converted.input INFO 2017-03-18 22:22:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1803862/mobley_1803862_converted.cms WARNING 2017-03-18 22:23:04 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:23:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1803862/mobley_1803862_converted.inp INFO 2017-03-18 22:23:04 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1803862/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1803862/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1803862/mobley_1803862_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1803862/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 5.75679898 5.75679898 0.00000000 0.00000000 0.00000000 0.00000000 -2.49261800 -2.49261800 coulomb total -2.48906160 -2.49413018 -0.00506858 -2.49413014 -0.00506854 -2.49413303 -0.00507143 -2.49261800 -0.00355640 coulomb-14 -8.25084800 -8.25092916 -0.00008116 0.00000000 8.25084800 -8.25092197 -0.00007397 0.00000000 8.25084800 proper 3.80074560 3.80071498 -0.00003062 3.80071736 -0.00002824 3.80073247 -0.00001313 3.80070376 -0.00004184 vdw (SR) 0.00000000 2.66611789 2.66611789 0.00000000 0.00000000 0.00000000 0.00000000 9.44194912 9.44194912 vdw total 9.44203280 9.44185135 -0.00018145 9.44185163 -0.00018117 9.44155531 -0.00047749 9.44194912 -0.00008368 vdw-14 6.77598800 6.77573346 -0.00025454 0.00000000 -6.77598800 6.77557429 -0.00041371 0.00000000 -6.77598800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.92043200 2.92033266 -0.00009934 2.92033267 -0.00009933 2.92036704 -0.00006496 2.92030648 -0.00012552 bond 0.56274800 0.56275569 0.00000769 0.56275570 0.00000770 0.56247257 -0.00027543 0.56274800 0.00000000 bonded 7.28392560 7.28380333 -0.00012227 7.28380573 -0.00011987 7.28357207 -0.00035353 7.28375824 -0.00016736 dihedral 3.80074560 3.80071498 -0.00003062 3.80071736 -0.00002824 3.80073247 -0.00001313 3.80070376 -0.00004184 nonbonded 6.95297120 6.94772117 -0.00525003 6.94772154 -0.00524966 6.94742228 -0.00554892 6.94933112 -0.00364008 potential 14.23689680 14.23152451 -0.00537229 14.23152705 -0.00536975 14.23096037 -0.00593643 14.23313120 -0.00376560 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 14.23689680 Difference in potential energy from amber=>gromacs conversion: -0.00537229 Difference in potential energy from amber=>lammps conversion: -0.00536975 Difference in potential energy from amber=>desmond conversion: -0.00593643 Difference in potential energy from amber=>charmm conversion: -0.00376560 ======================================================================= INFO 2017-03-18 22:23:04 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1803862.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1803862.inpcrd') INFO 2017-03-18 22:23:05 Beginning InterMol conversion INFO 2017-03-18 22:23:05 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:23:05 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:23:05 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1821184.inpcrd INFO 2017-03-18 22:23:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1821184/mobley_1821184_converted.input INFO 2017-03-18 22:23:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1821184/mobley_1821184_converted.cms WARNING 2017-03-18 22:23:20 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:23:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1821184/mobley_1821184_converted.inp INFO 2017-03-18 22:23:20 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1821184/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1821184/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1821184/mobley_1821184_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1821184/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -18.12247083 -18.12247083 0.00000000 0.00000000 0.00000000 0.00000000 -32.59432232 -32.59432232 coulomb total -32.62181120 -32.61403168 0.00777952 -32.61403147 0.00777973 -32.61403482 0.00777638 -32.59432232 0.02748888 coulomb-14 -14.49128400 -14.49156084 -0.00027684 0.00000000 14.49128400 -14.49155261 -0.00026861 0.00000000 14.49128400 improper 0.00000000 0.00011175 0.00011175 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00125520 0.00105768 -0.00019752 0.00116913 -0.00008607 0.00115840 -0.00009680 0.00104600 -0.00020920 vdw (SR) 0.00000000 -3.78000969 -3.78000969 0.00000000 0.00000000 0.00000000 0.00000000 10.39121504 10.39121504 vdw total 10.39138240 10.39125144 -0.00013096 10.39125144 -0.00013096 10.39097390 -0.00040850 10.39121504 -0.00016736 vdw-14 14.17120800 14.17126113 0.00005313 0.00000000 -14.17120800 14.17098081 -0.00022719 0.00000000 -14.17120800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 64.21686880 64.21699345 0.00012465 64.21699432 0.00012552 64.21716294 0.00029414 64.21699432 0.00012552 bond 4.50240240 4.50236634 -0.00003606 4.50236642 -0.00003598 4.50256591 0.00016351 4.50236056 -0.00004184 bonded 68.72052640 68.72052922 0.00000282 68.72052986 0.00000346 68.72088724 0.00036084 68.72052640 0.00000000 dihedral 0.00125520 0.00116943 -0.00008577 0.00116913 -0.00008607 0.00115840 -0.00009680 0.00117152 -0.00008368 nonbonded -22.23042880 -22.22278024 0.00764856 -22.22278003 0.00764877 -22.22306092 0.00736788 -22.20310728 0.02732152 potential 46.49009760 46.49774899 0.00765139 46.49775014 0.00765254 46.49775976 0.00766216 46.51746096 0.02736336 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 46.49009760 Difference in potential energy from amber=>gromacs conversion: 0.00765139 Difference in potential energy from amber=>lammps conversion: 0.00765254 Difference in potential energy from amber=>desmond conversion: 0.00766216 Difference in potential energy from amber=>charmm conversion: 0.02736336 ======================================================================= INFO 2017-03-18 22:23:20 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1821184.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1821184.inpcrd') INFO 2017-03-18 22:23:21 Beginning InterMol conversion INFO 2017-03-18 22:23:21 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:23:21 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:23:21 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1827204.inpcrd INFO 2017-03-18 22:23:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1827204/mobley_1827204_converted.input INFO 2017-03-18 22:23:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1827204/mobley_1827204_converted.cms WARNING 2017-03-18 22:23:36 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:23:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1827204/mobley_1827204_converted.inp INFO 2017-03-18 22:23:36 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1827204/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1827204/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1827204/mobley_1827204_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1827204/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -8.26596666 -8.26596666 0.00000000 0.00000000 0.00000000 0.00000000 -6.97799152 -6.97799152 coulomb total -6.98100400 -6.98141583 -0.00041183 -6.98141571 -0.00041171 -6.98152636 -0.00052236 -6.97799152 0.00301248 coulomb-14 1.28448800 1.28455082 0.00006282 0.00000000 -1.28448800 1.28452826 0.00004026 0.00000000 -1.28448800 improper 0.00000000 0.00353581 0.00353581 0.00000000 0.00000000 0.00000000 0.00000000 0.00355640 0.00355640 proper 6.60862800 6.60523186 -0.00339614 6.60876775 0.00013975 6.60876482 0.00013682 6.60523896 -0.00338904 vdw (SR) 0.00000000 -2.09022859 -2.09022859 0.00000000 0.00000000 0.00000000 0.00000000 5.27062664 5.27062664 vdw total 5.27058480 5.27051953 -0.00006527 5.27051953 -0.00006527 5.27053391 -0.00005089 5.27062664 0.00004184 vdw-14 7.36091120 7.36074812 -0.00016308 0.00000000 -7.36091120 7.36074710 -0.00016410 0.00000000 -7.36091120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.27900080 3.27894803 -0.00005277 3.27894804 -0.00005276 3.27903300 0.00003220 3.27891712 -0.00008368 bond 1.19118480 1.19127069 0.00008589 1.19127070 0.00008590 1.19143199 0.00024719 1.19126848 0.00008368 bonded 11.07881360 11.07898639 0.00017279 11.07898648 0.00017288 11.07922980 0.00041620 11.07898096 0.00016736 dihedral 6.60862800 6.60876766 0.00013966 6.60876775 0.00013975 6.60876482 0.00013682 6.60879536 0.00016736 nonbonded -1.71041920 -1.71089631 -0.00047711 -1.71089613 -0.00047693 -1.71099246 -0.00057326 -1.70736488 0.00305432 potential 9.36839440 9.36809008 -0.00030432 9.36809022 -0.00030418 9.36818809 -0.00020631 9.37161608 0.00322168 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 9.36839440 Difference in potential energy from amber=>gromacs conversion: -0.00030432 Difference in potential energy from amber=>lammps conversion: -0.00030418 Difference in potential energy from amber=>desmond conversion: -0.00020631 Difference in potential energy from amber=>charmm conversion: 0.00322168 ======================================================================= INFO 2017-03-18 22:23:36 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1827204.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1827204.inpcrd') INFO 2017-03-18 22:23:37 Beginning InterMol conversion INFO 2017-03-18 22:23:37 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:23:37 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:23:37 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1838110.inpcrd INFO 2017-03-18 22:23:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1838110/mobley_1838110_converted.input INFO 2017-03-18 22:23:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1838110/mobley_1838110_converted.cms WARNING 2017-03-18 22:23:52 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:23:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1838110/mobley_1838110_converted.inp INFO 2017-03-18 22:23:52 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1838110/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1838110/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1838110/mobley_1838110_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1838110/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 61.80738688 61.80738688 coulomb total 61.73408320 61.72501141 -0.00907179 61.72501229 -0.00907091 61.72503907 -0.00904413 61.80738688 0.07330368 coulomb-14 61.73408320 61.72501141 -0.00907179 0.00000000 -61.73408320 61.72503907 -0.00904413 0.00000000 -61.73408320 proper 6.73331120 6.73317394 -0.00013726 6.73317355 -0.00013765 6.73316321 -0.00014799 6.73318568 -0.00012552 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 6.08859864 6.08859864 vdw total 6.08855680 6.08869331 0.00013651 6.08869320 0.00013640 6.08876621 0.00020941 6.08859864 0.00004184 vdw-14 6.08855680 6.08869331 0.00013651 0.00000000 -6.08855680 6.08876621 0.00020941 0.00000000 -6.08855680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.30078160 2.30065797 -0.00012363 2.30065796 -0.00012364 2.30063143 -0.00015017 2.30065608 -0.00012552 bond 1.72380800 1.72394281 0.00013481 1.72394281 0.00013481 1.72400837 0.00020037 1.72393352 0.00012552 bonded 10.75790080 10.75777472 -0.00012608 10.75777432 -0.00012648 10.75780301 -0.00009779 10.75777528 -0.00012552 dihedral 6.73331120 6.73317394 -0.00013726 6.73317355 -0.00013765 6.73316321 -0.00014799 6.73318568 -0.00012552 nonbonded 67.82264000 67.81370471 -0.00893529 67.81370298 -0.00893702 67.81380527 -0.00883473 67.89598552 0.07334552 potential 78.58054080 78.57147943 -0.00906137 78.57147826 -0.00906254 78.57156068 -0.00898012 78.65380264 0.07326184 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 78.58054080 Difference in potential energy from amber=>gromacs conversion: -0.00906137 Difference in potential energy from amber=>lammps conversion: -0.00906254 Difference in potential energy from amber=>desmond conversion: -0.00898012 Difference in potential energy from amber=>charmm conversion: 0.07326184 ======================================================================= INFO 2017-03-18 22:23:52 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1838110.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1838110.inpcrd') INFO 2017-03-18 22:23:53 Beginning InterMol conversion INFO 2017-03-18 22:23:53 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:23:53 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:23:53 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1849020.inpcrd INFO 2017-03-18 22:23:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1849020/mobley_1849020_converted.input INFO 2017-03-18 22:23:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1849020/mobley_1849020_converted.cms WARNING 2017-03-18 22:24:09 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:24:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1849020/mobley_1849020_converted.inp INFO 2017-03-18 22:24:09 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1849020/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1849020/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1849020/mobley_1849020_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1849020/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -33.87150917 -33.87150917 0.00000000 0.00000000 0.00000000 0.00000000 -237.07836856 -237.07836856 coulomb total -237.04954080 -237.05759358 -0.00805278 -237.05759082 -0.00805002 -237.05784612 -0.00830532 -237.07836856 -0.02882776 coulomb-14 -203.17922400 -203.18608440 -0.00686040 0.00000000 203.17922400 -203.18608116 -0.00685716 0.00000000 203.17922400 improper 0.00000000 0.00005340 0.00005340 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 70.89997200 70.90010643 0.00013443 70.90015610 0.00018410 70.90032931 0.00035731 70.90009752 0.00012552 vdw (SR) 0.00000000 -0.73020878 -0.73020878 0.00000000 0.00000000 0.00000000 0.00000000 17.99873120 17.99873120 vdw total 17.99873120 17.99856819 -0.00016301 17.99856844 -0.00016276 17.99835476 -0.00037644 17.99873120 0.00000000 vdw-14 18.72883920 18.72877696 -0.00006224 0.00000000 -18.72883920 18.72874000 -0.00009920 0.00000000 -18.72883920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 14.24610160 14.24613535 0.00003375 14.24613549 0.00003389 14.24607704 -0.00002456 14.24597608 -0.00012552 bond 8.83242400 8.83247031 0.00004631 8.83247044 0.00004644 8.83178155 -0.00064245 8.83246584 0.00004184 bonded 93.97849760 93.97876548 0.00026788 93.97876203 0.00026443 93.97818790 -0.00030970 93.97858128 0.00008368 dihedral 70.89997200 70.90015983 0.00018783 70.90015610 0.00018410 70.90032931 0.00035731 70.90013936 0.00016736 nonbonded -219.05080960 -219.05902539 -0.00821579 -219.05902279 -0.00821319 -219.05949137 -0.00868177 -219.07963736 -0.02882776 potential -125.07231200 -125.08025991 -0.00794791 -125.08026160 -0.00794960 -125.08164943 -0.00933743 -125.10101424 -0.02870224 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -125.07231200 Difference in potential energy from amber=>gromacs conversion: -0.00794791 Difference in potential energy from amber=>lammps conversion: -0.00794960 Difference in potential energy from amber=>desmond conversion: -0.00933743 Difference in potential energy from amber=>charmm conversion: -0.02870224 ======================================================================= INFO 2017-03-18 22:24:09 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1849020.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1849020.inpcrd') INFO 2017-03-18 22:24:09 Beginning InterMol conversion INFO 2017-03-18 22:24:09 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:24:09 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1855337.inpcrd INFO 2017-03-18 22:24:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1855337/mobley_1855337_converted.input INFO 2017-03-18 22:24:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1855337/mobley_1855337_converted.cms INFO 2017-03-18 22:24:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1855337/mobley_1855337_converted.rst7 WARNING 2017-03-18 22:24:25 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:24:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1855337/mobley_1855337_converted.inp INFO 2017-03-18 22:24:25 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1855337/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1855337/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1855337/mobley_1855337_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_1855337/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1855337/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 11.07790406 11.07790406 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -18.94226504 -18.94226504 coulomb total -18.94431520 -18.94124534 0.00306986 -18.94124498 0.00307022 -18.94124297 0.00307223 -18.94431520 0.00000000 -18.94226504 0.00205016 coulomb-14 -30.01936320 -30.01914940 0.00021380 0.00000000 30.01936320 -30.01914793 0.00021527 -30.01936320 0.00000000 0.00000000 30.01936320 improper 0.00000000 0.00002658 0.00002658 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00032673 -0.00009167 0.00035332 -0.00006508 0.00035762 -0.00006078 0.00041840 0.00000000 0.00033472 -0.00008368 vdw (SR) 0.00000000 -2.94891380 -2.94891380 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 16.81332032 16.81332032 vdw total 16.81340400 16.81328049 -0.00012351 16.81328057 -0.00012343 16.81342421 0.00002021 16.81340400 0.00000000 16.81332032 -0.00008368 vdw-14 19.76228720 19.76219429 -0.00009291 0.00000000 -19.76228720 19.76234163 0.00005443 19.76228720 0.00000000 0.00000000 -19.76228720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.26814640 2.26819132 0.00004492 2.26819134 0.00004494 2.26834615 0.00019975 2.26814640 0.00000000 2.26823008 0.00008368 bond 0.93261360 0.93244672 -0.00016688 0.93244670 -0.00016690 0.93240653 -0.00020707 0.93261360 0.00000000 0.93244624 -0.00016736 bonded 3.20117840 3.20099135 -0.00018705 3.20099135 -0.00018705 3.20111029 -0.00006811 3.20117840 0.00000000 3.20105288 -0.00012552 dihedral 0.00041840 0.00035331 -0.00006509 0.00035332 -0.00006508 0.00035762 -0.00006078 0.00041840 0.00000000 0.00037656 -0.00004184 nonbonded -2.13091120 -2.12796485 0.00294635 -2.12796462 0.00294658 -2.12781876 0.00309244 -2.13091120 0.00000000 -2.12894472 0.00196648 potential 1.07026720 1.07302650 0.00275930 1.07302672 0.00275952 1.07319487 0.00292767 1.07026720 0.00000000 1.07206632 0.00179912 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 1.07026720 Difference in potential energy from amber=>gromacs conversion: 0.00275930 Difference in potential energy from amber=>lammps conversion: 0.00275952 Difference in potential energy from amber=>desmond conversion: 0.00292767 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00179912 ======================================================================= INFO 2017-03-18 22:24:25 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1855337.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1855337.inpcrd') INFO 2017-03-18 22:24:25 Beginning InterMol conversion INFO 2017-03-18 22:24:25 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:24:25 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:24:25 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1857976.inpcrd INFO 2017-03-18 22:24:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1857976/mobley_1857976_converted.input INFO 2017-03-18 22:24:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1857976/mobley_1857976_converted.cms WARNING 2017-03-18 22:24:41 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:24:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1857976/mobley_1857976_converted.inp INFO 2017-03-18 22:24:41 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1857976/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1857976/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1857976/mobley_1857976_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1857976/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 2.22869128 2.22869128 coulomb total 2.22672480 2.22683913 0.00011433 2.22683911 0.00011431 2.22683270 0.00010790 2.22869128 0.00196648 coulomb-14 2.22672480 2.22683913 0.00011433 0.00000000 -2.22672480 2.22683270 0.00010790 0.00000000 -2.22672480 proper 4.06266400 4.06275076 0.00008676 4.06274847 0.00008447 4.06275213 0.00008813 4.06274768 0.00008368 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.91177728 0.91177728 vdw total 0.91169360 0.91173737 0.00004377 0.91173736 0.00004376 0.91170512 0.00001152 0.91177728 0.00008368 vdw-14 0.91169360 0.91173737 0.00004377 0.00000000 -0.91169360 0.91170512 0.00001152 0.00000000 -0.91169360 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.40373200 1.40382286 0.00009086 1.40382288 0.00009088 1.40388067 0.00014867 1.40389936 0.00016736 bond 0.43095200 0.43105682 0.00010482 0.43105681 0.00010481 0.43106599 0.00011399 0.43107752 0.00012552 bonded 5.89734800 5.89763044 0.00028244 5.89762816 0.00028016 5.89769879 0.00035079 5.89772456 0.00037656 dihedral 4.06266400 4.06275076 0.00008676 4.06274847 0.00008447 4.06275213 0.00008813 4.06274768 0.00008368 nonbonded 3.13841840 3.13857650 0.00015810 3.13857647 0.00015807 3.13853782 0.00011942 3.14046856 0.00205016 potential 9.03576640 9.03620694 0.00044054 9.03620446 0.00043806 9.03621421 0.00044781 9.03815128 0.00238488 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 9.03576640 Difference in potential energy from amber=>gromacs conversion: 0.00044054 Difference in potential energy from amber=>lammps conversion: 0.00043806 Difference in potential energy from amber=>desmond conversion: 0.00044781 Difference in potential energy from amber=>charmm conversion: 0.00238488 ======================================================================= INFO 2017-03-18 22:24:41 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1857976.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1857976.inpcrd') INFO 2017-03-18 22:24:41 Beginning InterMol conversion INFO 2017-03-18 22:24:41 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:24:41 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:24:41 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1858644.inpcrd INFO 2017-03-18 22:24:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1858644/mobley_1858644_converted.input INFO 2017-03-18 22:24:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1858644/mobley_1858644_converted.cms WARNING 2017-03-18 22:24:57 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:24:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1858644/mobley_1858644_converted.inp INFO 2017-03-18 22:24:57 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1858644/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1858644/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1858644/mobley_1858644_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1858644/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 32.86987951 32.86987951 0.00000000 0.00000000 0.00000000 0.00000000 4.80553320 4.80553320 coulomb total 4.80699760 4.80030491 -0.00669269 4.80030487 -0.00669273 4.80023910 -0.00675850 4.80553320 -0.00146440 coulomb-14 -28.06794560 -28.06957460 -0.00162900 0.00000000 28.06794560 -28.06959062 -0.00164502 0.00000000 28.06794560 improper 0.00000000 0.00007041 0.00007041 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 1.56146880 1.56155658 0.00008778 1.56162691 0.00015811 1.56163660 0.00016780 1.56155248 0.00008368 vdw (SR) 0.00000000 -3.69736652 -3.69736652 0.00000000 0.00000000 0.00000000 0.00000000 16.22442232 16.22442232 vdw total 16.22429680 16.22437146 0.00007466 16.22437128 0.00007448 16.22430022 0.00000342 16.22442232 0.00012552 vdw-14 19.92169760 19.92173798 0.00004038 0.00000000 -19.92169760 19.92170689 0.00000929 0.00000000 -19.92169760 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.33302240 1.33317986 0.00015746 1.33317984 0.00015744 1.33333916 0.00031676 1.33314792 0.00012552 bond 1.67401840 1.67403941 0.00002101 1.67403940 0.00002100 1.67381092 -0.00020748 1.67406024 0.00004184 bonded 4.56850960 4.56884625 0.00033665 4.56884616 0.00033656 4.56878669 0.00027709 4.56884432 0.00033472 dihedral 1.56146880 1.56162699 0.00015819 1.56162691 0.00015811 1.56163660 0.00016780 1.56163616 0.00016736 nonbonded 21.03129440 21.02467637 -0.00661803 21.02467615 -0.00661825 21.02453932 -0.00675508 21.02995552 -0.00133888 potential 25.59980400 25.59352262 -0.00628138 25.59352256 -0.00628144 25.59326119 -0.00654281 25.59875800 -0.00104600 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 25.59980400 Difference in potential energy from amber=>gromacs conversion: -0.00628138 Difference in potential energy from amber=>lammps conversion: -0.00628144 Difference in potential energy from amber=>desmond conversion: -0.00654281 Difference in potential energy from amber=>charmm conversion: -0.00104600 ======================================================================= INFO 2017-03-18 22:24:57 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1858644.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1858644.inpcrd') INFO 2017-03-18 22:24:57 Beginning InterMol conversion INFO 2017-03-18 22:24:57 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:24:57 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:24:57 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_186894.inpcrd INFO 2017-03-18 22:24:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_186894/mobley_186894_converted.input INFO 2017-03-18 22:24:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_186894/mobley_186894_converted.cms WARNING 2017-03-18 22:25:13 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:25:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_186894/mobley_186894_converted.inp INFO 2017-03-18 22:25:13 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_186894/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_186894/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_186894/mobley_186894_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_186894/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 4.44785955 4.44785955 0.00000000 0.00000000 0.00000000 0.00000000 9.70968328 9.70968328 coulomb total 9.69767520 9.71157292 0.01389772 9.71157277 0.01389757 9.71155248 0.01387728 9.70968328 0.01200808 coulomb-14 5.25803280 5.26371337 0.00568057 0.00000000 -5.25803280 5.26369702 0.00566422 0.00000000 -5.25803280 proper 0.02343040 0.02353377 0.00010337 0.02353376 0.00010336 0.02353130 0.00010090 0.02351408 0.00008368 vdw (SR) 0.00000000 -0.50468469 -0.50468469 0.00000000 0.00000000 0.00000000 0.00000000 1.14562104 1.14562104 vdw total 1.14557920 1.14556169 -0.00001751 1.14556171 -0.00001749 1.14553032 -0.00004888 1.14562104 0.00004184 vdw-14 1.65016960 1.65024639 0.00007679 0.00000000 -1.65016960 1.65021588 0.00004628 0.00000000 -1.65016960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.14976320 1.14989726 0.00013406 1.14989726 0.00013406 1.14976013 -0.00000307 1.14984688 0.00008368 bond 0.50333520 0.50345368 0.00011848 0.50345369 0.00011849 0.50310444 -0.00023076 0.50346072 0.00012552 bonded 1.67652880 1.67688471 0.00035591 1.67688471 0.00035591 1.67639587 -0.00013293 1.67682168 0.00029288 dihedral 0.02343040 0.02353377 0.00010337 0.02353376 0.00010336 0.02353130 0.00010090 0.02351408 0.00008368 nonbonded 10.84325440 10.85713462 0.01388022 10.85713440 0.01388000 10.85708280 0.01382840 10.85530432 0.01204992 potential 12.51978320 12.53401932 0.01423612 12.53401926 0.01423606 12.53345342 0.01367022 12.53212600 0.01234280 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 12.51978320 Difference in potential energy from amber=>gromacs conversion: 0.01423612 Difference in potential energy from amber=>lammps conversion: 0.01423606 Difference in potential energy from amber=>desmond conversion: 0.01367022 Difference in potential energy from amber=>charmm conversion: 0.01234280 ======================================================================= INFO 2017-03-18 22:25:13 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_186894.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_186894.inpcrd') INFO 2017-03-18 22:25:13 Beginning InterMol conversion INFO 2017-03-18 22:25:13 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:25:13 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:25:13 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1873346.inpcrd INFO 2017-03-18 22:25:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1873346/mobley_1873346_converted.input INFO 2017-03-18 22:25:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1873346/mobley_1873346_converted.cms WARNING 2017-03-18 22:25:29 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:25:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1873346/mobley_1873346_converted.inp INFO 2017-03-18 22:25:29 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1873346/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1873346/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1873346/mobley_1873346_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1873346/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 13.20429372 13.20429372 0.00000000 0.00000000 0.00000000 0.00000000 -5.35095944 -5.35095944 coulomb total -5.34924400 -5.34928621 -0.00004221 -5.34928626 -0.00004226 -5.34930383 -0.00005983 -5.35095944 -0.00171544 coulomb-14 -18.55311120 -18.55357992 -0.00046872 0.00000000 18.55311120 -18.55359667 -0.00048547 0.00000000 18.55311120 improper 0.00000000 0.00001306 0.00001306 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00000000 0.00011956 0.00011956 0.00013261 0.00013261 0.00012918 0.00012918 0.00012552 0.00012552 vdw (SR) 0.00000000 -1.37254003 -1.37254003 0.00000000 0.00000000 0.00000000 0.00000000 16.30580112 16.30580112 vdw total 16.30588480 16.30582191 -0.00006289 16.30582204 -0.00006276 16.30591609 0.00003129 16.30580112 -0.00008368 vdw-14 17.67823680 17.67836194 0.00012514 0.00000000 -17.67823680 17.67845123 0.00021443 0.00000000 -17.67823680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.30166640 0.30174018 0.00007378 0.30174018 0.00007378 0.30168301 0.00001661 0.30175008 0.00008368 bond 1.37109680 1.37100080 -0.00009600 1.37100082 -0.00009598 1.37110241 0.00000561 1.37101312 -0.00008368 bonded 1.67276320 1.67287359 0.00011039 1.67287361 0.00011041 1.67291460 0.00015140 1.67288872 0.00012552 dihedral 0.00000000 0.00013262 0.00013262 0.00013261 0.00013261 0.00012918 0.00012918 0.00012552 0.00012552 nonbonded 10.95664080 10.95653570 -0.00010510 10.95653578 -0.00010502 10.95661226 -0.00002854 10.95484168 -0.00179912 potential 12.62940400 12.62940930 0.00000530 12.62940944 0.00000544 12.62948755 0.00008355 12.62773040 -0.00167360 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 12.62940400 Difference in potential energy from amber=>gromacs conversion: 0.00000530 Difference in potential energy from amber=>lammps conversion: 0.00000544 Difference in potential energy from amber=>desmond conversion: 0.00008355 Difference in potential energy from amber=>charmm conversion: -0.00167360 ======================================================================= INFO 2017-03-18 22:25:29 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1873346.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1873346.inpcrd') INFO 2017-03-18 22:25:29 Beginning InterMol conversion INFO 2017-03-18 22:25:29 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:25:29 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:25:29 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1875719.inpcrd INFO 2017-03-18 22:25:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1875719/mobley_1875719_converted.input INFO 2017-03-18 22:25:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1875719/mobley_1875719_converted.cms WARNING 2017-03-18 22:25:45 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:25:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1875719/mobley_1875719_converted.inp INFO 2017-03-18 22:25:45 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1875719/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1875719/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1875719/mobley_1875719_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1875719/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -66.93763876 -66.93763876 0.00000000 0.00000000 0.00000000 0.00000000 -16.59596152 -16.59596152 coulomb total -16.58370240 -16.58435773 -0.00065533 -16.58435761 -0.00065521 -16.58420155 -0.00049915 -16.59596152 -0.01225912 coulomb-14 50.35151120 50.35328104 0.00176984 0.00000000 -50.35151120 50.35336429 0.00185309 0.00000000 -50.35151120 improper 0.00000000 0.00000754 0.00000754 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 6.45549360 6.45541681 -0.00007679 6.45542456 -0.00006904 6.45539854 -0.00009506 6.45540992 -0.00008368 vdw (SR) 0.00000000 -0.90231503 -0.90231503 0.00000000 0.00000000 0.00000000 0.00000000 7.90177688 7.90177688 vdw total 7.90148400 7.90167279 0.00018879 7.90167312 0.00018912 7.90173075 0.00024675 7.90177688 0.00029288 vdw-14 8.80397280 8.80398781 0.00001501 0.00000000 -8.80397280 8.80402259 0.00004979 0.00000000 -8.80397280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.85978800 1.85959059 -0.00019741 1.85959060 -0.00019740 1.85945056 -0.00033744 1.85957880 -0.00020920 bond 1.89158640 1.89165326 0.00006686 1.89165326 0.00006686 1.89175412 0.00016772 1.89167008 0.00008368 bonded 10.20686800 10.20666821 -0.00019979 10.20666842 -0.00019958 10.20660322 -0.00026478 10.20665880 -0.00020920 dihedral 6.45549360 6.45542436 -0.00006924 6.45542456 -0.00006904 6.45539854 -0.00009506 6.45540992 -0.00008368 nonbonded -8.68221840 -8.68268494 -0.00046654 -8.68268450 -0.00046610 -8.68247080 -0.00025240 -8.69418464 -0.01196624 potential 1.52464960 1.52398327 -0.00066633 1.52398359 -0.00066601 1.52409368 -0.00055592 1.51247416 -0.01217544 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 1.52464960 Difference in potential energy from amber=>gromacs conversion: -0.00066633 Difference in potential energy from amber=>lammps conversion: -0.00066601 Difference in potential energy from amber=>desmond conversion: -0.00055592 Difference in potential energy from amber=>charmm conversion: -0.01217544 ======================================================================= INFO 2017-03-18 22:25:45 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1875719.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1875719.inpcrd') INFO 2017-03-18 22:25:45 Beginning InterMol conversion INFO 2017-03-18 22:25:45 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:25:45 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:25:45 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1881249.inpcrd INFO 2017-03-18 22:25:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1881249/mobley_1881249_converted.input INFO 2017-03-18 22:25:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1881249/mobley_1881249_converted.cms WARNING 2017-03-18 22:26:01 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:26:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1881249/mobley_1881249_converted.inp INFO 2017-03-18 22:26:01 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1881249/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1881249/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1881249/mobley_1881249_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1881249/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.37100743 0.37100743 0.00000000 0.00000000 0.00000000 0.00000000 -59.87228688 -59.87228688 coulomb total -59.81111680 -59.80684700 0.00426980 -59.80684494 0.00427186 -59.80675928 0.00435752 -59.87228688 -0.06117008 coulomb-14 -60.18349280 -60.17785443 0.00563837 0.00000000 60.18349280 -60.17784147 0.00565133 0.00000000 60.18349280 improper 0.00000000 0.00000024 0.00000024 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 14.29672800 14.29677211 0.00004411 14.29677361 0.00004561 14.29676009 0.00003209 14.29676984 0.00004184 vdw (SR) 0.00000000 -1.03482029 -1.03482029 0.00000000 0.00000000 0.00000000 0.00000000 6.08357784 6.08357784 vdw total 6.08353600 6.08348456 -0.00005144 6.08348454 -0.00005146 6.08357642 0.00004042 6.08357784 0.00004184 vdw-14 7.11823920 7.11830485 0.00006565 0.00000000 -7.11823920 7.11838296 0.00014376 0.00000000 -7.11823920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.67192640 1.67175285 -0.00017355 1.67175285 -0.00017355 1.67187433 -0.00005207 1.67175904 -0.00016736 bond 1.31503120 1.31485279 -0.00017841 1.31485279 -0.00017841 1.31501987 -0.00001133 1.31486384 -0.00016736 bonded 17.28368560 17.28337799 -0.00030761 17.28337925 -0.00030635 17.28365429 -0.00003131 17.28339272 -0.00029288 dihedral 14.29672800 14.29677235 0.00004435 14.29677361 0.00004561 14.29676009 0.00003209 14.29676984 0.00004184 nonbonded -53.72758080 -53.72336244 0.00421836 -53.72336333 0.00421747 -53.72318286 0.00439794 -53.78870904 -0.06112824 potential -36.44389520 -36.43998445 0.00391075 -36.43998232 0.00391288 -36.43956258 0.00433262 -36.50535816 -0.06146296 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -36.44389520 Difference in potential energy from amber=>gromacs conversion: 0.00391075 Difference in potential energy from amber=>lammps conversion: 0.00391288 Difference in potential energy from amber=>desmond conversion: 0.00433262 Difference in potential energy from amber=>charmm conversion: -0.06146296 ======================================================================= INFO 2017-03-18 22:26:01 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1881249.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1881249.inpcrd') INFO 2017-03-18 22:26:01 Beginning InterMol conversion INFO 2017-03-18 22:26:01 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:26:01 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:26:01 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1893815.inpcrd INFO 2017-03-18 22:26:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1893815/mobley_1893815_converted.input INFO 2017-03-18 22:26:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1893815/mobley_1893815_converted.cms WARNING 2017-03-18 22:26:17 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:26:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1893815/mobley_1893815_converted.inp INFO 2017-03-18 22:26:17 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1893815/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1893815/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1893815/mobley_1893815_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1893815/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -9.23584528 -9.23584528 coulomb total -9.24998720 -9.24719306 0.00279414 -9.24719312 0.00279408 -9.24720279 0.00278441 -9.23584528 0.01414192 coulomb-14 -9.24998720 -9.24719306 0.00279414 0.00000000 9.24998720 -9.24720279 0.00278441 0.00000000 9.24998720 proper 12.02690800 12.02680770 -0.00010030 12.02680758 -0.00010042 12.02681089 -0.00009711 12.02682432 -0.00008368 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.92173520 0.92173520 vdw total 0.92173520 0.92168778 -0.00004742 0.92168780 -0.00004740 0.92163005 -0.00010515 0.92173520 0.00000000 vdw-14 0.92173520 0.92168778 -0.00004742 0.00000000 -0.92173520 0.92163005 -0.00010515 0.00000000 -0.92173520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.93967840 2.93975446 0.00007606 2.93975447 0.00007607 2.93979528 0.00011688 2.93972024 0.00004184 bond 0.18911680 0.18925521 0.00013841 0.18925521 0.00013841 0.18924747 0.00013067 0.18924232 0.00012552 bonded 15.15570320 15.15581737 0.00011417 15.15581726 0.00011406 15.15585364 0.00015044 15.15578688 0.00008368 dihedral 12.02690800 12.02680770 -0.00010030 12.02680758 -0.00010042 12.02681089 -0.00009711 12.02682432 -0.00008368 nonbonded -8.32825200 -8.32550528 0.00274672 -8.32550520 0.00274680 -8.32557274 0.00267926 -8.31411008 0.01414192 potential 6.82745120 6.83031209 0.00286089 6.83031222 0.00286102 6.83023009 0.00277889 6.84167680 0.01422560 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 6.82745120 Difference in potential energy from amber=>gromacs conversion: 0.00286089 Difference in potential energy from amber=>lammps conversion: 0.00286102 Difference in potential energy from amber=>desmond conversion: 0.00277889 Difference in potential energy from amber=>charmm conversion: 0.01422560 ======================================================================= INFO 2017-03-18 22:26:17 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1893815.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1893815.inpcrd') INFO 2017-03-18 22:26:17 Beginning InterMol conversion INFO 2017-03-18 22:26:17 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:26:17 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:26:17 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1893937.inpcrd INFO 2017-03-18 22:26:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1893937/mobley_1893937_converted.input INFO 2017-03-18 22:26:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1893937/mobley_1893937_converted.cms WARNING 2017-03-18 22:26:33 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:26:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1893937/mobley_1893937_converted.inp INFO 2017-03-18 22:26:33 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1893937/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1893937/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1893937/mobley_1893937_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1893937/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 7.19831140 7.19831140 0.00000000 0.00000000 0.00000000 0.00000000 3.58698504 3.58698504 coulomb total 3.57606480 3.58200719 0.00594239 3.58200717 0.00594237 3.58197357 0.00590877 3.58698504 0.01092024 coulomb-14 -3.61790480 -3.61630421 0.00160059 0.00000000 3.61790480 -3.61630944 0.00159536 0.00000000 3.61790480 proper 8.34038560 8.34039600 0.00001040 8.34039606 0.00001046 8.34039702 0.00001142 8.34038560 0.00000000 vdw (SR) 0.00000000 -2.31275048 -2.31275048 0.00000000 0.00000000 0.00000000 0.00000000 4.00015504 4.00015504 vdw total 3.99990400 4.00006981 0.00016581 4.00006985 0.00016585 4.00009325 0.00018925 4.00015504 0.00025104 vdw-14 6.31281920 6.31282029 0.00000109 0.00000000 -6.31281920 6.31284041 0.00002121 0.00000000 -6.31281920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.38780880 2.38799660 0.00018780 2.38799662 0.00018782 2.38818458 0.00037578 2.38797616 0.00016736 bond 0.83763680 0.83767677 0.00003997 0.83767676 0.00003996 0.83764364 0.00000684 0.83767864 0.00004184 bonded 11.56583120 11.56606937 0.00023817 11.56606944 0.00023824 11.56622524 0.00039404 11.56604040 0.00020920 dihedral 8.34038560 8.34039600 0.00001040 8.34039606 0.00001046 8.34039702 0.00001142 8.34038560 0.00000000 nonbonded 7.57596880 7.58207700 0.00610820 7.58207702 0.00610822 7.58206682 0.00609802 7.58714008 0.01117128 potential 19.14180000 19.14814638 0.00634638 19.14814629 0.00634629 19.14822767 0.00642767 19.15322232 0.01142232 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 19.14180000 Difference in potential energy from amber=>gromacs conversion: 0.00634638 Difference in potential energy from amber=>lammps conversion: 0.00634629 Difference in potential energy from amber=>desmond conversion: 0.00642767 Difference in potential energy from amber=>charmm conversion: 0.01142232 ======================================================================= INFO 2017-03-18 22:26:33 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1893937.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1893937.inpcrd') INFO 2017-03-18 22:26:33 Beginning InterMol conversion INFO 2017-03-18 22:26:33 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:26:34 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:26:34 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1896013.inpcrd INFO 2017-03-18 22:26:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1896013/mobley_1896013_converted.input INFO 2017-03-18 22:26:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1896013/mobley_1896013_converted.cms WARNING 2017-03-18 22:26:49 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:26:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1896013/mobley_1896013_converted.inp INFO 2017-03-18 22:26:49 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1896013/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1896013/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1896013/mobley_1896013_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1896013/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -366.91973342 -366.91973342 0.00000000 0.00000000 0.00000000 0.00000000 85.80580672 85.80580672 coulomb total 85.99542560 85.99105836 -0.00436724 85.99105750 -0.00436810 85.99144996 -0.00397564 85.80580672 -0.18961888 coulomb-14 452.88871200 452.91079177 0.02207977 0.00000000 -452.88871200 452.91039349 0.02168149 0.00000000 -452.88871200 proper 50.57702880 50.57712718 0.00009838 50.57712922 0.00010042 50.57710495 0.00007615 50.57769824 0.00066944 vdw (SR) 0.00000000 -4.16872626 -4.16872626 0.00000000 0.00000000 0.00000000 0.00000000 12.75467296 12.75467296 vdw total 12.75492400 12.75447323 -0.00045077 12.75447380 -0.00045020 12.75445624 -0.00046776 12.75467296 -0.00025104 vdw-14 16.92344320 16.92319949 -0.00024371 0.00000000 -16.92344320 16.92314011 -0.00030309 0.00000000 -16.92344320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 8.01570720 8.01587386 0.00016666 8.01587372 0.00016652 8.01570051 -0.00000669 8.01583272 0.00012552 bond 1.07570640 1.07551038 -0.00019602 1.07551038 -0.00019602 1.07577033 0.00006393 1.07549720 -0.00020920 bonded 59.66844240 59.66851142 0.00006902 59.66851332 0.00007092 59.66857579 0.00013339 59.66902816 0.00058576 dihedral 50.57702880 50.57712718 0.00009838 50.57712922 0.00010042 50.57710495 0.00007615 50.57769824 0.00066944 nonbonded 98.75034960 98.74553158 -0.00481802 98.74552963 -0.00481997 98.74590620 -0.00444340 98.56047968 -0.18986992 potential 158.41879200 158.41404300 -0.00474900 158.41404316 -0.00474884 158.41437955 -0.00441245 158.22950784 -0.18928416 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 158.41879200 Difference in potential energy from amber=>gromacs conversion: -0.00474900 Difference in potential energy from amber=>lammps conversion: -0.00474884 Difference in potential energy from amber=>desmond conversion: -0.00441245 Difference in potential energy from amber=>charmm conversion: -0.18928416 ======================================================================= INFO 2017-03-18 22:26:49 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1896013.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1896013.inpcrd') INFO 2017-03-18 22:26:50 Beginning InterMol conversion INFO 2017-03-18 22:26:50 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:26:50 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:26:50 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1899443.inpcrd INFO 2017-03-18 22:26:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1899443/mobley_1899443_converted.input INFO 2017-03-18 22:26:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1899443/mobley_1899443_converted.cms WARNING 2017-03-18 22:27:05 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:27:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1899443/mobley_1899443_converted.inp INFO 2017-03-18 22:27:05 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1899443/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1899443/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1899443/mobley_1899443_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1899443/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 15.89984496 15.89984496 0.00000000 0.00000000 0.00000000 0.00000000 -8.81384704 -8.81384704 coulomb total -8.80732000 -8.81291618 -0.00559618 -8.81291610 -0.00559610 -8.81296702 -0.00564702 -8.81384704 -0.00652704 coulomb-14 -24.71363280 -24.71276114 0.00087166 0.00000000 24.71363280 -24.71278721 0.00084559 0.00000000 24.71363280 improper 0.00000000 0.00735726 0.00735726 0.00000000 0.00000000 0.00000000 0.00000000 0.00736384 0.00736384 proper 31.13481760 31.12734270 -0.00747490 31.13470589 -0.00011171 31.13466949 -0.00014811 31.12737008 -0.00744752 vdw (SR) 0.00000000 -1.10760420 -1.10760420 0.00000000 0.00000000 0.00000000 0.00000000 5.80500712 5.80500712 vdw total 5.80488160 5.80493381 0.00005221 5.80493390 0.00005230 5.80496644 0.00008484 5.80500712 0.00012552 vdw-14 6.91238640 6.91253801 0.00015161 0.00000000 -6.91238640 6.91255845 0.00017205 0.00000000 -6.91238640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.97024560 1.97024030 -0.00000530 1.97024029 -0.00000531 1.97019048 -0.00005512 1.97020376 -0.00004184 bond 1.41293680 1.41302622 0.00008942 1.41302621 0.00008941 1.41253726 -0.00039954 1.41302048 0.00008368 bonded 34.51800000 34.51796648 -0.00003352 34.51797239 -0.00002761 34.51739723 -0.00060277 34.51795816 -0.00004184 dihedral 31.13481760 31.13469996 -0.00011764 31.13470589 -0.00011171 31.13466949 -0.00014811 31.13473392 -0.00008368 nonbonded -3.00243840 -3.00798237 -0.00554397 -3.00798216 -0.00554376 -3.00800058 -0.00556218 -3.00883992 -0.00640152 potential 31.51556160 31.50998411 -0.00557749 31.50999019 -0.00557141 31.50935505 -0.00620655 31.50911824 -0.00644336 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 31.51556160 Difference in potential energy from amber=>gromacs conversion: -0.00557749 Difference in potential energy from amber=>lammps conversion: -0.00557141 Difference in potential energy from amber=>desmond conversion: -0.00620655 Difference in potential energy from amber=>charmm conversion: -0.00644336 ======================================================================= INFO 2017-03-18 22:27:05 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1899443.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1899443.inpcrd') INFO 2017-03-18 22:27:06 Beginning InterMol conversion INFO 2017-03-18 22:27:06 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:27:06 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:27:06 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1903702.inpcrd INFO 2017-03-18 22:27:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1903702/mobley_1903702_converted.input INFO 2017-03-18 22:27:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1903702/mobley_1903702_converted.cms WARNING 2017-03-18 22:27:21 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:27:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1903702/mobley_1903702_converted.inp INFO 2017-03-18 22:27:22 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1903702/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1903702/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1903702/mobley_1903702_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1903702/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 12.43448432 12.43448432 0.00000000 0.00000000 0.00000000 0.00000000 -38.77660072 -38.77660072 coulomb total -38.76434160 -38.76111774 0.00322386 -38.76111741 0.00322419 -38.76119996 0.00314164 -38.77660072 -0.01225912 coulomb-14 -51.19040320 -51.19560206 -0.00519886 0.00000000 51.19040320 -51.19564073 -0.00523753 0.00000000 51.19040320 proper 7.96089680 7.96071594 -0.00018086 7.96071605 -0.00018075 7.96070756 -0.00018924 7.96072944 -0.00016736 vdw (SR) 0.00000000 0.49572466 0.49572466 0.00000000 0.00000000 0.00000000 0.00000000 5.90784984 5.90784984 vdw total 5.90780800 5.90775780 -0.00005020 5.90775779 -0.00005021 5.90781013 0.00000213 5.90784984 0.00004184 vdw-14 5.41200400 5.41203314 0.00002914 0.00000000 -5.41200400 5.41207801 0.00007401 0.00000000 -5.41200400 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.46105280 1.46109242 0.00003962 1.46109242 0.00003962 1.46093135 -0.00012145 1.46105280 0.00000000 bond 0.56986080 0.56997297 0.00011217 0.56997297 0.00011217 0.56980991 -0.00005089 0.56998632 0.00012552 bonded 9.99181040 9.99178133 -0.00002907 9.99178145 -0.00002895 9.99144881 -0.00036159 9.99176856 -0.00004184 dihedral 7.96089680 7.96071594 -0.00018086 7.96071605 -0.00018075 7.96070756 -0.00018924 7.96072944 -0.00016736 nonbonded -32.85653360 -32.85335994 0.00317366 -32.85335920 0.00317440 -32.85338983 0.00314377 -32.86875088 -0.01221728 potential -22.86472320 -22.86157861 0.00314459 -22.86157809 0.00314511 -22.86196816 0.00275504 -22.87698232 -0.01225912 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -22.86472320 Difference in potential energy from amber=>gromacs conversion: 0.00314459 Difference in potential energy from amber=>lammps conversion: 0.00314511 Difference in potential energy from amber=>desmond conversion: 0.00275504 Difference in potential energy from amber=>charmm conversion: -0.01225912 ======================================================================= INFO 2017-03-18 22:27:22 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1903702.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1903702.inpcrd') INFO 2017-03-18 22:27:22 Beginning InterMol conversion INFO 2017-03-18 22:27:22 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:27:22 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:27:22 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1905088.inpcrd INFO 2017-03-18 22:27:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1905088/mobley_1905088_converted.input INFO 2017-03-18 22:27:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1905088/mobley_1905088_converted.cms WARNING 2017-03-18 22:27:37 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:27:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1905088/mobley_1905088_converted.inp INFO 2017-03-18 22:27:38 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1905088/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1905088/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1905088/mobley_1905088_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1905088/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 10.56029561 10.56029561 0.00000000 0.00000000 0.00000000 0.00000000 9.18362896 9.18362896 coulomb total 9.18388000 9.18430096 0.00042096 9.18430091 0.00042091 9.18428111 0.00040111 9.18362896 -0.00025104 coulomb-14 -1.37611760 -1.37599464 0.00012296 0.00000000 1.37611760 -1.37599544 0.00012216 0.00000000 1.37611760 improper 0.00000000 0.00007041 0.00007041 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00083680 0.00070627 -0.00013053 0.00077663 -0.00006017 0.00077659 -0.00006021 0.00071128 -0.00012552 vdw (SR) 0.00000000 -3.06099375 -3.06099375 0.00000000 0.00000000 0.00000000 0.00000000 13.42474056 13.42474056 vdw total 13.42478240 13.42476806 -0.00001434 13.42476817 -0.00001423 13.42481624 0.00003384 13.42474056 -0.00004184 vdw-14 16.48579680 16.48576181 -0.00003499 0.00000000 -16.48579680 16.48581157 0.00001477 0.00000000 -16.48579680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.47316240 2.47335828 0.00019588 2.47335829 0.00019589 2.47348941 0.00032701 2.47337160 0.00020920 bond 1.86648240 1.86645040 -0.00003200 1.86645039 -0.00003201 1.86575849 -0.00072391 1.86644056 -0.00004184 bonded 4.34048160 4.34058536 0.00010376 4.34058531 0.00010371 4.34002449 -0.00045711 4.34060712 0.00012552 dihedral 0.00083680 0.00077668 -0.00006012 0.00077663 -0.00006017 0.00077659 -0.00006021 0.00079496 -0.00004184 nonbonded 22.60866240 22.60906903 0.00040663 22.60906908 0.00040668 22.60909735 0.00043495 22.60836952 -0.00029288 potential 26.94914400 26.94965439 0.00051039 26.94965403 0.00051003 26.94906015 -0.00008385 26.94897664 -0.00016736 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 26.94914400 Difference in potential energy from amber=>gromacs conversion: 0.00051039 Difference in potential energy from amber=>lammps conversion: 0.00051003 Difference in potential energy from amber=>desmond conversion: -0.00008385 Difference in potential energy from amber=>charmm conversion: -0.00016736 ======================================================================= INFO 2017-03-18 22:27:38 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1905088.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1905088.inpcrd') INFO 2017-03-18 22:27:38 Beginning InterMol conversion INFO 2017-03-18 22:27:38 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:27:38 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:27:38 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1922649.inpcrd INFO 2017-03-18 22:27:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1922649/mobley_1922649_converted.input INFO 2017-03-18 22:27:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1922649/mobley_1922649_converted.cms WARNING 2017-03-18 22:27:54 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:27:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1922649/mobley_1922649_converted.inp INFO 2017-03-18 22:27:54 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1922649/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1922649/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1922649/mobley_1922649_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1922649/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -57.49508391 -57.49508391 0.00000000 0.00000000 0.00000000 0.00000000 -250.44181352 -250.44181352 coulomb total -250.42537040 -250.44143209 -0.01606169 -250.44142859 -0.01605819 -250.44086166 -0.01549126 -250.44181352 -0.01644312 coulomb-14 -192.92005600 -192.94634818 -0.02629218 0.00000000 192.92005600 -192.94624366 -0.02618766 0.00000000 192.92005600 improper 0.00000000 0.00001705 0.00001705 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 39.59026320 39.59033171 0.00006851 39.59033977 0.00007657 39.59038901 0.00012581 39.59030504 0.00004184 vdw (SR) 0.00000000 -1.34417093 -1.34417093 0.00000000 0.00000000 0.00000000 0.00000000 27.05328376 27.05328376 vdw total 27.05332560 27.05300490 -0.00032070 27.05300469 -0.00032091 27.05290025 -0.00042535 27.05328376 -0.00004184 vdw-14 28.39722640 28.39717583 -0.00005057 0.00000000 -28.39722640 28.39699661 -0.00022979 0.00000000 -28.39722640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.29741040 3.29751724 0.00010684 3.29751722 0.00010682 3.29776054 0.00035014 3.29761960 0.00020920 bond 16.48705200 16.48695557 -0.00009643 16.48695577 -0.00009623 16.48618759 -0.00086441 16.48696832 -0.00008368 bonded 59.37472560 59.37482157 0.00009597 59.37481275 0.00008715 59.37433714 -0.00038846 59.37489296 0.00016736 dihedral 39.59026320 39.59034877 0.00008557 39.59033977 0.00007657 39.59038901 0.00012581 39.59030504 0.00004184 nonbonded -223.37204480 -223.38842719 -0.01638239 -223.38842516 -0.01638036 -223.38796141 -0.01591661 -223.38852976 -0.01648496 potential -163.99731920 -164.01360562 -0.01628642 -164.01361170 -0.01629250 -164.01383638 -0.01651718 -164.01363680 -0.01631760 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -163.99731920 Difference in potential energy from amber=>gromacs conversion: -0.01628642 Difference in potential energy from amber=>lammps conversion: -0.01629250 Difference in potential energy from amber=>desmond conversion: -0.01651718 Difference in potential energy from amber=>charmm conversion: -0.01631760 ======================================================================= INFO 2017-03-18 22:27:54 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1922649.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1922649.inpcrd') INFO 2017-03-18 22:27:54 Beginning InterMol conversion INFO 2017-03-18 22:27:54 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:27:54 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:27:54 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1923244.inpcrd INFO 2017-03-18 22:27:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1923244/mobley_1923244_converted.input INFO 2017-03-18 22:27:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1923244/mobley_1923244_converted.cms WARNING 2017-03-18 22:28:10 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:28:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1923244/mobley_1923244_converted.inp INFO 2017-03-18 22:28:10 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1923244/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1923244/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1923244/mobley_1923244_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1923244/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 3.64817604 3.64817604 0.00000000 0.00000000 0.00000000 0.00000000 3.03628696 3.03628696 coulomb total 3.02419520 3.03396299 0.00976779 3.03396296 0.00976776 3.03394630 0.00975110 3.03628696 0.01209176 coulomb-14 -0.61755840 -0.61421305 0.00334535 0.00000000 0.61755840 -0.61421352 0.00334488 0.00000000 0.61755840 proper 1.71460320 1.71442962 -0.00017358 1.71442961 -0.00017359 1.71442829 -0.00017491 1.71443584 -0.00016736 vdw (SR) 0.00000000 -0.55162671 -0.55162671 0.00000000 0.00000000 0.00000000 0.00000000 3.09419352 3.09419352 vdw total 3.09448640 3.09414459 -0.00034181 3.09414465 -0.00034175 3.09414154 -0.00034486 3.09419352 -0.00029288 vdw-14 3.64593760 3.64577131 -0.00016629 0.00000000 -3.64593760 3.64577209 -0.00016551 0.00000000 -3.64593760 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.68575760 0.68595264 0.00019504 0.68595266 0.00019506 0.68602202 0.00026442 0.68596680 0.00020920 bond 0.82131920 0.82146780 0.00014860 0.82146782 0.00014862 0.82143510 0.00011590 0.82148656 0.00016736 bonded 3.22168000 3.22185005 0.00017005 3.22185008 0.00017008 3.22188541 0.00020541 3.22188920 0.00020920 dihedral 1.71460320 1.71442962 -0.00017358 1.71442961 -0.00017359 1.71442829 -0.00017491 1.71443584 -0.00016736 nonbonded 6.11868160 6.12810759 0.00942599 6.12810773 0.00942613 6.12808784 0.00940624 6.13048048 0.01179888 potential 9.34036160 9.34995764 0.00959604 9.34995760 0.00959600 9.34995087 0.00958927 9.35236968 0.01200808 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 9.34036160 Difference in potential energy from amber=>gromacs conversion: 0.00959604 Difference in potential energy from amber=>lammps conversion: 0.00959600 Difference in potential energy from amber=>desmond conversion: 0.00958927 Difference in potential energy from amber=>charmm conversion: 0.01200808 ======================================================================= INFO 2017-03-18 22:28:10 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1923244.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1923244.inpcrd') INFO 2017-03-18 22:28:10 Beginning InterMol conversion INFO 2017-03-18 22:28:10 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:28:10 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:28:10 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_194273.inpcrd INFO 2017-03-18 22:28:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_194273/mobley_194273_converted.input INFO 2017-03-18 22:28:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_194273/mobley_194273_converted.cms WARNING 2017-03-18 22:28:26 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:28:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_194273/mobley_194273_converted.inp INFO 2017-03-18 22:28:26 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_194273/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_194273/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_194273/mobley_194273_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_194273/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 470.75886489 470.75886489 0.00000000 0.00000000 0.00000000 0.00000000 -614.19668152 -614.19668152 coulomb total -614.00200000 -614.02133329 -0.01933329 -614.02133008 -0.01933008 -614.02085310 -0.01885310 -614.19668152 -0.19468152 coulomb-14 -1084.74384000 -1084.78019817 -0.03635817 0.00000000 1084.74384000 -1084.77999394 -0.03615394 0.00000000 1084.74384000 improper 0.00000000 0.00039391 0.00039391 0.00000000 0.00000000 0.00000000 0.00000000 0.00037656 0.00037656 proper 41.63749440 41.63711740 -0.00037700 41.63751155 0.00001715 41.63757214 0.00007774 41.63711784 -0.00037656 vdw (SR) 0.00000000 17.12123883 17.12123883 0.00000000 0.00000000 0.00000000 0.00000000 54.02903800 54.02903800 vdw total 54.02924720 54.02866947 -0.00057773 54.02866981 -0.00057739 54.02833919 -0.00090801 54.02903800 -0.00020920 vdw-14 36.90748240 36.90743064 -0.00005176 0.00000000 -36.90748240 36.90732010 -0.00016230 0.00000000 -36.90748240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 19.90998240 19.90986604 -0.00011636 19.90986608 -0.00011632 19.90939647 -0.00058593 19.90977320 -0.00020920 bond 23.84712640 23.84705583 -0.00007057 23.84705569 -0.00007071 23.84774044 0.00061404 23.84704272 -0.00008368 bonded 85.39460320 85.39443318 -0.00017002 85.39443333 -0.00016987 85.39470906 0.00010586 85.39431032 -0.00029288 dihedral 41.63749440 41.63751131 0.00001691 41.63751155 0.00001715 41.63757214 0.00007774 41.63749440 0.00000000 nonbonded -559.97275280 -559.99266382 -0.01991102 -559.99266864 -0.01991584 -559.99251392 -0.01976112 -560.16764352 -0.19489072 potential -474.57814960 -474.59823064 -0.02008104 -474.59823280 -0.02008320 -474.59796502 -0.01981542 -474.77324952 -0.19509992 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -474.57814960 Difference in potential energy from amber=>gromacs conversion: -0.02008104 Difference in potential energy from amber=>lammps conversion: -0.02008320 Difference in potential energy from amber=>desmond conversion: -0.01981542 Difference in potential energy from amber=>charmm conversion: -0.19509992 ======================================================================= INFO 2017-03-18 22:28:26 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_194273.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_194273.inpcrd') INFO 2017-03-18 22:28:26 Beginning InterMol conversion INFO 2017-03-18 22:28:26 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:28:26 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:28:26 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1944394.inpcrd INFO 2017-03-18 22:28:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1944394/mobley_1944394_converted.input INFO 2017-03-18 22:28:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1944394/mobley_1944394_converted.cms WARNING 2017-03-18 22:28:42 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:28:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1944394/mobley_1944394_converted.inp INFO 2017-03-18 22:28:42 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1944394/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1944394/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1944394/mobley_1944394_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1944394/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -85.45713739 -85.45713739 0.00000000 0.00000000 0.00000000 0.00000000 115.93541832 115.93541832 coulomb total 115.88257440 115.92209794 0.03952354 115.92209646 0.03952206 115.92202868 0.03945428 115.93541832 0.05284392 coulomb-14 201.36378640 201.37923533 0.01544893 0.00000000 -201.36378640 201.37916929 0.01538289 0.00000000 -201.36378640 improper 0.00000000 0.00020464 0.00020464 0.00000000 0.00000000 0.00000000 0.00000000 0.00020920 0.00020920 proper 15.23310720 15.23272780 -0.00037940 15.23292938 -0.00017782 15.23303984 -0.00006736 15.23243776 -0.00066944 vdw (SR) 0.00000000 -11.58123121 -11.58123121 0.00000000 0.00000000 0.00000000 0.00000000 41.49117992 41.49117992 vdw total 41.49105440 41.49096016 -0.00009424 41.49096026 -0.00009414 41.49127678 0.00022238 41.49117992 0.00012552 vdw-14 53.07236640 53.07219137 -0.00017503 0.00000000 -53.07236640 53.07256305 0.00019665 0.00000000 -53.07236640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.12124000 4.12105100 -0.00018900 4.12105101 -0.00018899 4.12123732 -0.00000268 4.12098896 -0.00025104 bond 3.31414640 3.31410619 -0.00004021 3.31410619 -0.00004021 3.31358156 -0.00056484 3.31410456 -0.00004184 bonded 22.66849360 22.66808964 -0.00040396 22.66808658 -0.00040702 22.66785872 -0.00063488 22.66774048 -0.00075312 dihedral 15.23310720 15.23293244 -0.00017476 15.23292938 -0.00017782 15.23303984 -0.00006736 15.23264696 -0.00046024 nonbonded 157.37362880 157.41305810 0.03942930 157.41305882 0.03943002 157.41330546 0.03967666 157.42659824 0.05296944 potential 180.04212240 180.08114774 0.03902534 180.08114238 0.03901998 180.08087377 0.03875137 180.09429688 0.05217448 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 180.04212240 Difference in potential energy from amber=>gromacs conversion: 0.03902534 Difference in potential energy from amber=>lammps conversion: 0.03901998 Difference in potential energy from amber=>desmond conversion: 0.03875137 Difference in potential energy from amber=>charmm conversion: 0.05217448 ======================================================================= INFO 2017-03-18 22:28:42 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1944394.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1944394.inpcrd') INFO 2017-03-18 22:28:42 Beginning InterMol conversion INFO 2017-03-18 22:28:42 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:28:42 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:28:42 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1952272.inpcrd INFO 2017-03-18 22:28:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1952272/mobley_1952272_converted.input INFO 2017-03-18 22:28:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1952272/mobley_1952272_converted.cms WARNING 2017-03-18 22:28:58 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:28:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1952272/mobley_1952272_converted.inp INFO 2017-03-18 22:28:58 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1952272/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1952272/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1952272/mobley_1952272_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1952272/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -49.87047672 -49.87047672 coulomb total -49.86993280 -49.87558714 -0.00565434 -49.87558538 -0.00565258 -49.87560547 -0.00567267 -49.87047672 -0.00054392 coulomb-14 -49.86993280 -49.87558714 -0.00565434 0.00000000 49.86993280 -49.87560547 -0.00567267 0.00000000 49.86993280 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.05729680 1.05729680 vdw total 1.05729680 1.05728640 -0.00001040 1.05728642 -0.00001038 1.05729524 -0.00000156 1.05729680 0.00000000 vdw-14 1.05729680 1.05728640 -0.00001040 0.00000000 -1.05729680 1.05729524 -0.00000156 0.00000000 -1.05729680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.69909840 2.69896047 -0.00013793 2.69896045 -0.00013795 2.69897067 -0.00012773 2.69905656 -0.00004184 bond 13.05784560 13.05772105 -0.00012455 13.05772092 -0.00012468 13.05769577 -0.00014983 13.05772008 -0.00012552 bonded 15.75694400 15.75668151 -0.00026249 15.75668137 -0.00026263 15.75666644 -0.00027756 15.75677664 -0.00016736 nonbonded -48.81263600 -48.81830074 -0.00566474 -48.81830114 -0.00566514 -48.81831022 -0.00567422 -48.81317992 -0.00054392 potential -33.05569200 -33.06161923 -0.00592723 -33.06161864 -0.00592664 -33.06165663 -0.00596463 -33.05640328 -0.00071128 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -33.05569200 Difference in potential energy from amber=>gromacs conversion: -0.00592723 Difference in potential energy from amber=>lammps conversion: -0.00592664 Difference in potential energy from amber=>desmond conversion: -0.00596463 Difference in potential energy from amber=>charmm conversion: -0.00071128 ======================================================================= INFO 2017-03-18 22:28:58 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1952272.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1952272.inpcrd') INFO 2017-03-18 22:28:58 Beginning InterMol conversion INFO 2017-03-18 22:28:58 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:28:59 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:28:59 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1963873.inpcrd INFO 2017-03-18 22:28:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1963873/mobley_1963873_converted.input INFO 2017-03-18 22:28:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1963873/mobley_1963873_converted.cms WARNING 2017-03-18 22:29:14 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:29:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1963873/mobley_1963873_converted.inp INFO 2017-03-18 22:29:14 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1963873/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1963873/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1963873/mobley_1963873_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1963873/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 1.65044503 1.65044503 0.00000000 0.00000000 0.00000000 0.00000000 -157.22057808 -157.22057808 coulomb total -157.15229520 -157.15456278 -0.00226758 -157.15456293 -0.00226773 -157.15468577 -0.00239057 -157.22057808 -0.06828288 coulomb-14 -158.80413840 -158.80500781 -0.00086941 0.00000000 158.80413840 -158.80501578 -0.00087738 0.00000000 158.80413840 improper 0.00000000 0.00016398 0.00016398 0.00000000 0.00000000 0.00000000 0.00000000 0.00016736 0.00016736 proper 11.01856400 11.01848792 -0.00007608 11.01865061 0.00008661 11.01867467 0.00011067 11.01848032 -0.00008368 vdw (SR) 0.00000000 -0.58742347 -0.58742347 0.00000000 0.00000000 0.00000000 0.00000000 2.47115408 2.47115408 vdw total 2.47107040 2.47111000 0.00003960 2.47111002 0.00003962 2.47113894 0.00006854 2.47115408 0.00008368 vdw-14 3.05850400 3.05853347 0.00002947 0.00000000 -3.05850400 3.05855389 0.00004989 0.00000000 -3.05850400 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 7.89897360 7.89887000 -0.00010360 7.89886984 -0.00010376 7.89882172 -0.00015188 7.89893176 -0.00004184 bond 4.09906480 4.09894950 -0.00011530 4.09894949 -0.00011531 4.09975145 0.00068665 4.09893928 -0.00012552 bonded 23.01660240 23.01647141 -0.00013099 23.01646993 -0.00013247 23.01724784 0.00064544 23.01651872 -0.00008368 dihedral 11.01856400 11.01865191 0.00008791 11.01865061 0.00008661 11.01867467 0.00011067 11.01864768 0.00008368 nonbonded -154.68122480 -154.68345278 -0.00222798 -154.68345069 -0.00222589 -154.68354683 -0.00232203 -154.74942400 -0.06819920 potential -131.66462240 -131.66698138 -0.00235898 -131.66698218 -0.00235978 -131.66632905 -0.00170665 -131.73290528 -0.06828288 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -131.66462240 Difference in potential energy from amber=>gromacs conversion: -0.00235898 Difference in potential energy from amber=>lammps conversion: -0.00235978 Difference in potential energy from amber=>desmond conversion: -0.00170665 Difference in potential energy from amber=>charmm conversion: -0.06828288 ======================================================================= INFO 2017-03-18 22:29:14 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1963873.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1963873.inpcrd') INFO 2017-03-18 22:29:14 Beginning InterMol conversion INFO 2017-03-18 22:29:14 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:29:15 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:29:15 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1967551.inpcrd INFO 2017-03-18 22:29:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1967551/mobley_1967551_converted.input INFO 2017-03-18 22:29:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1967551/mobley_1967551_converted.cms WARNING 2017-03-18 22:29:30 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:29:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1967551/mobley_1967551_converted.inp INFO 2017-03-18 22:29:30 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1967551/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1967551/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1967551/mobley_1967551_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1967551/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -41.80280424 -41.80280424 coulomb total -41.79272080 -41.79402325 -0.00130245 -41.79402286 -0.00130206 -41.79404658 -0.00132578 -41.80280424 -0.01008344 coulomb-14 -41.79272080 -41.79402325 -0.00130245 0.00000000 41.79272080 -41.79404658 -0.00132578 0.00000000 41.79272080 improper 0.00000000 0.00002015 0.00002015 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 11.04910720 11.04923941 0.00013221 11.04925824 0.00015104 11.04928916 0.00018196 11.04923272 0.00012552 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.33794168 0.33794168 vdw total 0.33806720 0.33793501 -0.00013219 0.33793501 -0.00013219 0.33794101 -0.00012619 0.33794168 -0.00012552 vdw-14 0.33806720 0.33793501 -0.00013219 0.00000000 -0.33806720 0.33794101 -0.00012619 0.00000000 -0.33806720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.35522160 0.35506373 -0.00015787 0.35506373 -0.00015787 0.35499217 -0.00022943 0.35509608 -0.00012552 bond 0.70876960 0.70888624 0.00011664 0.70888625 0.00011665 0.70851620 -0.00025340 0.70889512 0.00012552 bonded 12.11309840 12.11320953 0.00011113 12.11320822 0.00010982 12.11279753 -0.00030087 12.11322392 0.00012552 dihedral 11.04910720 11.04925956 0.00015236 11.04925824 0.00015104 11.04928916 0.00018196 11.04923272 0.00012552 nonbonded -41.45465360 -41.45608824 -0.00143464 -41.45608788 -0.00143428 -41.45610557 -0.00145197 -41.46486256 -0.01020896 potential -29.34155520 -29.34287871 -0.00132351 -29.34287944 -0.00132424 -29.34331503 -0.00175983 -29.35159680 -0.01004160 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -29.34155520 Difference in potential energy from amber=>gromacs conversion: -0.00132351 Difference in potential energy from amber=>lammps conversion: -0.00132424 Difference in potential energy from amber=>desmond conversion: -0.00175983 Difference in potential energy from amber=>charmm conversion: -0.01004160 ======================================================================= INFO 2017-03-18 22:29:30 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1967551.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1967551.inpcrd') INFO 2017-03-18 22:29:30 Beginning InterMol conversion INFO 2017-03-18 22:29:30 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:29:31 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:29:31 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_197466.inpcrd INFO 2017-03-18 22:29:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_197466/mobley_197466_converted.input INFO 2017-03-18 22:29:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_197466/mobley_197466_converted.cms WARNING 2017-03-18 22:29:46 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:29:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_197466/mobley_197466_converted.inp INFO 2017-03-18 22:29:46 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_197466/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_197466/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_197466/mobley_197466_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_197466/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -71.31747776 -71.31747776 0.00000000 0.00000000 0.00000000 0.00000000 -9.94913360 -9.94913360 coulomb total -9.93909200 -9.94108504 -0.00199304 -9.94108484 -0.00199284 -9.94111496 -0.00202296 -9.94913360 -0.01004160 coulomb-14 61.37467760 61.37639273 0.00171513 0.00000000 -61.37467760 61.37645162 0.00177402 0.00000000 -61.37467760 improper 0.00000000 0.00002705 0.00002705 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 38.01164000 38.01150060 -0.00013940 38.01152620 -0.00011380 38.01154954 -0.00009046 38.01938040 0.00774040 vdw (SR) 0.00000000 -1.11199465 -1.11199465 0.00000000 0.00000000 0.00000000 0.00000000 1.73364040 1.73364040 vdw total 1.73343120 1.73361696 0.00018576 1.73361697 0.00018577 1.73362127 0.00019007 1.73364040 0.00020920 vdw-14 2.84553840 2.84561162 0.00007322 0.00000000 -2.84553840 2.84560984 0.00007144 0.00000000 -2.84553840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.38532240 1.38529799 -0.00002441 1.38529801 -0.00002439 1.38542358 0.00010118 1.38528056 -0.00004184 bond 1.35017680 1.35013945 -0.00003735 1.35013944 -0.00003736 1.34976824 -0.00040856 1.35013496 -0.00004184 bonded 40.74713920 40.74696509 -0.00017411 40.74696364 -0.00017556 40.74674136 -0.00039784 40.75483776 0.00769856 dihedral 38.01164000 38.01152765 -0.00011235 38.01152620 -0.00011380 38.01154954 -0.00009046 38.01942224 0.00778224 nonbonded -8.20566080 -8.20746807 -0.00180727 -8.20746787 -0.00180707 -8.20749369 -0.00183289 -8.21549320 -0.00983240 potential 32.54147840 32.53949702 -0.00198138 32.53949560 -0.00198280 32.53921398 -0.00226442 32.53934456 -0.00213384 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 32.54147840 Difference in potential energy from amber=>gromacs conversion: -0.00198138 Difference in potential energy from amber=>lammps conversion: -0.00198280 Difference in potential energy from amber=>desmond conversion: -0.00226442 Difference in potential energy from amber=>charmm conversion: -0.00213384 ======================================================================= INFO 2017-03-18 22:29:46 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_197466.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_197466.inpcrd') INFO 2017-03-18 22:29:47 Beginning InterMol conversion INFO 2017-03-18 22:29:47 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:29:47 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:29:47 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1976156.inpcrd INFO 2017-03-18 22:29:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1976156/mobley_1976156_converted.input INFO 2017-03-18 22:29:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1976156/mobley_1976156_converted.cms WARNING 2017-03-18 22:30:02 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:30:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1976156/mobley_1976156_converted.inp INFO 2017-03-18 22:30:02 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1976156/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1976156/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1976156/mobley_1976156_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1976156/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -5.84479409 -5.84479409 0.00000000 0.00000000 0.00000000 0.00000000 -6.66963072 -6.66963072 coulomb total -6.68059280 -6.67687872 0.00371408 -6.67687866 0.00371414 -6.67692386 0.00366894 -6.66963072 0.01096208 coulomb-14 -0.83345280 -0.83208462 0.00136818 0.00000000 0.83345280 -0.83212468 0.00132812 0.00000000 0.83345280 improper 0.00000000 0.00404669 0.00404669 0.00000000 0.00000000 0.00000000 0.00000000 0.00405848 0.00405848 proper 11.74574320 11.74150279 -0.00424041 11.74554948 -0.00019372 11.74557028 -0.00017292 11.74151736 -0.00422584 vdw (SR) 0.00000000 -4.15051852 -4.15051852 0.00000000 0.00000000 0.00000000 0.00000000 7.66479512 7.66479512 vdw total 7.66466960 7.66464182 -0.00002778 7.66464199 -0.00002761 7.66453101 -0.00013859 7.66479512 0.00012552 vdw-14 11.81519760 11.81516034 -0.00003726 0.00000000 -11.81519760 11.81506267 -0.00013493 0.00000000 -11.81519760 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.62204080 5.62220736 0.00016656 5.62220732 0.00016652 5.62216427 0.00012347 5.62216632 0.00012552 bond 1.34934000 1.34918046 -0.00015954 1.34918046 -0.00015954 1.34908755 -0.00025245 1.34917264 -0.00016736 bonded 18.71712400 18.71693730 -0.00018670 18.71693727 -0.00018673 18.71682209 -0.00030191 18.71691480 -0.00020920 dihedral 11.74574320 11.74554949 -0.00019371 11.74554948 -0.00019372 11.74557028 -0.00017292 11.74557584 -0.00016736 nonbonded 0.98407680 0.98776310 0.00368630 0.98776328 0.00368648 0.98760715 0.00353035 0.99516440 0.01108760 potential 19.70120080 19.70470041 0.00349961 19.70470072 0.00349992 19.70431993 0.00311913 19.71207920 0.01087840 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 19.70120080 Difference in potential energy from amber=>gromacs conversion: 0.00349961 Difference in potential energy from amber=>lammps conversion: 0.00349992 Difference in potential energy from amber=>desmond conversion: 0.00311913 Difference in potential energy from amber=>charmm conversion: 0.01087840 ======================================================================= INFO 2017-03-18 22:30:02 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1976156.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1976156.inpcrd') INFO 2017-03-18 22:30:03 Beginning InterMol conversion INFO 2017-03-18 22:30:03 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:30:03 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:30:03 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1977493.inpcrd INFO 2017-03-18 22:30:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1977493/mobley_1977493_converted.input INFO 2017-03-18 22:30:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1977493/mobley_1977493_converted.cms WARNING 2017-03-18 22:30:18 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:30:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1977493/mobley_1977493_converted.inp INFO 2017-03-18 22:30:18 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1977493/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1977493/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1977493/mobley_1977493_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1977493/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -0.49502353 -0.49502353 0.00000000 0.00000000 0.00000000 0.00000000 4.13216024 4.13216024 coulomb total 4.13923120 4.13510743 -0.00412377 4.13510737 -0.00412383 4.13509585 -0.00413535 4.13216024 -0.00707096 coulomb-14 4.63294320 4.63013096 -0.00281224 0.00000000 -4.63294320 4.63013707 -0.00280613 0.00000000 -4.63294320 proper 3.25222320 3.25231096 0.00008776 3.25231094 0.00008774 3.25232046 0.00009726 3.25230688 0.00008368 vdw (SR) 0.00000000 -0.47691687 -0.47691687 0.00000000 0.00000000 0.00000000 0.00000000 0.72358096 0.72358096 vdw total 0.72341360 0.72353481 0.00012121 0.72353481 0.00012121 0.72349207 0.00007847 0.72358096 0.00016736 vdw-14 1.20038960 1.20045168 0.00006208 0.00000000 -1.20038960 1.20041254 0.00002294 0.00000000 -1.20038960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.06020160 2.06020535 0.00000375 2.06020537 0.00000377 2.06041815 0.00021655 2.06024344 0.00004184 bond 0.53597040 0.53576701 -0.00020339 0.53576702 -0.00020338 0.53588385 -0.00008655 0.53576120 -0.00020920 bonded 5.84839520 5.84828332 -0.00011188 5.84828332 -0.00011188 5.84862246 0.00022726 5.84831152 -0.00008368 dihedral 3.25222320 3.25231096 0.00008776 3.25231094 0.00008774 3.25232046 0.00009726 3.25230688 0.00008368 nonbonded 4.86264480 4.85864224 -0.00400256 4.85864239 -0.00400241 4.85858791 -0.00405689 4.85574120 -0.00690360 potential 10.71104000 10.70692556 -0.00411444 10.70692545 -0.00411455 10.70718821 -0.00385179 10.70405272 -0.00698728 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 10.71104000 Difference in potential energy from amber=>gromacs conversion: -0.00411444 Difference in potential energy from amber=>lammps conversion: -0.00411455 Difference in potential energy from amber=>desmond conversion: -0.00385179 Difference in potential energy from amber=>charmm conversion: -0.00698728 ======================================================================= INFO 2017-03-18 22:30:18 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1977493.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1977493.inpcrd') INFO 2017-03-18 22:30:19 Beginning InterMol conversion INFO 2017-03-18 22:30:19 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:30:19 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:30:19 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1987439.inpcrd INFO 2017-03-18 22:30:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1987439/mobley_1987439_converted.input INFO 2017-03-18 22:30:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1987439/mobley_1987439_converted.cms WARNING 2017-03-18 22:30:35 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:30:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1987439/mobley_1987439_converted.inp INFO 2017-03-18 22:30:35 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1987439/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1987439/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1987439/mobley_1987439_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1987439/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 37.27290299 37.27290299 0.00000000 0.00000000 0.00000000 0.00000000 -38.28715640 -38.28715640 coulomb total -38.28318160 -38.26400812 0.01917348 -38.26400758 0.01917402 -38.26404055 0.01914105 -38.28715640 -0.00397480 coulomb-14 -75.51617920 -75.53691111 -0.02073191 0.00000000 75.51617920 -75.53688414 -0.02070494 0.00000000 75.51617920 improper 0.00000000 0.00001117 0.00001117 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00000000 0.00012731 0.00012731 0.00013846 0.00013846 0.00014015 0.00014015 0.00012552 0.00012552 vdw (SR) 0.00000000 -3.29635523 -3.29635523 0.00000000 0.00000000 0.00000000 0.00000000 18.65269040 18.65269040 vdw total 18.65269040 18.65264837 -0.00004203 18.65264856 -0.00004184 18.65268081 -0.00000959 18.65269040 0.00000000 vdw-14 21.94884560 21.94900361 0.00015801 0.00000000 -21.94884560 21.94902982 0.00018422 0.00000000 -21.94884560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.93010320 0.92998033 -0.00012287 0.92998032 -0.00012288 0.92986012 -0.00024308 0.92997768 -0.00012552 bond 2.83675200 2.83669493 -0.00005707 2.83669493 -0.00005707 2.83648727 -0.00026473 2.83671016 -0.00004184 bonded 3.76685520 3.76681373 -0.00004147 3.76681371 -0.00004149 3.76648754 -0.00036766 3.76681336 -0.00004184 dihedral 0.00000000 0.00013848 0.00013848 0.00013846 0.00013846 0.00014015 0.00014015 0.00012552 0.00012552 nonbonded -19.63049120 -19.61135975 0.01913145 -19.61135944 0.01913176 -19.61135974 0.01913146 -19.63446600 -0.00397480 potential -15.86363600 -15.84454601 0.01908999 -15.84454566 0.01909034 -15.84494180 0.01869420 -15.86765264 -0.00401664 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -15.86363600 Difference in potential energy from amber=>gromacs conversion: 0.01908999 Difference in potential energy from amber=>lammps conversion: 0.01909034 Difference in potential energy from amber=>desmond conversion: 0.01869420 Difference in potential energy from amber=>charmm conversion: -0.00401664 ======================================================================= INFO 2017-03-18 22:30:35 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1987439.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1987439.inpcrd') INFO 2017-03-18 22:30:35 Beginning InterMol conversion INFO 2017-03-18 22:30:35 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:30:35 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2005792.inpcrd INFO 2017-03-18 22:30:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2005792/mobley_2005792_converted.input INFO 2017-03-18 22:30:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2005792/mobley_2005792_converted.cms INFO 2017-03-18 22:30:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2005792/mobley_2005792_converted.rst7 WARNING 2017-03-18 22:30:51 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:30:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2005792/mobley_2005792_converted.inp INFO 2017-03-18 22:30:51 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2005792/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2005792/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2005792/mobley_2005792_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_2005792/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2005792/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -11.72725050 -11.72725050 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 4.94142952 4.94142952 coulomb total 4.95845840 4.94176741 -0.01669099 4.94176717 -0.01669123 4.94175248 -0.01670592 4.95845840 0.00000000 4.94142952 -0.01702888 coulomb-14 16.67072960 16.66901792 -0.00171168 0.00000000 -16.67072960 16.66899077 -0.00173883 16.67072960 0.00000000 0.00000000 -16.67072960 improper 0.00000000 0.00027660 0.00027660 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00029288 0.00029288 proper 8.37553120 8.37519023 -0.00034097 8.37548727 -0.00004393 8.37542011 -0.00011109 8.37553120 0.00000000 8.37519648 -0.00033472 vdw (SR) 0.00000000 4.94966547 4.94966547 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 42.75579392 42.75579392 vdw total 42.75587760 42.75577031 -0.00010729 42.75576882 -0.00010878 42.75587559 -0.00000201 42.75587760 0.00000000 42.75579392 -0.00008368 vdw-14 37.80620560 37.80610484 -0.00010076 0.00000000 -37.80620560 37.80623501 0.00002941 37.80620560 0.00000000 0.00000000 -37.80620560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.39578240 1.39562542 -0.00015698 1.39562542 -0.00015698 1.39561772 -0.00016468 1.39578240 0.00000000 1.39561504 -0.00016736 bond 3.77857040 3.77849005 -0.00008035 3.77849007 -0.00008033 3.77792373 -0.00064667 3.77857040 0.00000000 3.77848672 -0.00008368 bonded 13.54988400 13.54958231 -0.00030169 13.54960275 -0.00028125 13.54896156 -0.00092244 13.54988400 0.00000000 13.54959112 -0.00029288 dihedral 8.37553120 8.37546684 -0.00006436 8.37548727 -0.00004393 8.37542011 -0.00011109 8.37553120 0.00000000 8.37548936 -0.00004184 nonbonded 47.71433600 47.69753772 -0.01679828 47.69753724 -0.01679876 47.69762807 -0.01670793 47.71433600 0.00000000 47.69722344 -0.01711256 potential 61.26422000 61.24712003 -0.01709997 61.24714091 -0.01707909 61.24648946 -0.01773054 61.26422000 0.00000000 61.24681456 -0.01740544 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 61.26422000 Difference in potential energy from amber=>gromacs conversion: -0.01709997 Difference in potential energy from amber=>lammps conversion: -0.01707909 Difference in potential energy from amber=>desmond conversion: -0.01773054 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.01740544 ======================================================================= INFO 2017-03-18 22:30:51 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2005792.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2005792.inpcrd') INFO 2017-03-18 22:30:51 Beginning InterMol conversion INFO 2017-03-18 22:30:51 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:30:51 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:30:51 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2008055.inpcrd INFO 2017-03-18 22:30:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2008055/mobley_2008055_converted.input INFO 2017-03-18 22:30:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2008055/mobley_2008055_converted.cms WARNING 2017-03-18 22:31:07 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:31:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2008055/mobley_2008055_converted.inp INFO 2017-03-18 22:31:07 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2008055/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2008055/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2008055/mobley_2008055_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2008055/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 3.83434312 3.83434312 coulomb total 3.82501280 3.83125587 0.00624307 3.83125583 0.00624303 3.83125982 0.00624702 3.83434312 0.00933032 coulomb-14 3.82501280 3.83125587 0.00624307 0.00000000 -3.82501280 3.83125982 0.00624702 0.00000000 -3.82501280 proper 0.00000000 0.00000461 0.00000461 0.00000461 0.00000461 0.00000474 0.00000474 0.00000000 0.00000000 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.36647656 0.36647656 vdw total 0.36651840 0.36647943 -0.00003897 0.36647943 -0.00003897 0.36649149 -0.00002691 0.36647656 -0.00004184 vdw-14 0.36651840 0.36647943 -0.00003897 0.00000000 -0.36651840 0.36649149 -0.00002691 0.00000000 -0.36651840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.09748720 0.09769095 0.00020375 0.09769096 0.00020376 0.09769778 0.00021058 0.09769640 0.00020920 bond 0.70082000 0.70093564 0.00011564 0.70093565 0.00011565 0.70096386 0.00014386 0.70094552 0.00012552 bonded 0.79830720 0.79863120 0.00032400 0.79863121 0.00032401 0.79866639 0.00035919 0.79864192 0.00033472 dihedral 0.00000000 0.00000461 0.00000461 0.00000461 0.00000461 0.00000474 0.00000474 0.00000000 0.00000000 nonbonded 4.19153120 4.19773530 0.00620410 4.19773524 0.00620404 4.19775131 0.00622011 4.20081968 0.00928848 potential 4.98983840 4.99636650 0.00652810 4.99636628 0.00652788 4.99641159 0.00657319 4.99950344 0.00966504 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 4.98983840 Difference in potential energy from amber=>gromacs conversion: 0.00652810 Difference in potential energy from amber=>lammps conversion: 0.00652788 Difference in potential energy from amber=>desmond conversion: 0.00657319 Difference in potential energy from amber=>charmm conversion: 0.00966504 ======================================================================= INFO 2017-03-18 22:31:07 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2008055.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2008055.inpcrd') INFO 2017-03-18 22:31:07 Beginning InterMol conversion INFO 2017-03-18 22:31:07 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:31:07 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:31:07 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2023925.inpcrd INFO 2017-03-18 22:31:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2023925/mobley_2023925_converted.input INFO 2017-03-18 22:31:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2023925/mobley_2023925_converted.cms WARNING 2017-03-18 22:31:23 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:31:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2023925/mobley_2023925_converted.inp INFO 2017-03-18 22:31:23 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2023925/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2023925/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2023925/mobley_2023925_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2023925/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -137.99439752 -137.99439752 0.00000000 0.00000000 0.00000000 0.00000000 74.05859912 74.05859912 coulomb total 74.00115280 73.99984611 -0.00130669 73.99984321 -0.00130959 73.99986036 -0.00129244 74.05859912 0.05744632 coulomb-14 211.98905440 211.99424363 0.00518923 0.00000000 -211.98905440 211.99428356 0.00522916 0.00000000 -211.98905440 proper 5.00992160 5.00973522 -0.00018638 5.00973458 -0.00018702 5.00975416 -0.00016744 5.00946136 -0.00046024 vdw (SR) 0.00000000 -0.77801573 -0.77801573 0.00000000 0.00000000 0.00000000 0.00000000 8.68527272 8.68527272 vdw total 8.68556560 8.68533195 -0.00023365 8.68533213 -0.00023347 8.68544973 -0.00011587 8.68527272 -0.00029288 vdw-14 9.46337120 9.46334768 -0.00002352 0.00000000 -9.46337120 9.46339476 0.00002356 0.00000000 -9.46337120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.34385280 3.34364241 -0.00021039 3.34364243 -0.00021037 3.34353546 -0.00031734 3.34364360 -0.00020920 bond 1.96104080 1.96092287 -0.00011793 1.96092285 -0.00011795 1.96069722 -0.00034358 1.96091528 -0.00012552 bonded 10.31481520 10.31430050 -0.00051470 10.31429986 -0.00051534 10.31398684 -0.00082836 10.31402024 -0.00079496 dihedral 5.00992160 5.00973522 -0.00018638 5.00973458 -0.00018702 5.00975416 -0.00016744 5.00946136 -0.00046024 nonbonded 82.68671840 82.68517806 -0.00154034 82.68517869 -0.00153971 82.68531009 -0.00140831 82.74387184 0.05715344 potential 93.00153360 92.99947856 -0.00205504 92.99947926 -0.00205434 92.99925834 -0.00227526 93.05789208 0.05635848 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 93.00153360 Difference in potential energy from amber=>gromacs conversion: -0.00205504 Difference in potential energy from amber=>lammps conversion: -0.00205434 Difference in potential energy from amber=>desmond conversion: -0.00227526 Difference in potential energy from amber=>charmm conversion: 0.05635848 ======================================================================= INFO 2017-03-18 22:31:23 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2023925.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2023925.inpcrd') INFO 2017-03-18 22:31:23 Beginning InterMol conversion INFO 2017-03-18 22:31:23 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:31:23 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:31:23 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2043882.inpcrd INFO 2017-03-18 22:31:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2043882/mobley_2043882_converted.input INFO 2017-03-18 22:31:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2043882/mobley_2043882_converted.cms WARNING 2017-03-18 22:31:39 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:31:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2043882/mobley_2043882_converted.inp INFO 2017-03-18 22:31:39 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2043882/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2043882/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2043882/mobley_2043882_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2043882/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -0.64136672 -0.64136672 0.00000000 0.00000000 0.00000000 0.00000000 -33.94491752 -33.94491752 coulomb total -33.93014800 -33.93055824 -0.00041024 -33.93055803 -0.00041003 -33.93058929 -0.00044129 -33.94491752 -0.01476952 coulomb-14 -33.28832240 -33.28919152 -0.00086912 0.00000000 33.28832240 -33.28917606 -0.00085366 0.00000000 33.28832240 improper 0.00000000 0.00000718 0.00000718 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 26.10272080 26.10262056 -0.00010024 26.10262624 -0.00009456 26.10251578 -0.00020502 26.10297184 0.00025104 vdw (SR) 0.00000000 0.95419583 0.95419583 0.00000000 0.00000000 0.00000000 0.00000000 23.02325496 23.02325496 vdw total 23.02329680 23.02306587 -0.00023093 23.02306626 -0.00023054 23.02311598 -0.00018082 23.02325496 -0.00004184 vdw-14 22.06892640 22.06887005 -0.00005635 0.00000000 -22.06892640 22.06897657 0.00005017 0.00000000 -22.06892640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.18188400 5.18198234 0.00009834 5.18198232 0.00009832 5.18289808 0.00101408 5.18188400 0.00000000 bond 1.65226160 1.65235115 0.00008955 1.65235114 0.00008954 1.65284118 0.00057958 1.65234528 0.00008368 bonded 32.93686640 32.93696123 0.00009483 32.93695970 0.00009330 32.93825504 0.00138864 32.93720112 0.00033472 dihedral 26.10272080 26.10262775 -0.00009305 26.10262624 -0.00009456 26.10251578 -0.00020502 26.10297184 0.00025104 nonbonded -10.90685120 -10.90749236 -0.00064116 -10.90749135 -0.00064015 -10.90747330 -0.00062210 -10.92166256 -0.01481136 potential 22.03001520 22.02946886 -0.00054634 22.02946835 -0.00054685 22.03070405 0.00068885 22.01558040 -0.01443480 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 22.03001520 Difference in potential energy from amber=>gromacs conversion: -0.00054634 Difference in potential energy from amber=>lammps conversion: -0.00054685 Difference in potential energy from amber=>desmond conversion: 0.00068885 Difference in potential energy from amber=>charmm conversion: -0.01443480 ======================================================================= INFO 2017-03-18 22:31:39 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2043882.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2043882.inpcrd') INFO 2017-03-18 22:31:39 Beginning InterMol conversion INFO 2017-03-18 22:31:39 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:31:39 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:31:39 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2049967.inpcrd INFO 2017-03-18 22:31:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2049967/mobley_2049967_converted.input INFO 2017-03-18 22:31:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2049967/mobley_2049967_converted.cms WARNING 2017-03-18 22:31:55 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:31:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2049967/mobley_2049967_converted.inp INFO 2017-03-18 22:31:55 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2049967/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2049967/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2049967/mobley_2049967_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2049967/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 9.67634688 9.67634688 0.00000000 0.00000000 0.00000000 0.00000000 -0.27668792 -0.27668792 coulomb total -0.28242000 -0.27778392 0.00463608 -0.27778391 0.00463609 -0.27778476 0.00463524 -0.27668792 0.00573208 coulomb-14 -9.95373600 -9.95413079 -0.00039479 0.00000000 9.95373600 -9.95412135 -0.00038535 0.00000000 9.95373600 proper 0.01464400 0.01475546 0.00011146 0.01475545 0.00011145 0.01475198 0.00010798 0.01476952 0.00012552 vdw (SR) 0.00000000 -0.57656233 -0.57656233 0.00000000 0.00000000 0.00000000 0.00000000 -0.18125088 -0.18125088 vdw total -0.18116720 -0.18126374 -0.00009654 -0.18126375 -0.00009655 -0.18127332 -0.00010612 -0.18125088 -0.00008368 vdw-14 0.39538800 0.39529860 -0.00008940 0.00000000 -0.39538800 0.39528809 -0.00009991 0.00000000 -0.39538800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.03428480 1.03414700 -0.00013780 1.03414698 -0.00013782 1.03421743 -0.00006737 1.03411744 -0.00016736 bond 0.68784960 0.68769088 -0.00015872 0.68769090 -0.00015870 0.68741637 -0.00043323 0.68768224 -0.00016736 bonded 1.73677840 1.73659334 -0.00018506 1.73659333 -0.00018507 1.73638579 -0.00039261 1.73656920 -0.00020920 dihedral 0.01464400 0.01475546 0.00011146 0.01475545 0.00011145 0.01475198 0.00010798 0.01476952 0.00012552 nonbonded -0.46358720 -0.45904765 0.00453955 -0.45904764 0.00453956 -0.45905808 0.00452912 -0.45793880 0.00564840 potential 1.27319120 1.27754569 0.00435449 1.27754566 0.00435446 1.27730395 0.00411275 1.27867224 0.00548104 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 1.27319120 Difference in potential energy from amber=>gromacs conversion: 0.00435449 Difference in potential energy from amber=>lammps conversion: 0.00435446 Difference in potential energy from amber=>desmond conversion: 0.00411275 Difference in potential energy from amber=>charmm conversion: 0.00548104 ======================================================================= INFO 2017-03-18 22:31:55 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2049967.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2049967.inpcrd') INFO 2017-03-18 22:31:55 Beginning InterMol conversion INFO 2017-03-18 22:31:55 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:31:55 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_20524.inpcrd INFO 2017-03-18 22:31:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_20524/mobley_20524_converted.input INFO 2017-03-18 22:31:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_20524/mobley_20524_converted.cms INFO 2017-03-18 22:32:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_20524/mobley_20524_converted.rst7 WARNING 2017-03-18 22:32:11 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:32:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_20524/mobley_20524_converted.inp INFO 2017-03-18 22:32:11 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_20524/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_20524/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_20524/mobley_20524_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_20524/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_20524/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 39.77805842 39.77805842 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -65.20542248 -65.20542248 coulomb total -65.17333120 -65.17558100 -0.00224980 -65.17558219 -0.00225099 -65.17610779 -0.00277659 -65.17333120 0.00000000 -65.20542248 -0.03209128 coulomb-14 -104.95020080 -104.95363942 -0.00343862 0.00000000 104.95020080 -104.95362708 -0.00342628 -104.95020080 0.00000000 0.00000000 104.95020080 improper 0.00000000 0.00010172 0.00010172 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00125520 0.00103617 -0.00021903 0.00113782 -0.00011738 0.00113570 -0.00011950 0.00125520 0.00000000 0.00104600 -0.00020920 vdw (SR) 0.00000000 -1.08236759 -1.08236759 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 14.72554616 14.72554616 vdw total 14.72558800 14.72556590 -0.00002210 14.72556582 -0.00002218 14.72563026 0.00004226 14.72558800 0.00000000 14.72554616 -0.00004184 vdw-14 15.80798880 15.80793349 -0.00005531 0.00000000 -15.80798880 15.80799788 0.00000908 15.80798880 0.00000000 0.00000000 -15.80798880 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.07573040 0.07558583 -0.00014457 0.07558583 -0.00014457 0.07558593 -0.00014447 0.07573040 0.00000000 0.07560488 -0.00012552 bond 0.74642560 0.74653132 0.00010572 0.74653133 0.00010573 0.74642816 0.00000256 0.74642560 0.00000000 0.74655112 0.00012552 bonded 0.82341120 0.82325504 -0.00015616 0.82325498 -0.00015622 0.82314980 -0.00026140 0.82341120 0.00000000 0.82328568 -0.00012552 dihedral 0.00125520 0.00113789 -0.00011731 0.00113782 -0.00011738 0.00113570 -0.00011950 0.00125520 0.00000000 0.00112968 -0.00012552 nonbonded -50.44774320 -50.45001510 -0.00227190 -50.45001511 -0.00227191 -50.45047753 -0.00273433 -50.44774320 0.00000000 -50.47987632 -0.03213312 potential -49.62433200 -49.62676006 -0.00242806 -49.62675872 -0.00242672 -49.62735787 -0.00302587 -49.62433200 0.00000000 -49.65659064 -0.03225864 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -49.62433200 Difference in potential energy from amber=>gromacs conversion: -0.00242806 Difference in potential energy from amber=>lammps conversion: -0.00242672 Difference in potential energy from amber=>desmond conversion: -0.00302587 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.03225864 ======================================================================= INFO 2017-03-18 22:32:11 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_20524.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_20524.inpcrd') INFO 2017-03-18 22:32:11 Beginning InterMol conversion INFO 2017-03-18 22:32:11 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:32:11 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:32:11 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2068538.inpcrd INFO 2017-03-18 22:32:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2068538/mobley_2068538_converted.input INFO 2017-03-18 22:32:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2068538/mobley_2068538_converted.cms WARNING 2017-03-18 22:32:27 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:32:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2068538/mobley_2068538_converted.inp INFO 2017-03-18 22:32:27 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2068538/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2068538/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2068538/mobley_2068538_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2068538/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 3.90545764 3.90545764 0.00000000 0.00000000 0.00000000 0.00000000 3.09988376 3.09988376 coulomb total 3.09574160 3.10450442 0.00876282 3.10450436 0.00876276 3.10449333 0.00875173 3.09988376 0.00414216 coulomb-14 -0.80500160 -0.80095323 0.00404837 0.00000000 0.80500160 -0.80095769 0.00404391 0.00000000 0.80500160 proper 0.02133840 0.02118526 -0.00015314 0.02118526 -0.00015314 0.02118751 -0.00015089 0.02117104 -0.00016736 vdw (SR) 0.00000000 -0.13326517 -0.13326517 0.00000000 0.00000000 0.00000000 0.00000000 2.05785856 2.05785856 vdw total 2.05769120 2.05781161 0.00012041 2.05781166 0.00012046 2.05777260 0.00008140 2.05785856 0.00016736 vdw-14 2.19116080 2.19107678 -0.00008402 0.00000000 -2.19116080 2.19103597 -0.00012483 0.00000000 -2.19116080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.55186960 0.55203062 0.00016102 0.55203060 0.00016100 0.55208767 0.00021807 0.55203696 0.00016736 bond 2.27902480 2.27916104 0.00013624 2.27916103 0.00013623 2.27904078 0.00001598 2.27915032 0.00012552 bonded 2.85223280 2.85237693 0.00014413 2.85237689 0.00014409 2.85231595 0.00008315 2.85235832 0.00012552 dihedral 0.02133840 0.02118526 -0.00015314 0.02118526 -0.00015314 0.02118751 -0.00015089 0.02117104 -0.00016736 nonbonded 5.15343280 5.16231603 0.00888323 5.16231585 0.00888305 5.16226593 0.00883313 5.15774232 0.00430952 potential 8.00566560 8.01469296 0.00902736 8.01469300 0.00902740 8.01456911 0.00890351 8.01010064 0.00443504 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 8.00566560 Difference in potential energy from amber=>gromacs conversion: 0.00902736 Difference in potential energy from amber=>lammps conversion: 0.00902740 Difference in potential energy from amber=>desmond conversion: 0.00890351 Difference in potential energy from amber=>charmm conversion: 0.00443504 ======================================================================= INFO 2017-03-18 22:32:27 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2068538.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2068538.inpcrd') INFO 2017-03-18 22:32:27 Beginning InterMol conversion INFO 2017-03-18 22:32:27 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:32:27 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:32:27 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2078467.inpcrd INFO 2017-03-18 22:32:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2078467/mobley_2078467_converted.input INFO 2017-03-18 22:32:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2078467/mobley_2078467_converted.cms WARNING 2017-03-18 22:32:43 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:32:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2078467/mobley_2078467_converted.inp INFO 2017-03-18 22:32:43 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2078467/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2078467/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2078467/mobley_2078467_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2078467/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 8.29282839 8.29282839 0.00000000 0.00000000 0.00000000 0.00000000 -92.06766480 -92.06766480 coulomb total -92.02624320 -92.03932209 -0.01307889 -92.03932238 -0.01307918 -92.03949640 -0.01325320 -92.06766480 -0.04142160 coulomb-14 -100.33064640 -100.33215047 -0.00150407 0.00000000 100.33064640 -100.33225515 -0.00160875 0.00000000 100.33064640 improper 0.00000000 0.00018794 0.00018794 0.00000000 0.00000000 0.00000000 0.00000000 0.00016736 0.00016736 proper 0.97738240 0.97718826 -0.00019414 0.97737571 -0.00000669 0.97737498 -0.00000742 0.97721504 -0.00016736 vdw (SR) 0.00000000 -8.53740007 -8.53740007 0.00000000 0.00000000 0.00000000 0.00000000 24.25703288 24.25703288 vdw total 24.25674000 24.25687710 0.00013710 24.25687724 0.00013724 24.25650883 -0.00023117 24.25703288 0.00029288 vdw-14 32.79419200 32.79427717 0.00008517 0.00000000 -32.79419200 32.79389933 -0.00029267 0.00000000 -32.79419200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 9.02405120 9.02396639 -0.00008481 9.02396626 -0.00008494 9.02393890 -0.00011230 9.02396752 -0.00008368 bond 8.07386480 8.07388186 0.00001706 8.07388195 0.00001715 8.07369162 -0.00017318 8.07386480 0.00000000 bonded 18.07529840 18.07522445 -0.00007395 18.07522392 -0.00007448 18.07500551 -0.00029289 18.07521472 -0.00008368 dihedral 0.97738240 0.97737620 -0.00000620 0.97737571 -0.00000669 0.97737498 -0.00000742 0.97738240 -0.00000000 nonbonded -67.76950320 -67.78244499 -0.01294179 -67.78244431 -0.01294111 -67.78298756 -0.01348436 -67.81063192 -0.04112872 potential -49.69420480 -49.70722054 -0.01301574 -49.70722122 -0.01301642 -49.70816890 -0.01396410 -49.73541720 -0.04121240 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -49.69420480 Difference in potential energy from amber=>gromacs conversion: -0.01301574 Difference in potential energy from amber=>lammps conversion: -0.01301642 Difference in potential energy from amber=>desmond conversion: -0.01396410 Difference in potential energy from amber=>charmm conversion: -0.04121240 ======================================================================= INFO 2017-03-18 22:32:43 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2078467.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2078467.inpcrd') INFO 2017-03-18 22:32:43 Beginning InterMol conversion INFO 2017-03-18 22:32:43 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:32:44 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:32:44 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2099370.inpcrd INFO 2017-03-18 22:32:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2099370/mobley_2099370_converted.input INFO 2017-03-18 22:32:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2099370/mobley_2099370_converted.cms WARNING 2017-03-18 22:32:59 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:32:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2099370/mobley_2099370_converted.inp INFO 2017-03-18 22:32:59 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2099370/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2099370/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2099370/mobley_2099370_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2099370/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -65.96088055 -65.96088055 0.00000000 0.00000000 0.00000000 0.00000000 -8.04934656 -8.04934656 coulomb total -7.99771600 -8.00465210 -0.00693610 -8.00465182 -0.00693582 -8.00507984 -0.00736384 -8.04934656 -0.05163056 coulomb-14 57.96011520 57.95622844 -0.00388676 0.00000000 -57.96011520 57.95629688 -0.00381832 0.00000000 -57.96011520 improper 0.00000000 0.00018150 0.00018150 0.00000000 0.00000000 0.00000000 0.00000000 0.00016736 0.00016736 proper 35.04769440 35.04753023 -0.00016417 35.04771155 0.00001715 35.04771001 0.00001561 35.04752704 -0.00016736 vdw (SR) 0.00000000 -8.22581842 -8.22581842 0.00000000 0.00000000 0.00000000 0.00000000 39.41989072 39.41989072 vdw total 39.41997440 39.41975421 -0.00022019 39.41975432 -0.00022008 39.41965391 -0.00032049 39.41989072 -0.00008368 vdw-14 47.64571840 47.64557263 -0.00014577 0.00000000 -47.64571840 47.64554100 -0.00017740 0.00000000 -47.64571840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 12.04573600 12.04559287 -0.00014313 12.04559291 -0.00014309 12.04497581 -0.00076019 12.04556864 -0.00016736 bond 11.80975840 11.80972359 -0.00003481 11.80972367 -0.00003473 11.80875796 -0.00100044 11.80971656 -0.00004184 bonded 58.90318880 58.90302819 -0.00016061 58.90302813 -0.00016067 58.90144378 -0.00174502 58.90297960 -0.00020920 dihedral 35.04769440 35.04771172 0.00001732 35.04771155 0.00001715 35.04771001 0.00001561 35.04769440 0.00000000 nonbonded 31.42225840 31.41510210 -0.00715630 31.41510209 -0.00715631 31.41457407 -0.00768433 31.37054416 -0.05171424 potential 90.32544720 90.31813029 -0.00731691 90.31812938 -0.00731782 90.31577463 -0.00967257 90.27356560 -0.05188160 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 90.32544720 Difference in potential energy from amber=>gromacs conversion: -0.00731691 Difference in potential energy from amber=>lammps conversion: -0.00731782 Difference in potential energy from amber=>desmond conversion: -0.00967257 Difference in potential energy from amber=>charmm conversion: -0.05188160 ======================================================================= INFO 2017-03-18 22:32:59 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2099370.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2099370.inpcrd') INFO 2017-03-18 22:33:00 Beginning InterMol conversion INFO 2017-03-18 22:33:00 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:33:00 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:33:00 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_210639.inpcrd INFO 2017-03-18 22:33:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_210639/mobley_210639_converted.input INFO 2017-03-18 22:33:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_210639/mobley_210639_converted.cms WARNING 2017-03-18 22:33:15 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:33:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_210639/mobley_210639_converted.inp INFO 2017-03-18 22:33:15 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_210639/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_210639/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_210639/mobley_210639_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_210639/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 8.03147929 8.03147929 0.00000000 0.00000000 0.00000000 0.00000000 -18.07693016 -18.07693016 coulomb total -18.07948240 -18.07991396 -0.00043156 -18.07991377 -0.00043137 -18.07989406 -0.00041166 -18.07693016 0.00255224 coulomb-14 -26.11067040 -26.11139324 -0.00072284 0.00000000 26.11067040 -26.11135791 -0.00068751 0.00000000 26.11067040 proper 0.02008320 0.02011296 0.00002976 0.02011295 0.00002975 0.02011147 0.00002827 0.02012504 0.00004184 vdw (SR) 0.00000000 -0.15674481 -0.15674481 0.00000000 0.00000000 0.00000000 0.00000000 1.30921544 1.30921544 vdw total 1.30917360 1.30916009 -0.00001351 1.30916013 -0.00001347 1.30915417 -0.00001943 1.30921544 0.00004184 vdw-14 1.46607360 1.46590490 -0.00016870 0.00000000 -1.46607360 1.46590046 -0.00017314 0.00000000 -1.46607360 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.65477200 1.65470135 -0.00007065 1.65470133 -0.00007067 1.65463747 -0.00013453 1.65473016 -0.00004184 bond 0.34099600 0.34118716 0.00019116 0.34118715 0.00019115 0.34128893 0.00029293 0.34120520 0.00020920 bonded 2.01585120 2.01600146 0.00015026 2.01600143 0.00015023 2.01603788 0.00018668 2.01606040 0.00020920 dihedral 0.02008320 0.02011296 0.00002976 0.02011295 0.00002975 0.02011147 0.00002827 0.02012504 0.00004184 nonbonded -16.77030880 -16.77075386 -0.00044506 -16.77075356 -0.00044476 -16.77073989 -0.00043109 -16.76771472 0.00259408 potential -14.75445760 -14.75475240 -0.00029480 -14.75475215 -0.00029455 -14.75473764 -0.00028004 -14.75169616 0.00276144 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -14.75445760 Difference in potential energy from amber=>gromacs conversion: -0.00029480 Difference in potential energy from amber=>lammps conversion: -0.00029455 Difference in potential energy from amber=>desmond conversion: -0.00028004 Difference in potential energy from amber=>charmm conversion: 0.00276144 ======================================================================= INFO 2017-03-18 22:33:15 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_210639.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_210639.inpcrd') INFO 2017-03-18 22:33:16 Beginning InterMol conversion INFO 2017-03-18 22:33:16 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:33:16 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2123854.inpcrd INFO 2017-03-18 22:33:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2123854/mobley_2123854_converted.input INFO 2017-03-18 22:33:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2123854/mobley_2123854_converted.cms INFO 2017-03-18 22:33:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2123854/mobley_2123854_converted.rst7 WARNING 2017-03-18 22:33:31 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:33:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2123854/mobley_2123854_converted.inp INFO 2017-03-18 22:33:31 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2123854/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2123854/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2123854/mobley_2123854_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_2123854/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2123854/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 33.69795613 33.69795613 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -59.00025760 -59.00025760 coulomb total -58.95423360 -58.96299072 -0.00875712 -58.96299071 -0.00875711 -58.96344522 -0.00921162 -58.95381520 0.00041840 -59.00025760 -0.04602400 coulomb-14 -92.65760880 -92.66094684 -0.00333804 0.00000000 92.65760880 -92.66083466 -0.00322586 -92.65719040 0.00041840 0.00000000 92.65760880 improper 0.00000000 0.00002571 0.00002571 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00028848 -0.00012992 0.00031417 -0.00010423 0.00031622 -0.00010218 0.00041840 0.00000000 0.00029288 -0.00012552 vdw (SR) 0.00000000 -2.57702967 -2.57702967 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 14.08464104 14.08464104 vdw total 14.08459920 14.08463323 0.00003403 14.08463309 0.00003389 14.08469500 0.00009580 14.08459920 0.00000000 14.08464104 0.00004184 vdw-14 16.66152480 16.66166290 0.00013810 0.00000000 -16.66152480 16.66172551 0.00020071 16.66152480 0.00000000 0.00000000 -16.66152480 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.54894080 0.27401249 -0.27492831 0.27401249 -0.27492831 0.27410688 -0.27483392 0.54894080 0.00000000 0.27401016 -0.27493064 bond 2.34094800 2.34105147 0.00010347 2.34105147 0.00010347 2.34212594 0.00117794 2.34094800 0.00000000 2.34103168 0.00008368 bonded 2.89030720 2.61537815 -0.27492905 2.61537814 -0.27492906 2.61654904 -0.27375816 2.89030720 0.00000000 2.61537656 -0.27493064 dihedral 0.00041840 0.00031419 -0.00010421 0.00031417 -0.00010423 0.00031622 -0.00010218 0.00041840 0.00000000 0.00033472 -0.00008368 nonbonded -44.86963440 -44.87835749 -0.00872309 -44.87835804 -0.00872364 -44.87875022 -0.00911582 -44.86921600 0.00041840 -44.91561656 -0.04598216 potential -41.97932720 -42.26297933 -0.28365213 -42.26297730 -0.28365010 -42.26226685 -0.28293965 -41.97890880 0.00041840 -42.30024000 -0.32091280 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -41.97932720 Difference in potential energy from amber=>gromacs conversion: -0.28365213 Difference in potential energy from amber=>lammps conversion: -0.28365010 Difference in potential energy from amber=>desmond conversion: -0.28293965 Difference in potential energy from amber=>amber conversion: 0.00041840 Difference in potential energy from amber=>charmm conversion: -0.32091280 ======================================================================= INFO 2017-03-18 22:33:31 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2123854.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2123854.inpcrd') INFO 2017-03-18 22:33:32 Beginning InterMol conversion INFO 2017-03-18 22:33:32 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:33:32 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:33:32 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2126135.inpcrd INFO 2017-03-18 22:33:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2126135/mobley_2126135_converted.input INFO 2017-03-18 22:33:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2126135/mobley_2126135_converted.cms WARNING 2017-03-18 22:33:48 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:33:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2126135/mobley_2126135_converted.inp INFO 2017-03-18 22:33:48 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2126135/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2126135/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2126135/mobley_2126135_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2126135/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -9.58387925 -9.58387925 0.00000000 0.00000000 0.00000000 0.00000000 -51.55487144 -51.55487144 coulomb total -51.54144080 -51.54912260 -0.00768180 -51.54912262 -0.00768182 -51.54973462 -0.00829382 -51.55487144 -0.01343064 coulomb-14 -41.96426480 -41.96524335 -0.00097855 0.00000000 41.96426480 -41.96533046 -0.00106566 0.00000000 41.96426480 improper 0.00000000 0.00008581 0.00008581 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.02050160 0.02038694 -0.00011466 0.02047267 -0.00002893 0.02046635 -0.00003525 0.02037608 -0.00012552 vdw (SR) 0.00000000 -2.03975526 -2.03975526 0.00000000 0.00000000 0.00000000 0.00000000 19.45053736 19.45053736 vdw total 19.45057920 19.45047058 -0.00010862 19.45047083 -0.00010837 19.45059537 0.00001617 19.45053736 -0.00004184 vdw-14 21.49027920 21.49022584 -0.00005336 0.00000000 -21.49027920 21.49032778 0.00004858 0.00000000 -21.49027920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.86023040 0.86033021 0.00009981 0.86033023 0.00009983 0.86030174 0.00007134 0.86031408 0.00008368 bond 1.62381040 1.62383937 0.00002897 1.62383935 0.00002895 1.62356614 -0.00024426 1.62385224 0.00004184 bonded 2.50454240 2.50464234 0.00009994 2.50464225 0.00009985 2.50433423 -0.00020817 2.50462608 0.00008368 dihedral 0.02050160 0.02047275 -0.00002885 0.02047267 -0.00002893 0.02046635 -0.00003525 0.02045976 -0.00004184 nonbonded -32.09086160 -32.09865202 -0.00779042 -32.09865137 -0.00778977 -32.09913925 -0.00827765 -32.10433408 -0.01347248 potential -29.58631920 -29.59400968 -0.00769048 -29.59400897 -0.00768977 -29.59486628 -0.00854708 -29.59970800 -0.01338880 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -29.58631920 Difference in potential energy from amber=>gromacs conversion: -0.00769048 Difference in potential energy from amber=>lammps conversion: -0.00768977 Difference in potential energy from amber=>desmond conversion: -0.00854708 Difference in potential energy from amber=>charmm conversion: -0.01338880 ======================================================================= INFO 2017-03-18 22:33:48 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2126135.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2126135.inpcrd') INFO 2017-03-18 22:33:48 Beginning InterMol conversion INFO 2017-03-18 22:33:48 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:33:48 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:33:48 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2143011.inpcrd INFO 2017-03-18 22:33:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2143011/mobley_2143011_converted.input INFO 2017-03-18 22:33:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2143011/mobley_2143011_converted.cms WARNING 2017-03-18 22:34:04 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:34:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2143011/mobley_2143011_converted.inp INFO 2017-03-18 22:34:04 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2143011/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2143011/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2143011/mobley_2143011_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2143011/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 5.46915644 5.46915644 0.00000000 0.00000000 0.00000000 0.00000000 -0.80027368 -0.80027368 coulomb total -0.81420640 -0.80313346 0.01107294 -0.80313344 0.01107296 -0.80318491 0.01102149 -0.80027368 0.01393272 coulomb-14 -6.27014240 -6.27228989 -0.00214749 0.00000000 6.27014240 -6.27230674 -0.00216434 0.00000000 6.27014240 improper 0.00000000 0.00001144 0.00001144 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 9.66755040 9.66747441 -0.00007599 9.66748555 -0.00006485 9.66749710 -0.00005330 9.66746672 -0.00008368 vdw (SR) 0.00000000 -1.16659573 -1.16659573 0.00000000 0.00000000 0.00000000 0.00000000 3.49008360 3.49008360 vdw total 3.49029280 3.49002414 -0.00026866 3.49002419 -0.00026861 3.49003372 -0.00025908 3.49008360 -0.00020920 vdw-14 4.65679200 4.65661987 -0.00017213 0.00000000 -4.65679200 4.65663954 -0.00015246 0.00000000 -4.65679200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.79702800 1.79685568 -0.00017232 1.79685570 -0.00017230 1.79664208 -0.00038592 1.79681880 -0.00020920 bond 0.87152720 0.87145365 -0.00007355 0.87145365 -0.00007355 0.87092366 -0.00060354 0.87144352 -0.00008368 bonded 12.33610560 12.33579518 -0.00031042 12.33579490 -0.00031070 12.33506283 -0.00104277 12.33572904 -0.00037656 dihedral 9.66755040 9.66748585 -0.00006455 9.66748555 -0.00006485 9.66749710 -0.00005330 9.66746672 -0.00008368 nonbonded 2.67608640 2.68689068 0.01080428 2.68689074 0.01080434 2.68684882 0.01076242 2.68980992 0.01372352 potential 15.01219200 15.02268587 0.01049387 15.02268589 0.01049389 15.02188445 0.00969245 15.02558080 0.01338880 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 15.01219200 Difference in potential energy from amber=>gromacs conversion: 0.01049387 Difference in potential energy from amber=>lammps conversion: 0.01049389 Difference in potential energy from amber=>desmond conversion: 0.00969245 Difference in potential energy from amber=>charmm conversion: 0.01338880 ======================================================================= INFO 2017-03-18 22:34:04 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2143011.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2143011.inpcrd') INFO 2017-03-18 22:34:04 Beginning InterMol conversion INFO 2017-03-18 22:34:04 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:34:04 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:34:04 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2178600.inpcrd INFO 2017-03-18 22:34:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2178600/mobley_2178600_converted.input INFO 2017-03-18 22:34:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2178600/mobley_2178600_converted.cms WARNING 2017-03-18 22:34:20 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:34:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2178600/mobley_2178600_converted.inp INFO 2017-03-18 22:34:20 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2178600/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2178600/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2178600/mobley_2178600_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2178600/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 3.28083510 3.28083510 0.00000000 0.00000000 0.00000000 0.00000000 4.32198832 4.32198832 coulomb total 4.32583760 4.32124343 -0.00459417 4.32124357 -0.00459403 4.32123410 -0.00460350 4.32198832 -0.00384928 coulomb-14 1.04223440 1.04040833 -0.00182607 0.00000000 -1.04223440 1.04040995 -0.00182445 0.00000000 -1.04223440 proper 5.03418880 5.03416185 -0.00002695 5.03416202 -0.00002678 5.03416386 -0.00002494 5.03418880 0.00000000 vdw (SR) 0.00000000 -0.97276137 -0.97276137 0.00000000 0.00000000 0.00000000 0.00000000 3.65074920 3.65074920 vdw total 3.65054000 3.65065851 0.00011851 3.65065857 0.00011857 3.65063719 0.00009719 3.65074920 0.00020920 vdw-14 4.62332000 4.62341988 0.00009988 0.00000000 -4.62332000 4.62346506 0.00014506 0.00000000 -4.62332000 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.38648160 5.38638223 -0.00009937 5.38638202 -0.00009958 5.38613675 -0.00034485 5.38639792 -0.00008368 bond 0.68241040 0.68249386 0.00008346 0.68249387 0.00008347 0.68245366 0.00004326 0.68249408 0.00008368 bonded 11.10308080 11.10303794 -0.00004286 11.10303791 -0.00004289 11.10275428 -0.00032652 11.10308080 0.00000000 dihedral 5.03418880 5.03416185 -0.00002695 5.03416202 -0.00002678 5.03416386 -0.00002494 5.03418880 0.00000000 nonbonded 7.97637760 7.97190193 -0.00447567 7.97190198 -0.00447562 7.97187129 -0.00450631 7.97273752 -0.00364008 potential 19.07945840 19.07493987 -0.00451853 19.07493968 -0.00451872 19.07457764 -0.00488076 19.07577648 -0.00368192 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 19.07945840 Difference in potential energy from amber=>gromacs conversion: -0.00451853 Difference in potential energy from amber=>lammps conversion: -0.00451872 Difference in potential energy from amber=>desmond conversion: -0.00488076 Difference in potential energy from amber=>charmm conversion: -0.00368192 ======================================================================= INFO 2017-03-18 22:34:20 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2178600.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2178600.inpcrd') INFO 2017-03-18 22:34:20 Beginning InterMol conversion INFO 2017-03-18 22:34:20 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:34:20 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:34:20 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2183616.inpcrd INFO 2017-03-18 22:34:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2183616/mobley_2183616_converted.input INFO 2017-03-18 22:34:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2183616/mobley_2183616_converted.cms WARNING 2017-03-18 22:34:36 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:34:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2183616/mobley_2183616_converted.inp INFO 2017-03-18 22:34:36 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2183616/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2183616/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2183616/mobley_2183616_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2183616/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -8.53891288 -8.53891288 0.00000000 0.00000000 0.00000000 0.00000000 -4.14006800 -4.14006800 coulomb total -4.14885440 -4.14873367 0.00012073 -4.14873361 0.00012079 -4.14887913 -0.00002473 -4.14006800 0.00878640 coulomb-14 4.38985280 4.39017921 0.00032641 0.00000000 -4.38985280 4.39013342 0.00028062 0.00000000 -4.38985280 improper 0.00000000 0.00006133 0.00006133 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 1.90037280 1.90017226 -0.00020054 1.90023372 -0.00013908 1.90021195 -0.00016085 1.90020544 -0.00016736 vdw (SR) 0.00000000 4.47654992 4.47654992 0.00000000 0.00000000 0.00000000 0.00000000 29.39967096 29.39967096 vdw total 29.39929440 29.39955765 0.00026325 29.39955799 0.00026359 29.39983476 0.00054036 29.39967096 0.00037656 vdw-14 24.92283280 24.92300773 0.00017493 0.00000000 -24.92283280 24.92308685 0.00025405 0.00000000 -24.92283280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.36393600 3.36393223 -0.00000377 3.36393223 -0.00000377 3.36362905 -0.00030695 3.36389416 -0.00004184 bond 1.21796240 1.21793252 -0.00002988 1.21793253 -0.00002987 1.21753764 -0.00042476 1.21792056 -0.00004184 bonded 6.48227120 6.48209835 -0.00017285 6.48209848 -0.00017272 6.48137864 -0.00089256 6.48206200 -0.00020920 dihedral 1.90037280 1.90023360 -0.00013920 1.90023372 -0.00013908 1.90021195 -0.00016085 1.90024728 -0.00012552 nonbonded 25.25044000 25.25082398 0.00038398 25.25082409 0.00038409 25.25095564 0.00051564 25.25960296 0.00916296 potential 31.73271120 31.73292233 0.00021113 31.73292249 0.00021129 31.73224326 -0.00046794 31.74166496 0.00895376 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 31.73271120 Difference in potential energy from amber=>gromacs conversion: 0.00021113 Difference in potential energy from amber=>lammps conversion: 0.00021129 Difference in potential energy from amber=>desmond conversion: -0.00046794 Difference in potential energy from amber=>charmm conversion: 0.00895376 ======================================================================= INFO 2017-03-18 22:34:36 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2183616.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2183616.inpcrd') INFO 2017-03-18 22:34:36 Beginning InterMol conversion INFO 2017-03-18 22:34:36 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:34:36 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:34:36 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2197088.inpcrd INFO 2017-03-18 22:34:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2197088/mobley_2197088_converted.input INFO 2017-03-18 22:34:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2197088/mobley_2197088_converted.cms WARNING 2017-03-18 22:34:52 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:34:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2197088/mobley_2197088_converted.inp INFO 2017-03-18 22:34:52 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2197088/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2197088/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2197088/mobley_2197088_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2197088/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 8.62309914 8.62309914 0.00000000 0.00000000 0.00000000 0.00000000 3.82576592 3.82576592 coulomb total 3.84928000 3.81953239 -0.02974761 3.81953235 -0.02974765 3.81948134 -0.02979866 3.82576592 -0.02351408 coulomb-14 -4.79779280 -4.80356675 -0.00577395 0.00000000 4.79779280 -4.80355735 -0.00576455 0.00000000 4.79779280 proper 11.99636480 11.99633266 -0.00003214 11.99633258 -0.00003222 11.99634459 -0.00002021 11.99632296 -0.00004184 vdw (SR) 0.00000000 -4.64828743 -4.64828743 0.00000000 0.00000000 0.00000000 0.00000000 7.72270168 7.72270168 vdw total 7.72240880 7.72251923 0.00011043 7.72251926 0.00011046 7.72260139 0.00019259 7.72270168 0.00029288 vdw-14 12.37083280 12.37080666 -0.00002614 0.00000000 -12.37083280 12.37089133 0.00005853 0.00000000 -12.37083280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.13627840 5.13648658 0.00020818 5.13648676 0.00020836 5.13688223 0.00060383 5.13644576 0.00016736 bond 1.21043120 1.21029411 -0.00013709 1.21029413 -0.00013707 1.21039035 -0.00004085 1.21030568 -0.00012552 bonded 18.34307440 18.34311336 0.00003896 18.34311348 0.00003908 18.34361718 0.00054278 18.34307440 0.00000000 dihedral 11.99636480 11.99633266 -0.00003214 11.99633258 -0.00003222 11.99634459 -0.00002021 11.99632296 -0.00004184 nonbonded 11.57168880 11.54205162 -0.02963718 11.54205185 -0.02963695 11.54208273 -0.02960607 11.54846760 -0.02322120 potential 29.91476320 29.88516498 -0.02959822 29.88516517 -0.02959803 29.88557013 -0.02919307 29.89154200 -0.02322120 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 29.91476320 Difference in potential energy from amber=>gromacs conversion: -0.02959822 Difference in potential energy from amber=>lammps conversion: -0.02959803 Difference in potential energy from amber=>desmond conversion: -0.02919307 Difference in potential energy from amber=>charmm conversion: -0.02322120 ======================================================================= INFO 2017-03-18 22:34:52 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2197088.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2197088.inpcrd') INFO 2017-03-18 22:34:52 Beginning InterMol conversion INFO 2017-03-18 22:34:52 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:34:52 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:34:52 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2198613.inpcrd INFO 2017-03-18 22:34:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2198613/mobley_2198613_converted.input INFO 2017-03-18 22:34:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2198613/mobley_2198613_converted.cms WARNING 2017-03-18 22:35:08 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:35:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2198613/mobley_2198613_converted.inp INFO 2017-03-18 22:35:08 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2198613/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2198613/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2198613/mobley_2198613_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2198613/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -2.99038848 -2.99038848 coulomb total -2.99407040 -2.99407015 0.00000025 -2.99407011 0.00000029 -2.99407994 -0.00000954 -2.99038848 0.00368192 coulomb-14 -2.99407040 -2.99407015 0.00000025 0.00000000 2.99407040 -2.99407994 -0.00000954 0.00000000 2.99407040 proper 3.12670320 3.12677527 0.00007207 3.12677525 0.00007205 3.12677624 0.00007304 3.12678688 0.00008368 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.35036816 0.35036816 vdw total 0.35020080 0.35035657 0.00015577 0.35035657 0.00015577 0.35036273 0.00016193 0.35036816 0.00016736 vdw-14 0.35020080 0.35035657 0.00015577 0.00000000 -0.35020080 0.35036273 0.00016193 0.00000000 -0.35020080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.71128000 0.71135593 0.00007593 0.71135594 0.00007594 0.71139683 0.00011683 0.71140552 0.00012552 bond 0.68533920 0.68515857 -0.00018063 0.68515858 -0.00018062 0.68523978 -0.00009942 0.68517184 -0.00016736 bonded 4.52332240 4.52328978 -0.00003262 4.52328976 -0.00003264 4.52341285 0.00009045 4.52336424 0.00004184 dihedral 3.12670320 3.12677527 0.00007207 3.12677525 0.00007205 3.12677624 0.00007304 3.12678688 0.00008368 nonbonded -2.64386960 -2.64371358 0.00015602 -2.64371354 0.00015606 -2.64371720 0.00015240 -2.64002032 0.00384928 potential 1.87945280 1.87957620 0.00012340 1.87957623 0.00012343 1.87968256 0.00022976 1.88330208 0.00384928 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 1.87945280 Difference in potential energy from amber=>gromacs conversion: 0.00012340 Difference in potential energy from amber=>lammps conversion: 0.00012343 Difference in potential energy from amber=>desmond conversion: 0.00022976 Difference in potential energy from amber=>charmm conversion: 0.00384928 ======================================================================= INFO 2017-03-18 22:35:08 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2198613.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2198613.inpcrd') INFO 2017-03-18 22:35:08 Beginning InterMol conversion INFO 2017-03-18 22:35:08 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:35:08 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:35:08 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2213823.inpcrd INFO 2017-03-18 22:35:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2213823/mobley_2213823_converted.input INFO 2017-03-18 22:35:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2213823/mobley_2213823_converted.cms WARNING 2017-03-18 22:35:24 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:35:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2213823/mobley_2213823_converted.inp INFO 2017-03-18 22:35:24 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2213823/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2213823/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2213823/mobley_2213823_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2213823/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.48365394 0.48365394 0.00000000 0.00000000 0.00000000 0.00000000 -1.95325856 -1.95325856 coulomb total -1.96145920 -1.95637677 0.00508243 -1.95637677 0.00508243 -1.95638107 0.00507813 -1.95325856 0.00820064 coulomb-14 -2.44010880 -2.44003071 0.00007809 0.00000000 2.44010880 -2.44004842 0.00006038 0.00000000 2.44010880 proper 7.39940400 7.39948993 0.00008593 7.39949019 0.00008619 7.39952140 0.00011740 7.39948768 0.00008368 vdw (SR) 0.00000000 8.17643381 8.17643381 0.00000000 0.00000000 0.00000000 0.00000000 16.98536640 16.98536640 vdw total 16.98536640 16.98516463 -0.00020177 16.98516473 -0.00020167 16.98578564 0.00041924 16.98536640 0.00000000 vdw-14 8.80899360 8.80873082 -0.00026278 0.00000000 -8.80899360 8.80884482 -0.00014878 0.00000000 -8.80899360 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.78733280 4.78715940 -0.00017340 4.78715958 -0.00017322 4.78675495 -0.00057785 4.78716544 -0.00016736 bond 0.91796960 0.91798923 0.00001963 0.91798922 0.00001962 0.91778150 -0.00018810 0.91796960 0.00000000 bonded 13.10470640 13.10463856 -0.00006784 13.10463900 -0.00006740 13.10405785 -0.00064855 13.10462272 -0.00008368 dihedral 7.39940400 7.39948993 0.00008593 7.39949019 0.00008619 7.39952140 0.00011740 7.39948768 0.00008368 nonbonded 15.02390720 15.02878786 0.00488066 15.02878825 0.00488105 15.02940457 0.00549737 15.03210784 0.00820064 potential 28.12861360 28.13342641 0.00481281 28.13342687 0.00481327 28.13341374 0.00480014 28.13673056 0.00811696 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 28.12861360 Difference in potential energy from amber=>gromacs conversion: 0.00481281 Difference in potential energy from amber=>lammps conversion: 0.00481327 Difference in potential energy from amber=>desmond conversion: 0.00480014 Difference in potential energy from amber=>charmm conversion: 0.00811696 ======================================================================= INFO 2017-03-18 22:35:24 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2213823.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2213823.inpcrd') INFO 2017-03-18 22:35:24 Beginning InterMol conversion INFO 2017-03-18 22:35:24 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:35:25 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:35:25 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2245668.inpcrd INFO 2017-03-18 22:35:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2245668/mobley_2245668_converted.input INFO 2017-03-18 22:35:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2245668/mobley_2245668_converted.cms WARNING 2017-03-18 22:35:40 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:35:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2245668/mobley_2245668_converted.inp INFO 2017-03-18 22:35:40 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2245668/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2245668/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2245668/mobley_2245668_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2245668/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -29.04686172 -29.04686172 0.00000000 0.00000000 0.00000000 0.00000000 -0.75763872 -0.75763872 coulomb total -0.75019120 -0.75014295 0.00004825 -0.75014296 0.00004824 -0.75009731 0.00009389 -0.75763872 -0.00744752 coulomb-14 28.29555520 28.29671878 0.00116358 0.00000000 -28.29555520 28.29670643 0.00115123 0.00000000 -28.29555520 proper 1.69870400 1.69850269 -0.00020131 1.69850267 -0.00020133 1.69851598 -0.00018802 1.69849480 -0.00020920 vdw (SR) 0.00000000 0.45572272 0.45572272 0.00000000 0.00000000 0.00000000 0.00000000 6.27432640 6.27432640 vdw total 6.27432640 6.27422287 -0.00010353 6.27422306 -0.00010334 6.27421053 -0.00011587 6.27432640 0.00000000 vdw-14 5.81868880 5.81850015 -0.00018865 0.00000000 -5.81868880 5.81846157 -0.00022723 0.00000000 -5.81868880 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.74807520 1.74823149 0.00015629 1.74823151 0.00015631 1.74825781 0.00018261 1.74820072 0.00012552 bond 0.33764880 0.33776030 0.00011150 0.33776030 0.00011150 0.33777304 0.00012424 0.33777432 0.00012552 bonded 3.78442800 3.78449448 0.00006648 3.78449448 0.00006648 3.78454683 0.00011883 3.78446984 0.00004184 dihedral 1.69870400 1.69850269 -0.00020131 1.69850267 -0.00020133 1.69851598 -0.00018802 1.69849480 -0.00020920 nonbonded 5.52413520 5.52407992 -0.00005528 5.52407997 -0.00005523 5.52411322 -0.00002198 5.51668768 -0.00744752 potential 9.30856320 9.30857440 0.00001120 9.30857450 0.00001130 9.30863136 0.00006816 9.30115752 -0.00740568 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 9.30856320 Difference in potential energy from amber=>gromacs conversion: 0.00001120 Difference in potential energy from amber=>lammps conversion: 0.00001130 Difference in potential energy from amber=>desmond conversion: 0.00006816 Difference in potential energy from amber=>charmm conversion: -0.00740568 ======================================================================= INFO 2017-03-18 22:35:40 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2245668.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2245668.inpcrd') INFO 2017-03-18 22:35:41 Beginning InterMol conversion INFO 2017-03-18 22:35:41 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:35:41 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:35:41 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2261979.inpcrd INFO 2017-03-18 22:35:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2261979/mobley_2261979_converted.input INFO 2017-03-18 22:35:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2261979/mobley_2261979_converted.cms WARNING 2017-03-18 22:35:56 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:35:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2261979/mobley_2261979_converted.inp INFO 2017-03-18 22:35:56 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2261979/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2261979/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2261979/mobley_2261979_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2261979/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -9.28962084 -9.28962084 0.00000000 0.00000000 0.00000000 0.00000000 -10.37908144 -10.37908144 coulomb total -10.40351600 -10.37998854 0.02352746 -10.37998853 0.02352747 -10.38002098 0.02349502 -10.37908144 0.02443456 coulomb-14 -1.08742160 -1.09036769 -0.00294609 0.00000000 1.08742160 -1.09038080 -0.00295920 0.00000000 1.08742160 improper 0.00000000 0.00006217 0.00006217 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 11.52231760 11.52231264 -0.00000496 11.52237492 0.00005732 11.52237513 0.00005753 11.52420040 0.00188280 vdw (SR) 0.00000000 -6.09673216 -6.09673216 0.00000000 0.00000000 0.00000000 0.00000000 25.19408152 25.19408152 vdw total 25.19395600 25.19412659 0.00017059 25.19412671 0.00017071 25.19397445 0.00001845 25.19408152 0.00012552 vdw-14 31.29088080 31.29085876 -0.00002204 0.00000000 -31.29088080 31.29070599 -0.00017481 0.00000000 -31.29088080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 59.86592720 59.86574424 -0.00018296 59.86574310 -0.00018410 59.86622636 0.00029916 59.86563432 -0.00029288 bond 7.11321840 7.11332375 0.00010535 7.11332384 0.00010544 7.11327689 0.00005849 7.11334392 0.00012552 bonded 78.50146320 78.50144280 -0.00002040 78.50144186 -0.00002134 78.50187838 0.00041518 78.50322048 0.00175728 dihedral 11.52231760 11.52237481 0.00005721 11.52237492 0.00005732 11.52237513 0.00005753 11.52424224 0.00192464 nonbonded 14.79044000 14.81413806 0.02369806 14.81413818 0.02369818 14.81395347 0.02351347 14.81500008 0.02456008 potential 93.29190320 93.31558086 0.02367766 93.31558046 0.02367726 93.31572606 0.02382286 93.31826240 0.02635920 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 93.29190320 Difference in potential energy from amber=>gromacs conversion: 0.02367766 Difference in potential energy from amber=>lammps conversion: 0.02367726 Difference in potential energy from amber=>desmond conversion: 0.02382286 Difference in potential energy from amber=>charmm conversion: 0.02635920 ======================================================================= INFO 2017-03-18 22:35:56 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2261979.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2261979.inpcrd') INFO 2017-03-18 22:35:57 Beginning InterMol conversion INFO 2017-03-18 22:35:57 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:35:57 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:35:57 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2269032.inpcrd INFO 2017-03-18 22:35:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2269032/mobley_2269032_converted.input INFO 2017-03-18 22:35:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2269032/mobley_2269032_converted.cms WARNING 2017-03-18 22:36:12 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:36:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2269032/mobley_2269032_converted.inp INFO 2017-03-18 22:36:12 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2269032/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2269032/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2269032/mobley_2269032_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2269032/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -4.86422084 -4.86422084 0.00000000 0.00000000 0.00000000 0.00000000 -125.69321760 -125.69321760 coulomb total -125.68359440 -125.69293898 -0.00934458 -125.69293727 -0.00934287 -125.69296631 -0.00937191 -125.69321760 -0.00962320 coulomb-14 -120.82597040 -120.82871814 -0.00274774 0.00000000 120.82597040 -120.82863226 -0.00266186 0.00000000 120.82597040 improper 0.00000000 0.00019524 0.00019524 0.00000000 0.00000000 0.00000000 0.00000000 0.00020920 0.00020920 proper 0.88156880 0.88152457 -0.00004423 0.88171921 0.00015041 0.88171061 0.00014181 0.88152696 -0.00004184 vdw (SR) 0.00000000 4.86833158 4.86833158 0.00000000 0.00000000 0.00000000 0.00000000 54.72651080 54.72651080 vdw total 54.72672000 54.72635473 -0.00036527 54.72635599 -0.00036401 54.72642407 -0.00029593 54.72651080 -0.00020920 vdw-14 49.85821760 49.85802315 -0.00019445 0.00000000 -49.85821760 49.85827952 0.00006192 0.00000000 -49.85821760 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 7.86550160 7.86569403 0.00019243 7.86569406 0.00019246 7.86618246 0.00068086 7.86575264 0.00025104 bond 12.07293200 12.07298238 0.00005038 12.07298221 0.00005021 12.07267293 -0.00025907 12.07297384 0.00004184 bonded 20.82000240 20.82039622 0.00039382 20.82039549 0.00039309 20.82056600 0.00056360 20.82046264 0.00046024 dihedral 0.88156880 0.88171981 0.00015101 0.88171921 0.00015041 0.88171061 0.00014181 0.88173616 0.00016736 nonbonded -70.95687440 -70.96658425 -0.00970985 -70.96658128 -0.00970688 -70.96654224 -0.00966784 -70.96670680 -0.00983240 potential -50.13687200 -50.14618803 -0.00931603 -50.14618558 -0.00931358 -50.14617847 -0.00930647 -50.14624416 -0.00937216 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -50.13687200 Difference in potential energy from amber=>gromacs conversion: -0.00931603 Difference in potential energy from amber=>lammps conversion: -0.00931358 Difference in potential energy from amber=>desmond conversion: -0.00930647 Difference in potential energy from amber=>charmm conversion: -0.00937216 ======================================================================= INFO 2017-03-18 22:36:12 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2269032.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2269032.inpcrd') INFO 2017-03-18 22:36:13 Beginning InterMol conversion INFO 2017-03-18 22:36:13 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:36:13 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:36:13 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2279874.inpcrd INFO 2017-03-18 22:36:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2279874/mobley_2279874_converted.input INFO 2017-03-18 22:36:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2279874/mobley_2279874_converted.cms WARNING 2017-03-18 22:36:28 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:36:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2279874/mobley_2279874_converted.inp INFO 2017-03-18 22:36:28 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2279874/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2279874/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2279874/mobley_2279874_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2279874/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -55.90055681 -55.90055681 0.00000000 0.00000000 0.00000000 0.00000000 -88.95849256 -88.95849256 coulomb total -88.95142160 -88.93623451 0.01518709 -88.93623368 0.01518792 -88.93614301 0.01527859 -88.95849256 -0.00707096 coulomb-14 -33.06196800 -33.03567771 0.02629029 0.00000000 33.06196800 -33.03568926 0.02627874 0.00000000 33.06196800 proper 66.05280800 66.05288836 0.00008036 66.05290842 0.00010042 66.05289377 0.00008577 66.05276616 -0.00004184 vdw (SR) 0.00000000 -2.52730758 -2.52730758 0.00000000 0.00000000 0.00000000 0.00000000 6.93769960 6.93769960 vdw total 6.93790880 6.93758510 -0.00032370 6.93758538 -0.00032342 6.93760305 -0.00030575 6.93769960 -0.00020920 vdw-14 9.46504480 9.46489268 -0.00015212 0.00000000 -9.46504480 9.46494957 -0.00009523 0.00000000 -9.46504480 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.91282880 5.91265145 -0.00017735 5.91265140 -0.00017740 5.91328067 0.00045187 5.91261960 -0.00020920 bond 1.25101600 1.25095076 -0.00006524 1.25095077 -0.00006523 1.25101715 0.00000115 1.25093232 -0.00008368 bonded 73.21665280 73.21649057 -0.00016223 73.21651059 -0.00014221 73.21719160 0.00053880 73.21631808 -0.00033472 dihedral 66.05280800 66.05288836 0.00008036 66.05290842 0.00010042 66.05289377 0.00008577 66.05276616 -0.00004184 nonbonded -82.01351280 -81.99864942 0.01486338 -81.99864705 0.01486575 -81.99853997 0.01497283 -82.02079296 -0.00728016 potential -8.79686000 -8.78215884 0.01470116 -8.78213692 0.01472308 -8.78138694 0.01547306 -8.80443304 -0.00757304 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -8.79686000 Difference in potential energy from amber=>gromacs conversion: 0.01470116 Difference in potential energy from amber=>lammps conversion: 0.01472308 Difference in potential energy from amber=>desmond conversion: 0.01547306 Difference in potential energy from amber=>charmm conversion: -0.00757304 ======================================================================= INFO 2017-03-18 22:36:28 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2279874.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2279874.inpcrd') INFO 2017-03-18 22:36:29 Beginning InterMol conversion INFO 2017-03-18 22:36:29 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:36:29 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:36:29 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2294995.inpcrd INFO 2017-03-18 22:36:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2294995/mobley_2294995_converted.input INFO 2017-03-18 22:36:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2294995/mobley_2294995_converted.cms WARNING 2017-03-18 22:36:44 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:36:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2294995/mobley_2294995_converted.inp INFO 2017-03-18 22:36:45 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2294995/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2294995/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2294995/mobley_2294995_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2294995/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 1.24979625 1.24979625 0.00000000 0.00000000 0.00000000 0.00000000 -37.03354632 -37.03354632 coulomb total -37.02965520 -37.02738686 0.00226834 -37.02738664 0.00226856 -37.02721277 0.00244243 -37.03354632 -0.00389112 coulomb-14 -38.28401840 -38.27718311 0.00683529 0.00000000 38.28401840 -38.27709622 0.00692218 0.00000000 38.28401840 improper 0.00000000 0.00000007 0.00000007 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 9.86503520 9.86511582 0.00008062 9.86511595 0.00008075 9.86511143 0.00007623 9.86511888 0.00008368 vdw (SR) 0.00000000 -0.77126136 -0.77126136 0.00000000 0.00000000 0.00000000 0.00000000 5.27104504 5.27104504 vdw total 5.27100320 5.27099020 -0.00001300 5.27099023 -0.00001297 5.27071852 -0.00028468 5.27104504 0.00004184 vdw-14 6.04211440 6.04225156 0.00013716 0.00000000 -6.04211440 6.04199704 -0.00011736 0.00000000 -6.04211440 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.94681520 1.94666467 -0.00015053 1.94666466 -0.00015054 1.94660770 -0.00020750 1.94673152 -0.00008368 bond 1.86773760 1.86785165 0.00011405 1.86785166 0.00011406 1.86793737 0.00019977 1.86786312 0.00012552 bonded 13.67958800 13.67963222 0.00004422 13.67963227 0.00004427 13.67965650 0.00006850 13.67971352 0.00012552 dihedral 9.86503520 9.86511589 0.00008069 9.86511595 0.00008075 9.86511143 0.00007623 9.86511888 0.00008368 nonbonded -31.75865200 -31.75639666 0.00225534 -31.75639599 0.00225601 -31.75649425 0.00215775 -31.76250128 -0.00384928 potential -18.07906400 -18.07676444 0.00229956 -18.07676406 0.00229994 -18.07685794 0.00220606 -18.08282960 -0.00376560 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -18.07906400 Difference in potential energy from amber=>gromacs conversion: 0.00229956 Difference in potential energy from amber=>lammps conversion: 0.00229994 Difference in potential energy from amber=>desmond conversion: 0.00220606 Difference in potential energy from amber=>charmm conversion: -0.00376560 ======================================================================= INFO 2017-03-18 22:36:45 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2294995.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2294995.inpcrd') INFO 2017-03-18 22:36:45 Beginning InterMol conversion INFO 2017-03-18 22:36:45 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:36:45 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:36:45 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2295058.inpcrd INFO 2017-03-18 22:36:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2295058/mobley_2295058_converted.input INFO 2017-03-18 22:36:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2295058/mobley_2295058_converted.cms WARNING 2017-03-18 22:37:01 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:37:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2295058/mobley_2295058_converted.inp INFO 2017-03-18 22:37:01 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2295058/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2295058/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2295058/mobley_2295058_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2295058/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -15.46111594 -15.46111594 0.00000000 0.00000000 0.00000000 0.00000000 -113.21113224 -113.21113224 coulomb total -113.04665920 -113.05780635 -0.01114715 -113.05780538 -0.01114618 -113.05792232 -0.01126312 -113.21113224 -0.16447304 coulomb-14 -97.58552400 -97.59669041 -0.01116641 0.00000000 97.58552400 -97.59668356 -0.01115956 0.00000000 97.58552400 improper 0.00000000 0.00003777 0.00003777 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 8.36632640 8.36632381 -0.00000259 8.36634146 0.00001506 8.36632494 -0.00000146 8.36628456 -0.00004184 vdw (SR) 0.00000000 -1.46732805 -1.46732805 0.00000000 0.00000000 0.00000000 0.00000000 26.89090272 26.89090272 vdw total 26.89098640 26.89081189 -0.00017451 26.89081193 -0.00017447 26.89067021 -0.00031619 26.89090272 -0.00008368 vdw-14 28.35831520 28.35813994 -0.00017526 0.00000000 -28.35831520 28.35808232 -0.00023288 0.00000000 -28.35831520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.46853600 3.46860102 0.00006502 3.46860102 0.00006502 3.46853537 -0.00000063 3.46861968 0.00008368 bond 2.84428320 2.84448137 0.00019817 2.84448135 0.00019815 2.84475301 0.00046981 2.84449240 0.00020920 bonded 14.67914560 14.67944398 0.00029838 14.67942384 0.00027824 14.67961332 0.00046772 14.67943848 0.00029288 dihedral 8.36632640 8.36636158 0.00003518 8.36634146 0.00001506 8.36632494 -0.00000146 8.36632640 0.00000000 nonbonded -86.15567280 -86.16699446 -0.01132166 -86.16699470 -0.01132190 -86.16725211 -0.01157931 -86.32022952 -0.16455672 potential -71.47652720 -71.48755048 -0.01102328 -71.48756878 -0.01104158 -71.48772358 -0.01119638 -71.64079104 -0.16426384 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -71.47652720 Difference in potential energy from amber=>gromacs conversion: -0.01102328 Difference in potential energy from amber=>lammps conversion: -0.01104158 Difference in potential energy from amber=>desmond conversion: -0.01119638 Difference in potential energy from amber=>charmm conversion: -0.16426384 ======================================================================= INFO 2017-03-18 22:37:01 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2295058.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2295058.inpcrd') INFO 2017-03-18 22:37:01 Beginning InterMol conversion INFO 2017-03-18 22:37:01 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:37:01 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:37:01 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2310185.inpcrd INFO 2017-03-18 22:37:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2310185/mobley_2310185_converted.input INFO 2017-03-18 22:37:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2310185/mobley_2310185_converted.cms WARNING 2017-03-18 22:37:17 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:37:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2310185/mobley_2310185_converted.inp INFO 2017-03-18 22:37:17 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2310185/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2310185/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2310185/mobley_2310185_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2310185/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 20.10500285 20.10500285 0.00000000 0.00000000 0.00000000 0.00000000 -17.60681592 -17.60681592 coulomb total -17.58702560 -17.59334987 -0.00632427 -17.59334972 -0.00632412 -17.59332394 -0.00629834 -17.60681592 -0.01979032 coulomb-14 -37.69700320 -37.69835271 -0.00134951 0.00000000 37.69700320 -37.69830112 -0.00129792 0.00000000 37.69700320 proper 3.16979840 3.16983529 0.00003689 3.16983530 0.00003690 3.16983067 0.00003227 3.16984024 0.00004184 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.77688512 0.77688512 vdw total 0.77696880 0.77685662 -0.00011218 0.77685663 -0.00011217 0.77683108 -0.00013772 0.77688512 -0.00008368 vdw-14 0.77696880 0.77685662 -0.00011218 0.00000000 -0.77696880 0.77683108 -0.00013772 0.00000000 -0.77696880 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.52802080 0.52786527 -0.00015553 0.52786528 -0.00015552 0.52798479 -0.00003601 0.52785344 -0.00016736 bond 0.67780800 0.67767303 -0.00013497 0.67767302 -0.00013498 0.67786132 0.00005332 0.67768248 -0.00012552 bonded 4.37562720 4.37537359 -0.00025361 4.37537361 -0.00025359 4.37567678 0.00004958 4.37537616 -0.00025104 dihedral 3.16979840 3.16983529 0.00003689 3.16983530 0.00003690 3.16983067 0.00003227 3.16984024 0.00004184 nonbonded -16.81005680 -16.81649325 -0.00643645 -16.81649305 -0.00643625 -16.81649286 -0.00643606 -16.82993080 -0.01987400 potential -12.43442960 -12.44111965 -0.00669005 -12.44111940 -0.00668980 -12.44082556 -0.00639596 -12.45459648 -0.02016688 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -12.43442960 Difference in potential energy from amber=>gromacs conversion: -0.00669005 Difference in potential energy from amber=>lammps conversion: -0.00668980 Difference in potential energy from amber=>desmond conversion: -0.00639596 Difference in potential energy from amber=>charmm conversion: -0.02016688 ======================================================================= INFO 2017-03-18 22:37:17 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2310185.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2310185.inpcrd') INFO 2017-03-18 22:37:17 Beginning InterMol conversion INFO 2017-03-18 22:37:17 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:37:17 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:37:17 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2316618.inpcrd INFO 2017-03-18 22:37:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2316618/mobley_2316618_converted.input INFO 2017-03-18 22:37:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2316618/mobley_2316618_converted.cms WARNING 2017-03-18 22:37:33 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:37:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2316618/mobley_2316618_converted.inp INFO 2017-03-18 22:37:33 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2316618/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2316618/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2316618/mobley_2316618_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2316618/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -144.25503259 -144.25503259 0.00000000 0.00000000 0.00000000 0.00000000 57.99446584 57.99446584 coulomb total 57.85007600 57.84370225 -0.00637375 57.84369958 -0.00637642 57.84541502 -0.00466098 57.99446584 0.14438984 coulomb-14 202.09682320 202.09873484 0.00191164 0.00000000 -202.09682320 202.09893445 0.00211125 0.00000000 -202.09682320 improper 0.00000000 0.00044770 0.00044770 0.00000000 0.00000000 0.00000000 0.00000000 0.00046024 0.00046024 proper 1.56439760 1.56385691 -0.00054069 1.56430488 -0.00009272 1.56430771 -0.00008989 1.56385368 -0.00054392 vdw (SR) 0.00000000 13.50925354 13.50925354 0.00000000 0.00000000 0.00000000 0.00000000 73.38577008 73.38577008 vdw total 73.38568640 73.38565394 -0.00003246 73.38565293 -0.00003347 73.38517838 -0.00050802 73.38577008 0.00008368 vdw-14 59.87638720 59.87640041 0.00001321 0.00000000 -59.87638720 59.87599390 -0.00039330 0.00000000 -59.87638720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 11.88381520 11.88361674 -0.00019846 11.88361688 -0.00019832 11.88283807 -0.00097713 11.88356416 -0.00025104 bond 10.84953040 10.84947605 -0.00005435 10.84947601 -0.00005439 10.85016557 0.00063517 10.84948856 -0.00004184 bonded 24.29774320 24.29739741 -0.00034579 24.29739777 -0.00034543 24.29731135 -0.00043185 24.29736664 -0.00037656 dihedral 1.56439760 1.56430461 -0.00009299 1.56430488 -0.00009272 1.56430771 -0.00008989 1.56431392 -0.00008368 nonbonded 131.23576240 131.22935619 -0.00640621 131.22935670 -0.00640570 131.23059340 -0.00516900 131.38023592 0.14447352 potential 155.53350560 155.52675360 -0.00675200 155.52675262 -0.00675298 155.52766181 -0.00584379 155.67756072 0.14405512 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 155.53350560 Difference in potential energy from amber=>gromacs conversion: -0.00675200 Difference in potential energy from amber=>lammps conversion: -0.00675298 Difference in potential energy from amber=>desmond conversion: -0.00584379 Difference in potential energy from amber=>charmm conversion: 0.14405512 ======================================================================= INFO 2017-03-18 22:37:33 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2316618.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2316618.inpcrd') INFO 2017-03-18 22:37:33 Beginning InterMol conversion INFO 2017-03-18 22:37:33 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:37:33 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:37:33 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2328633.inpcrd INFO 2017-03-18 22:37:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2328633/mobley_2328633_converted.input INFO 2017-03-18 22:37:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2328633/mobley_2328633_converted.cms WARNING 2017-03-18 22:37:49 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:37:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2328633/mobley_2328633_converted.inp INFO 2017-03-18 22:37:49 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2328633/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2328633/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2328633/mobley_2328633_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2328633/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 12.98615743 12.98615743 0.00000000 0.00000000 0.00000000 0.00000000 -0.51994568 -0.51994568 coulomb total -0.51756080 -0.52429381 -0.00673301 -0.52429382 -0.00673302 -0.52433005 -0.00676925 -0.51994568 -0.00238488 coulomb-14 -13.50888080 -13.51045124 -0.00157044 0.00000000 13.50888080 -13.51045557 -0.00157477 0.00000000 13.50888080 proper 45.90308240 45.90302315 -0.00005925 45.90302382 -0.00005858 45.90302926 -0.00005314 45.90304056 -0.00004184 vdw (SR) 0.00000000 -3.30969499 -3.30969499 0.00000000 0.00000000 0.00000000 0.00000000 9.78700360 9.78700360 vdw total 9.78721280 9.78678918 -0.00042362 9.78678938 -0.00042342 9.78679443 -0.00041837 9.78700360 -0.00020920 vdw-14 13.09675680 13.09648417 -0.00027263 0.00000000 -13.09675680 13.09656605 -0.00019075 0.00000000 -13.09675680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 19.96814000 19.96802679 -0.00011321 19.96802661 -0.00011339 19.96829167 0.00015167 19.96784712 -0.00029288 bond 1.68949920 1.68944083 -0.00005837 1.68944083 -0.00005837 1.68980079 0.00030159 1.68945736 -0.00004184 bonded 67.56072160 67.56049077 -0.00023083 67.56049127 -0.00023033 67.56112172 0.00040012 67.56034504 -0.00037656 dihedral 45.90308240 45.90302315 -0.00005925 45.90302382 -0.00005858 45.90302926 -0.00005314 45.90304056 -0.00004184 nonbonded 9.26965200 9.26249537 -0.00715663 9.26249569 -0.00715631 9.26246438 -0.00718762 9.26705792 -0.00259408 potential 76.83037360 76.82298614 -0.00738746 76.82298884 -0.00738476 76.82346456 -0.00690904 76.82736112 -0.00301248 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 76.83037360 Difference in potential energy from amber=>gromacs conversion: -0.00738746 Difference in potential energy from amber=>lammps conversion: -0.00738476 Difference in potential energy from amber=>desmond conversion: -0.00690904 Difference in potential energy from amber=>charmm conversion: -0.00301248 ======================================================================= INFO 2017-03-18 22:37:49 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2328633.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2328633.inpcrd') INFO 2017-03-18 22:37:49 Beginning InterMol conversion INFO 2017-03-18 22:37:49 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:37:50 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:37:50 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2341732.inpcrd INFO 2017-03-18 22:37:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2341732/mobley_2341732_converted.input INFO 2017-03-18 22:37:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2341732/mobley_2341732_converted.cms WARNING 2017-03-18 22:38:05 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:38:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2341732/mobley_2341732_converted.inp INFO 2017-03-18 22:38:05 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2341732/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2341732/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2341732/mobley_2341732_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2341732/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -47.88327110 -47.88327110 0.00000000 0.00000000 0.00000000 0.00000000 -64.43807688 -64.43807688 coulomb total -64.40514880 -64.40779006 -0.00264126 -64.40778890 -0.00264010 -64.40776154 -0.00261274 -64.43807688 -0.03292808 coulomb-14 -16.52052400 -16.52451897 -0.00399497 0.00000000 16.52052400 -16.52461202 -0.00408802 0.00000000 16.52052400 improper 0.00000000 0.00002258 0.00002258 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 4.96557120 4.96572767 0.00015647 4.96575028 0.00017908 4.96571831 0.00014711 4.96573856 0.00016736 vdw (SR) 0.00000000 -2.45069319 -2.45069319 0.00000000 0.00000000 0.00000000 0.00000000 11.09429440 11.09429440 vdw total 11.09429440 11.09414360 -0.00015080 11.09414378 -0.00015062 11.09421313 -0.00008127 11.09429440 0.00000000 vdw-14 13.54486320 13.54483679 -0.00002641 0.00000000 -13.54486320 13.54493542 0.00007222 0.00000000 -13.54486320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.04720720 3.04707988 -0.00012732 3.04707988 -0.00012732 3.04702717 -0.00018003 3.04708168 -0.00012552 bond 1.90413840 1.90401736 -0.00012104 1.90401736 -0.00012104 1.90442692 0.00028852 1.90401288 -0.00012552 bonded 9.91691680 9.91684749 -0.00006931 9.91684751 -0.00006929 9.91717240 0.00025560 9.91687496 -0.00004184 dihedral 4.96557120 4.96575025 0.00017905 4.96575028 0.00017908 4.96571831 0.00014711 4.96578040 0.00020920 nonbonded -53.31085440 -53.31364646 -0.00279206 -53.31364513 -0.00279073 -53.31354841 -0.00269401 -53.34378248 -0.03292808 potential -43.39393760 -43.39679897 -0.00286137 -43.39679946 -0.00286186 -43.39644674 -0.00250914 -43.42694936 -0.03301176 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -43.39393760 Difference in potential energy from amber=>gromacs conversion: -0.00286137 Difference in potential energy from amber=>lammps conversion: -0.00286186 Difference in potential energy from amber=>desmond conversion: -0.00250914 Difference in potential energy from amber=>charmm conversion: -0.03301176 ======================================================================= INFO 2017-03-18 22:38:05 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2341732.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2341732.inpcrd') INFO 2017-03-18 22:38:06 Beginning InterMol conversion INFO 2017-03-18 22:38:06 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:38:06 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:38:06 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2354112.inpcrd INFO 2017-03-18 22:38:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2354112/mobley_2354112_converted.input INFO 2017-03-18 22:38:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2354112/mobley_2354112_converted.cms WARNING 2017-03-18 22:38:21 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:38:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2354112/mobley_2354112_converted.inp INFO 2017-03-18 22:38:21 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2354112/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2354112/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2354112/mobley_2354112_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2354112/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 55.10300146 55.10300146 0.00000000 0.00000000 0.00000000 0.00000000 -87.64517680 -87.64517680 coulomb total -87.63680880 -87.64661336 -0.00980456 -87.64661191 -0.00980311 -87.64713910 -0.01033030 -87.64517680 -0.00836800 coulomb-14 -142.74720160 -142.74961483 -0.00241323 0.00000000 142.74720160 -142.74956974 -0.00236814 0.00000000 142.74720160 improper 0.00000000 0.00001019 0.00001019 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.01966480 0.01982070 0.00015590 0.01983085 0.00016605 0.01983696 0.00017216 0.01983216 0.00016736 vdw (SR) 0.00000000 -3.76336112 -3.76336112 0.00000000 0.00000000 0.00000000 0.00000000 15.59493952 15.59493952 vdw total 15.59460480 15.59492659 0.00032179 15.59492655 0.00032175 15.59496379 0.00035899 15.59493952 0.00033472 vdw-14 19.35811280 19.35828771 0.00017491 0.00000000 -19.35811280 19.35832878 0.00021598 0.00000000 -19.35811280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.67195040 0.67188453 -0.00006587 0.67188454 -0.00006586 0.67193775 -0.00001265 0.67186672 -0.00008368 bond 1.70330640 1.70336455 0.00005815 1.70336456 0.00005816 1.70337033 0.00006393 1.70334824 0.00004184 bonded 2.39492160 2.39507996 0.00015836 2.39507995 0.00015835 2.39514504 0.00022344 2.39504712 0.00012552 dihedral 0.01966480 0.01983089 0.00016609 0.01983085 0.00016605 0.01983696 0.00017216 0.01983216 0.00016736 nonbonded -72.04220400 -72.05168677 -0.00948277 -72.05168494 -0.00948094 -72.05217531 -0.00997131 -72.05023728 -0.00803328 potential -69.64728240 -69.65660681 -0.00932441 -69.65660435 -0.00932195 -69.65709179 -0.00980939 -69.65514832 -0.00786592 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -69.64728240 Difference in potential energy from amber=>gromacs conversion: -0.00932441 Difference in potential energy from amber=>lammps conversion: -0.00932195 Difference in potential energy from amber=>desmond conversion: -0.00980939 Difference in potential energy from amber=>charmm conversion: -0.00786592 ======================================================================= INFO 2017-03-18 22:38:21 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2354112.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2354112.inpcrd') INFO 2017-03-18 22:38:22 Beginning InterMol conversion INFO 2017-03-18 22:38:22 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:38:22 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:38:22 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2364370.inpcrd INFO 2017-03-18 22:38:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2364370/mobley_2364370_converted.input INFO 2017-03-18 22:38:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2364370/mobley_2364370_converted.cms WARNING 2017-03-18 22:38:37 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:38:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2364370/mobley_2364370_converted.inp INFO 2017-03-18 22:38:37 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2364370/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2364370/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2364370/mobley_2364370_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2364370/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 7.80219077 7.80219077 0.00000000 0.00000000 0.00000000 0.00000000 -122.07727928 -122.07727928 coulomb total -122.03263600 -122.03782584 -0.00518984 -122.03782416 -0.00518816 -122.03778747 -0.00515147 -122.07727928 -0.04464328 coulomb-14 -129.83077520 -129.84001662 -0.00924142 0.00000000 129.83077520 -129.83996703 -0.00919183 0.00000000 129.83077520 improper 0.00000000 0.00000001 0.00000001 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 22.71284400 22.71290089 0.00005689 22.71290216 0.00005816 22.71285756 0.00001356 22.71292768 0.00008368 vdw (SR) 0.00000000 -3.02071120 -3.02071120 0.00000000 0.00000000 0.00000000 0.00000000 7.78680056 7.78680056 vdw total 7.78684240 7.78667997 -0.00016243 7.78668006 -0.00016234 7.78668770 -0.00015470 7.78680056 -0.00004184 vdw-14 10.80769040 10.80739117 -0.00029923 0.00000000 -10.80769040 10.80739664 -0.00029376 0.00000000 -10.80769040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.40621840 2.40623400 0.00001560 2.40623401 0.00001561 2.40632528 0.00010688 2.40626024 0.00004184 bond 2.53508560 2.53497978 -0.00010582 2.53497979 -0.00010581 2.53472852 -0.00035708 2.53496008 -0.00012552 bonded 27.65414800 27.65411467 -0.00003333 27.65411595 -0.00003205 27.65391135 -0.00023665 27.65414800 0.00000000 dihedral 22.71284400 22.71290089 0.00005689 22.71290216 0.00005816 22.71285756 0.00001356 22.71292768 0.00008368 nonbonded -114.24579360 -114.25114587 -0.00535227 -114.25114494 -0.00535134 -114.25109977 -0.00530617 -114.29047872 -0.04468512 potential -86.59164560 -86.59703119 -0.00538559 -86.59703041 -0.00538481 -86.59725174 -0.00560614 -86.63633072 -0.04468512 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -86.59164560 Difference in potential energy from amber=>gromacs conversion: -0.00538559 Difference in potential energy from amber=>lammps conversion: -0.00538481 Difference in potential energy from amber=>desmond conversion: -0.00560614 Difference in potential energy from amber=>charmm conversion: -0.04468512 ======================================================================= INFO 2017-03-18 22:38:37 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2364370.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2364370.inpcrd') INFO 2017-03-18 22:38:38 Beginning InterMol conversion INFO 2017-03-18 22:38:38 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:38:38 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:38:38 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2371092.inpcrd INFO 2017-03-18 22:38:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2371092/mobley_2371092_converted.input INFO 2017-03-18 22:38:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2371092/mobley_2371092_converted.cms WARNING 2017-03-18 22:38:53 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:38:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2371092/mobley_2371092_converted.inp INFO 2017-03-18 22:38:54 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2371092/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2371092/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2371092/mobley_2371092_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2371092/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 26.42734760 26.42734760 0.00000000 0.00000000 0.00000000 0.00000000 -81.16503944 -81.16503944 coulomb total -81.15119040 -81.13765661 0.01353379 -81.13765516 0.01353524 -81.13776558 0.01342482 -81.16503944 -0.01384904 coulomb-14 -107.56143520 -107.56500421 -0.00356901 0.00000000 107.56143520 -107.56508072 -0.00364552 0.00000000 107.56143520 improper 0.00000000 0.00008912 0.00008912 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00083680 0.00079228 -0.00004452 0.00088144 0.00004464 0.00087684 0.00004004 0.00079496 -0.00004184 vdw (SR) 0.00000000 18.92102637 18.92102637 0.00000000 0.00000000 0.00000000 0.00000000 44.05392176 44.05392176 vdw total 44.05375440 44.05369287 -0.00006153 44.05369164 -0.00006276 44.05416255 0.00040815 44.05392176 0.00016736 vdw-14 25.13245120 25.13266651 0.00021531 0.00000000 -25.13245120 25.13300290 0.00055170 0.00000000 -25.13245120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.20413120 2.20412377 -0.00000743 2.20412375 -0.00000745 2.20403067 -0.00010053 2.20413120 0.00000000 bond 2.02631120 2.02616786 -0.00014334 2.02616786 -0.00014334 2.02568969 -0.00062151 2.02618568 -0.00012552 bonded 4.23127920 4.23117303 -0.00010617 4.23117305 -0.00010615 4.23059720 -0.00068200 4.23119552 -0.00008368 dihedral 0.00083680 0.00088140 0.00004460 0.00088144 0.00004464 0.00087684 0.00004004 0.00087864 0.00004184 nonbonded -37.09743600 -37.08396374 0.01347226 -37.08396268 0.01347332 -37.08360303 0.01383297 -37.11111768 -0.01368168 potential -32.86615680 -32.85279071 0.01336609 -32.85278934 0.01336746 -32.85305498 0.01310182 -32.87996400 -0.01380720 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -32.86615680 Difference in potential energy from amber=>gromacs conversion: 0.01336609 Difference in potential energy from amber=>lammps conversion: 0.01336746 Difference in potential energy from amber=>desmond conversion: 0.01310182 Difference in potential energy from amber=>charmm conversion: -0.01380720 ======================================================================= INFO 2017-03-18 22:38:54 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2371092.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2371092.inpcrd') INFO 2017-03-18 22:38:54 Beginning InterMol conversion INFO 2017-03-18 22:38:54 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:38:54 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:38:54 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2390199.inpcrd INFO 2017-03-18 22:38:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2390199/mobley_2390199_converted.input INFO 2017-03-18 22:38:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2390199/mobley_2390199_converted.cms WARNING 2017-03-18 22:39:10 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:39:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2390199/mobley_2390199_converted.inp INFO 2017-03-18 22:39:10 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2390199/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2390199/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2390199/mobley_2390199_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2390199/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -11.87843174 -11.87843174 0.00000000 0.00000000 0.00000000 0.00000000 -23.08091048 -23.08091048 coulomb total -22.95426080 -22.95417915 0.00008165 -22.95417879 0.00008201 -22.95413879 0.00012201 -23.08091048 -0.12664968 coulomb-14 -11.07170080 -11.07574741 -0.00404661 0.00000000 11.07170080 -11.07582832 -0.00412752 0.00000000 11.07170080 improper 0.00000000 0.00000246 0.00000246 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 6.46469840 6.46484144 0.00014304 6.46484400 0.00014560 6.46483986 0.00014146 6.46482392 0.00012552 vdw (SR) 0.00000000 -2.28926010 -2.28926010 0.00000000 0.00000000 0.00000000 0.00000000 9.74637696 9.74637696 vdw total 9.74662800 9.74622475 -0.00040325 9.74622508 -0.00040292 9.74631420 -0.00031380 9.74637696 -0.00025104 vdw-14 12.03569440 12.03548485 -0.00020955 0.00000000 -12.03569440 12.03554461 -0.00014979 0.00000000 -12.03569440 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.37944080 2.37940041 -0.00004039 2.37940042 -0.00004038 2.37955294 0.00011214 2.37935712 -0.00008368 bond 2.12128800 2.12110125 -0.00018675 2.12110127 -0.00018673 2.12146626 0.00017826 2.12112064 -0.00016736 bonded 10.96542720 10.96534556 -0.00008164 10.96534570 -0.00008150 10.96585906 0.00043186 10.96530168 -0.00012552 dihedral 6.46469840 6.46484390 0.00014550 6.46484400 0.00014560 6.46483986 0.00014146 6.46482392 0.00012552 nonbonded -13.20763280 -13.20795440 -0.00032160 -13.20795413 -0.00032133 -13.20782459 -0.00019179 -13.33453352 -0.12690072 potential -2.24220560 -2.24260884 -0.00040324 -2.24260844 -0.00040284 -2.24203902 0.00016658 -2.36923184 -0.12702624 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -2.24220560 Difference in potential energy from amber=>gromacs conversion: -0.00040324 Difference in potential energy from amber=>lammps conversion: -0.00040284 Difference in potential energy from amber=>desmond conversion: 0.00016658 Difference in potential energy from amber=>charmm conversion: -0.12702624 ======================================================================= INFO 2017-03-18 22:39:10 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2390199.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2390199.inpcrd') INFO 2017-03-18 22:39:10 Beginning InterMol conversion INFO 2017-03-18 22:39:10 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:39:10 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:39:10 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2402487.inpcrd INFO 2017-03-18 22:39:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2402487/mobley_2402487_converted.input INFO 2017-03-18 22:39:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2402487/mobley_2402487_converted.cms WARNING 2017-03-18 22:39:26 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:39:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2402487/mobley_2402487_converted.inp INFO 2017-03-18 22:39:26 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2402487/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2402487/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2402487/mobley_2402487_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2402487/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 340.59624079 340.59624079 0.00000000 0.00000000 0.00000000 0.00000000 -370.21165864 -370.21165864 coulomb total -370.08986240 -370.10724945 -0.01738705 -370.10724692 -0.01738452 -370.10797410 -0.01811170 -370.21165864 -0.12179624 coulomb-14 -710.67875920 -710.70349024 -0.02473104 0.00000000 710.67875920 -710.70355358 -0.02479438 0.00000000 710.67875920 improper 0.00000000 0.00006742 0.00006742 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 26.30564480 26.30566009 0.00001529 26.30572764 0.00008284 26.30572329 0.00007849 26.30564480 0.00000000 vdw (SR) 0.00000000 -1.18924233 -1.18924233 0.00000000 0.00000000 0.00000000 0.00000000 15.78731984 15.78731984 vdw total 15.78748720 15.78711198 -0.00037522 15.78711231 -0.00037489 15.78707369 -0.00041351 15.78731984 -0.00016736 vdw-14 16.97658000 16.97635431 -0.00022569 0.00000000 -16.97658000 16.97641285 -0.00016715 0.00000000 -16.97658000 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 7.87052240 7.87033261 -0.00018979 7.87033245 -0.00018995 7.87016099 -0.00036141 7.87039688 -0.00012552 bond 4.08483920 4.08476174 -0.00007746 4.08476175 -0.00007745 4.08537003 0.00053083 4.08475552 -0.00008368 bonded 38.26100640 38.26082186 -0.00018454 38.26082184 -0.00018456 38.26125431 0.00024791 38.26088088 -0.00012552 dihedral 26.30564480 26.30572751 0.00008271 26.30572764 0.00008284 26.30572329 0.00007849 26.30572848 0.00008368 nonbonded -354.30237520 -354.32013747 -0.01776227 -354.32013210 -0.01775690 -354.32090041 -0.01852521 -354.42433880 -0.12196360 potential -316.04136880 -316.05931562 -0.01794682 -316.05930979 -0.01794099 -316.05974242 -0.01837362 -316.16345792 -0.12208912 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -316.04136880 Difference in potential energy from amber=>gromacs conversion: -0.01794682 Difference in potential energy from amber=>lammps conversion: -0.01794099 Difference in potential energy from amber=>desmond conversion: -0.01837362 Difference in potential energy from amber=>charmm conversion: -0.12208912 ======================================================================= INFO 2017-03-18 22:39:26 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2402487.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2402487.inpcrd') INFO 2017-03-18 22:39:26 Beginning InterMol conversion INFO 2017-03-18 22:39:26 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:39:26 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:39:26 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2410897.inpcrd INFO 2017-03-18 22:39:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2410897/mobley_2410897_converted.input INFO 2017-03-18 22:39:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2410897/mobley_2410897_converted.cms WARNING 2017-03-18 22:39:42 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:39:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2410897/mobley_2410897_converted.inp INFO 2017-03-18 22:39:42 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2410897/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2410897/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2410897/mobley_2410897_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2410897/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 31.30450737 31.30450737 0.00000000 0.00000000 0.00000000 0.00000000 -9.74441048 -9.74441048 coulomb total -9.72487120 -9.73527468 -0.01040348 -9.73527472 -0.01040352 -9.73530024 -0.01042904 -9.74441048 -0.01953928 coulomb-14 -41.03792720 -41.03978206 -0.00185486 0.00000000 41.03792720 -41.03975628 -0.00182908 0.00000000 41.03792720 proper 4.96724480 4.96735317 0.00010837 4.96735317 0.00010837 4.96735789 0.00011309 4.96737032 0.00012552 vdw (SR) 0.00000000 -0.06332761 -0.06332761 0.00000000 0.00000000 0.00000000 0.00000000 0.94437064 0.94437064 vdw total 0.94432880 0.94437134 0.00004254 0.94437135 0.00004255 0.94437108 0.00004228 0.94437064 0.00004184 vdw-14 1.00750720 1.00769895 0.00019175 0.00000000 -1.00750720 1.00769825 0.00019105 0.00000000 -1.00750720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 20.19784160 20.19803554 0.00019394 20.19803574 0.00019414 20.19802703 0.00018543 20.19821816 0.00037656 bond 4.33378720 4.33396179 0.00017459 4.33396167 0.00017447 4.33397623 0.00018903 4.33395456 0.00016736 bonded 29.49887360 29.49935051 0.00047691 29.49935058 0.00047698 29.49936116 0.00048756 29.49954304 0.00066944 dihedral 4.96724480 4.96735317 0.00010837 4.96735317 0.00010837 4.96735789 0.00011309 4.96737032 0.00012552 nonbonded -8.78054240 -8.79090334 -0.01036094 -8.79090324 -0.01036084 -8.79092916 -0.01038676 -8.80003984 -0.01949744 potential 20.71833120 20.70844717 -0.00988403 20.70844734 -0.00988386 20.70842027 -0.00991093 20.69950320 -0.01882800 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 20.71833120 Difference in potential energy from amber=>gromacs conversion: -0.00988403 Difference in potential energy from amber=>lammps conversion: -0.00988386 Difference in potential energy from amber=>desmond conversion: -0.00991093 Difference in potential energy from amber=>charmm conversion: -0.01882800 ======================================================================= INFO 2017-03-18 22:39:42 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2410897.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2410897.inpcrd') INFO 2017-03-18 22:39:42 Beginning InterMol conversion INFO 2017-03-18 22:39:42 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:39:42 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:39:42 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2422586.inpcrd INFO 2017-03-18 22:39:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2422586/mobley_2422586_converted.input INFO 2017-03-18 22:39:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2422586/mobley_2422586_converted.cms WARNING 2017-03-18 22:39:58 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:39:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2422586/mobley_2422586_converted.inp INFO 2017-03-18 22:39:58 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2422586/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2422586/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2422586/mobley_2422586_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2422586/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -4.78530111 -4.78530111 0.00000000 0.00000000 0.00000000 0.00000000 2.15446712 2.15446712 coulomb total 2.16647520 2.16653707 0.00006187 2.16653704 0.00006184 2.16651972 0.00004452 2.15446712 -0.01200808 coulomb-14 6.95171600 6.95183819 0.00012219 0.00000000 -6.95171600 6.95183847 0.00012247 0.00000000 -6.95171600 proper 3.24552880 3.24573128 0.00020248 3.24573126 0.00020246 3.24572623 0.00019743 3.24573800 0.00020920 vdw (SR) 0.00000000 -1.16754164 -1.16754164 0.00000000 0.00000000 0.00000000 0.00000000 3.61928552 3.61928552 vdw total 3.61957840 3.61920233 -0.00037607 3.61920238 -0.00037602 3.61920369 -0.00037471 3.61928552 -0.00029288 vdw-14 4.78691440 4.78674398 -0.00017042 0.00000000 -4.78691440 4.78673633 -0.00017807 0.00000000 -4.78691440 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.82341120 0.82349396 0.00008276 0.82349396 0.00008276 0.82327417 -0.00013703 0.82349488 0.00008368 bond 1.59703280 1.59718103 0.00014823 1.59718104 0.00014824 1.59703787 0.00000507 1.59720016 0.00016736 bonded 5.66597280 5.66640628 0.00043348 5.66640626 0.00043346 5.66603828 0.00006548 5.66643304 0.00046024 dihedral 3.24552880 3.24573128 0.00020248 3.24573126 0.00020246 3.24572623 0.00019743 3.24573800 0.00020920 nonbonded 5.78605360 5.78573941 -0.00031419 5.78573938 -0.00031422 5.78572340 -0.00033020 5.77375264 -0.01230096 potential 11.45202640 11.45214569 0.00011929 11.45214564 0.00011924 11.45173381 -0.00029259 11.44014384 -0.01188256 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 11.45202640 Difference in potential energy from amber=>gromacs conversion: 0.00011929 Difference in potential energy from amber=>lammps conversion: 0.00011924 Difference in potential energy from amber=>desmond conversion: -0.00029259 Difference in potential energy from amber=>charmm conversion: -0.01188256 ======================================================================= INFO 2017-03-18 22:39:58 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2422586.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2422586.inpcrd') INFO 2017-03-18 22:39:58 Beginning InterMol conversion INFO 2017-03-18 22:39:58 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:39:58 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_242480.inpcrd INFO 2017-03-18 22:39:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_242480/mobley_242480_converted.input INFO 2017-03-18 22:39:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_242480/mobley_242480_converted.cms INFO 2017-03-18 22:40:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_242480/mobley_242480_converted.rst7 WARNING 2017-03-18 22:40:14 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:40:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_242480/mobley_242480_converted.inp INFO 2017-03-18 22:40:14 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_242480/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_242480/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_242480/mobley_242480_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_242480/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_242480/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 134.08083960 134.08083960 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -126.97858424 -126.97858424 coulomb total -127.17226160 -127.17278487 -0.00052327 -127.17278460 -0.00052300 -127.17497827 -0.00271667 -127.17226160 0.00000000 -126.97858424 0.19367736 coulomb-14 -261.23975520 -261.25362446 -0.01386926 0.00000000 261.23975520 -261.25375486 -0.01399966 -261.23975520 0.00000000 0.00000000 261.23975520 improper 0.00000000 0.22865277 0.22865277 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.22865560 0.22865560 proper 0.43722800 0.20841462 -0.22881338 0.43706478 -0.00016322 0.43706813 -0.00015987 0.43722800 0.00000000 0.20840504 -0.22882296 vdw (SR) 0.00000000 25.44956958 25.44956958 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 80.42363464 80.42363464 vdw total 80.42359280 80.42360892 0.00001612 80.42360954 0.00001674 80.42301507 -0.00057773 80.42359280 0.00000000 80.42363464 0.00004184 vdw-14 54.97399440 54.97403933 0.00004493 0.00000000 -54.97399440 54.97371951 -0.00027489 54.97399440 0.00000000 0.00000000 -54.97399440 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 15.45904320 15.45913683 0.00009363 15.45913692 0.00009372 15.45804737 -0.00099583 15.45904320 0.00000000 15.45916872 0.00012552 bond 14.48919200 14.48920484 0.00001284 14.48920497 0.00001297 14.48866151 -0.00053049 14.48919200 0.00000000 14.48919200 0.00000000 bonded 30.38546320 30.38540906 -0.00005414 30.38540667 -0.00005653 30.38377701 -0.00168619 30.38546320 0.00000000 30.38542136 -0.00004184 dihedral 0.43722800 0.43706739 -0.00016061 0.43706478 -0.00016322 0.43706813 -0.00015987 0.43722800 0.00000000 0.43706064 -0.00016736 nonbonded -46.74866880 -46.74917595 -0.00050715 -46.74917506 -0.00050626 -46.75196320 -0.00329440 -46.74866880 0.00000000 -46.55494960 0.19371920 potential -16.36320560 -16.36376689 -0.00056129 -16.36376793 -0.00056233 -16.36842418 -0.00521858 -16.36320560 0.00000000 -16.16948640 0.19371920 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -16.36320560 Difference in potential energy from amber=>gromacs conversion: -0.00056129 Difference in potential energy from amber=>lammps conversion: -0.00056233 Difference in potential energy from amber=>desmond conversion: -0.00521858 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.19371920 ======================================================================= INFO 2017-03-18 22:40:14 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_242480.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_242480.inpcrd') INFO 2017-03-18 22:40:14 Beginning InterMol conversion INFO 2017-03-18 22:40:14 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:40:14 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2451097.inpcrd INFO 2017-03-18 22:40:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2451097/mobley_2451097_converted.input INFO 2017-03-18 22:40:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2451097/mobley_2451097_converted.cms INFO 2017-03-18 22:40:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2451097/mobley_2451097_converted.rst7 WARNING 2017-03-18 22:40:30 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:40:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2451097/mobley_2451097_converted.inp INFO 2017-03-18 22:40:30 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2451097/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2451097/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2451097/mobley_2451097_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_2451097/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2451097/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -6.00633265 -6.00633265 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 30.74821600 30.74821600 coulomb total 30.73984800 30.73512992 -0.00471808 30.73512970 -0.00471830 30.73511163 -0.00473637 30.73984800 0.00000000 30.74821600 0.00836800 coulomb-14 36.74430640 36.74146257 -0.00284383 0.00000000 -36.74430640 36.74147710 -0.00282930 36.74430640 0.00000000 0.00000000 -36.74430640 improper 0.00000000 0.00007821 0.00007821 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00083680 0.00070609 -0.00013071 0.00078426 -0.00005254 0.00078557 -0.00005123 0.00083680 0.00000000 0.00071128 -0.00012552 vdw (SR) 0.00000000 -2.08084206 -2.08084206 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 14.29672800 14.29672800 vdw total 14.29672800 14.29675978 0.00003178 14.29675980 0.00003180 14.29686221 0.00013421 14.29672800 0.00000000 14.29672800 0.00000000 vdw-14 16.37743120 16.37760184 0.00017064 0.00000000 -16.37743120 16.37770655 0.00027535 16.37743120 0.00000000 0.00000000 -16.37743120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.47446560 0.19694782 -0.27751778 0.19694782 -0.27751778 0.19689924 -0.27756636 0.47446560 0.00000000 0.19694088 -0.27752472 bond 2.32128320 2.32124560 -0.00003760 2.32124559 -0.00003761 2.32093226 -0.00035094 2.32128320 0.00000000 2.32124136 -0.00004184 bonded 2.79658560 2.51897771 -0.27760789 2.51897766 -0.27760794 2.51861707 -0.27796853 2.79658560 0.00000000 2.51897720 -0.27760840 dihedral 0.00083680 0.00078430 -0.00005250 0.00078426 -0.00005254 0.00078557 -0.00005123 0.00083680 0.00000000 0.00079496 -0.00004184 nonbonded 45.03657600 45.03188970 -0.00468630 45.03188992 -0.00468608 45.03197383 -0.00460217 45.03657600 0.00000000 45.04494400 0.00836800 potential 47.83316160 47.55086741 -0.28229419 47.55086712 -0.28229448 47.55054202 -0.28261958 47.83316160 0.00000000 47.56392120 -0.26924040 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 47.83316160 Difference in potential energy from amber=>gromacs conversion: -0.28229419 Difference in potential energy from amber=>lammps conversion: -0.28229448 Difference in potential energy from amber=>desmond conversion: -0.28261958 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.26924040 ======================================================================= INFO 2017-03-18 22:40:30 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2451097.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2451097.inpcrd') INFO 2017-03-18 22:40:30 Beginning InterMol conversion INFO 2017-03-18 22:40:30 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:40:31 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:40:31 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2457863.inpcrd INFO 2017-03-18 22:40:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2457863/mobley_2457863_converted.input INFO 2017-03-18 22:40:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2457863/mobley_2457863_converted.cms WARNING 2017-03-18 22:40:46 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:40:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2457863/mobley_2457863_converted.inp INFO 2017-03-18 22:40:46 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2457863/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2457863/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2457863/mobley_2457863_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2457863/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 112.35831292 112.35831292 0.00000000 0.00000000 0.00000000 0.00000000 -162.14522976 -162.14522976 coulomb total -162.10740640 -162.09852617 0.00888023 -162.09852377 0.00888263 -162.09906852 0.00833788 -162.14522976 -0.03782336 coulomb-14 -274.44153040 -274.45683909 -0.01530869 0.00000000 274.44153040 -274.45676936 -0.01523896 0.00000000 274.44153040 improper 0.00000000 0.00005090 0.00005090 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00251040 0.00233413 -0.00017627 0.00238500 -0.00012540 0.00238887 -0.00012153 0.00234304 -0.00016736 vdw (SR) 0.00000000 13.72393577 13.72393577 0.00000000 0.00000000 0.00000000 0.00000000 39.99929104 39.99929104 vdw total 39.99904000 39.99919138 0.00015138 39.99919188 0.00015188 39.99936593 0.00032593 39.99929104 0.00025104 vdw-14 26.27510160 26.27525560 0.00015400 0.00000000 -26.27510160 26.27525298 0.00015138 0.00000000 -26.27510160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.36986560 0.36968737 -0.00017823 0.36968737 -0.00017823 0.36974222 -0.00012338 0.36969824 -0.00016736 bond 1.29285600 1.29274492 -0.00011108 1.29274491 -0.00011109 1.29281086 -0.00004514 1.29273048 -0.00012552 bonded 1.66523200 1.66481733 -0.00041467 1.66481729 -0.00041471 1.66494195 -0.00029005 1.66481360 -0.00041840 dihedral 0.00251040 0.00238503 -0.00012537 0.00238500 -0.00012540 0.00238887 -0.00012153 0.00238488 -0.00012552 nonbonded -122.10836640 -122.09933479 0.00903161 -122.09933314 0.00903326 -122.09970259 0.00866381 -122.14593872 -0.03757232 potential -120.44313440 -120.43451747 0.00861693 -120.43451536 0.00861904 -120.43481410 0.00832030 -120.48112512 -0.03799072 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -120.44313440 Difference in potential energy from amber=>gromacs conversion: 0.00861693 Difference in potential energy from amber=>lammps conversion: 0.00861904 Difference in potential energy from amber=>desmond conversion: 0.00832030 Difference in potential energy from amber=>charmm conversion: -0.03799072 ======================================================================= INFO 2017-03-18 22:40:46 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2457863.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2457863.inpcrd') INFO 2017-03-18 22:40:47 Beginning InterMol conversion INFO 2017-03-18 22:40:47 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:40:47 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:40:47 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2481002.inpcrd INFO 2017-03-18 22:40:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2481002/mobley_2481002_converted.input INFO 2017-03-18 22:40:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2481002/mobley_2481002_converted.cms WARNING 2017-03-18 22:41:02 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:41:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2481002/mobley_2481002_converted.inp INFO 2017-03-18 22:41:02 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2481002/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2481002/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2481002/mobley_2481002_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2481002/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 12.68542776 12.68542776 coulomb total 12.68128560 12.68187972 0.00059412 12.68187973 0.00059413 12.68187128 0.00058568 12.68542776 0.00414216 coulomb-14 12.68128560 12.68187972 0.00059412 0.00000000 -12.68128560 12.68187128 0.00058568 0.00000000 -12.68128560 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 10.89563808 10.89563808 vdw total 10.89555440 10.89550915 -0.00004525 10.89550921 -0.00004519 10.89525717 -0.00029723 10.89563808 0.00008368 vdw-14 10.89555440 10.89550915 -0.00004525 0.00000000 -10.89555440 10.89525717 -0.00029723 0.00000000 -10.89555440 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.15057600 2.15056783 -0.00000817 2.15056784 -0.00000816 2.15060765 0.00003165 2.15057600 0.00000000 bond 5.15217760 5.15202523 -0.00015237 5.15202530 -0.00015230 5.15313703 0.00095943 5.15201024 -0.00016736 bonded 7.30275360 7.30259306 -0.00016054 7.30259314 -0.00016046 7.30374468 0.00099108 7.30258624 -0.00016736 nonbonded 23.57684000 23.57738887 0.00054887 23.57738894 0.00054894 23.57712844 0.00028844 23.58106584 0.00422584 potential 30.87959360 30.87998193 0.00038833 30.87998188 0.00038828 30.88082252 0.00122892 30.88365208 0.00405848 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 30.87959360 Difference in potential energy from amber=>gromacs conversion: 0.00038833 Difference in potential energy from amber=>lammps conversion: 0.00038828 Difference in potential energy from amber=>desmond conversion: 0.00122892 Difference in potential energy from amber=>charmm conversion: 0.00405848 ======================================================================= INFO 2017-03-18 22:41:02 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2481002.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2481002.inpcrd') INFO 2017-03-18 22:41:03 Beginning InterMol conversion INFO 2017-03-18 22:41:03 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:41:03 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:41:03 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2484519.inpcrd INFO 2017-03-18 22:41:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2484519/mobley_2484519_converted.input INFO 2017-03-18 22:41:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2484519/mobley_2484519_converted.cms WARNING 2017-03-18 22:41:18 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:41:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2484519/mobley_2484519_converted.inp INFO 2017-03-18 22:41:18 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2484519/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2484519/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2484519/mobley_2484519_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2484519/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 9.34927251 9.34927251 0.00000000 0.00000000 0.00000000 0.00000000 12.68777080 12.68777080 coulomb total 12.69090880 12.68401590 -0.00689290 12.68401566 -0.00689314 12.68401189 -0.00689691 12.68777080 -0.00313800 coulomb-14 3.33590320 3.33474339 -0.00115981 0.00000000 -3.33590320 3.33476243 -0.00114077 0.00000000 -3.33590320 improper 0.00000000 0.00007041 0.00007041 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00083680 0.00070627 -0.00013053 0.00077663 -0.00006017 0.00077659 -0.00006021 0.00071128 -0.00012552 vdw (SR) 0.00000000 -2.68323022 -2.68323022 0.00000000 0.00000000 0.00000000 0.00000000 14.03589744 14.03589744 vdw total 14.03606480 14.03591390 -0.00015090 14.03591376 -0.00015104 14.03596123 -0.00010357 14.03589744 -0.00016736 vdw-14 16.71926400 16.71914413 -0.00011987 0.00000000 -16.71926400 16.71919597 -0.00006803 0.00000000 -16.71926400 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.94767600 0.94752938 -0.00014662 0.94752939 -0.00014661 0.94756169 -0.00011431 0.94755048 -0.00012552 bond 1.53929360 1.53934331 0.00004971 1.53934331 0.00004971 1.53894997 -0.00034363 1.53933544 0.00004184 bonded 2.48780640 2.48764938 -0.00015702 2.48764932 -0.00015708 2.48728825 -0.00051815 2.48768088 -0.00012552 dihedral 0.00083680 0.00077668 -0.00006012 0.00077663 -0.00006017 0.00077659 -0.00006021 0.00079496 -0.00004184 nonbonded 26.72697360 26.71992980 -0.00704380 26.71992984 -0.00704376 26.71997312 -0.00700048 26.72366824 -0.00330536 potential 29.21478000 29.20757918 -0.00720082 29.20757892 -0.00720108 29.20721035 -0.00756965 29.21134912 -0.00343088 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 29.21478000 Difference in potential energy from amber=>gromacs conversion: -0.00720082 Difference in potential energy from amber=>lammps conversion: -0.00720108 Difference in potential energy from amber=>desmond conversion: -0.00756965 Difference in potential energy from amber=>charmm conversion: -0.00343088 ======================================================================= INFO 2017-03-18 22:41:18 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2484519.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2484519.inpcrd') INFO 2017-03-18 22:41:19 Beginning InterMol conversion INFO 2017-03-18 22:41:19 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:41:19 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:41:19 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2487143.inpcrd INFO 2017-03-18 22:41:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2487143/mobley_2487143_converted.input INFO 2017-03-18 22:41:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2487143/mobley_2487143_converted.cms WARNING 2017-03-18 22:41:34 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:41:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2487143/mobley_2487143_converted.inp INFO 2017-03-18 22:41:35 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2487143/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2487143/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2487143/mobley_2487143_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2487143/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -5.28637393 -5.28637393 0.00000000 0.00000000 0.00000000 0.00000000 -59.29932992 -59.29932992 coulomb total -59.28351440 -59.28557066 -0.00205626 -59.28556874 -0.00205434 -59.28554322 -0.00202882 -59.29932992 -0.01581552 coulomb-14 -53.99744880 -53.99919672 -0.00174792 0.00000000 53.99744880 -53.99914625 -0.00169745 0.00000000 53.99744880 improper 0.00000000 0.00003991 0.00003991 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 15.96237840 15.96240040 0.00002200 15.96244158 0.00006318 15.96248861 0.00011021 15.96242024 0.00004184 vdw (SR) 0.00000000 -1.68697840 -1.68697840 0.00000000 0.00000000 0.00000000 0.00000000 6.49536712 6.49536712 vdw total 6.49524160 6.49527625 0.00003465 6.49527633 0.00003473 6.49529528 0.00005368 6.49536712 0.00012552 vdw-14 8.18223040 8.18225464 0.00002424 0.00000000 -8.18223040 8.18225458 0.00002418 0.00000000 -8.18223040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.34008720 3.34021226 0.00012506 3.34021226 0.00012506 3.34025623 0.00016903 3.34021272 0.00012552 bond 3.85890320 3.85880475 -0.00009845 3.85880475 -0.00009845 3.85880548 -0.00009772 3.85881952 -0.00008368 bonded 23.16136880 23.16145732 0.00008852 23.16145859 0.00008979 23.16155032 0.00018152 23.16149432 0.00012552 dihedral 15.96237840 15.96244031 0.00006191 15.96244158 0.00006318 15.96248861 0.00011021 15.96246208 0.00008368 nonbonded -52.78827280 -52.79029441 -0.00202161 -52.79029367 -0.00202087 -52.79024794 -0.00197514 -52.80396280 -0.01569000 potential -29.62690400 -29.62883709 -0.00193309 -29.62883492 -0.00193092 -29.62875316 -0.00184916 -29.64251032 -0.01560632 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -29.62690400 Difference in potential energy from amber=>gromacs conversion: -0.00193309 Difference in potential energy from amber=>lammps conversion: -0.00193092 Difference in potential energy from amber=>desmond conversion: -0.00184916 Difference in potential energy from amber=>charmm conversion: -0.01560632 ======================================================================= INFO 2017-03-18 22:41:35 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2487143.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2487143.inpcrd') INFO 2017-03-18 22:41:35 Beginning InterMol conversion INFO 2017-03-18 22:41:35 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:41:35 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2489709.inpcrd INFO 2017-03-18 22:41:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2489709/mobley_2489709_converted.input INFO 2017-03-18 22:41:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2489709/mobley_2489709_converted.cms INFO 2017-03-18 22:41:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2489709/mobley_2489709_converted.rst7 WARNING 2017-03-18 22:41:51 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:41:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2489709/mobley_2489709_converted.inp INFO 2017-03-18 22:41:51 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2489709/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2489709/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2489709/mobley_2489709_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_2489709/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2489709/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -2.17908653 -2.17908653 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 13.53837800 13.53837800 coulomb total 13.53356640 13.53965348 0.00608708 13.53965328 0.00608688 13.53966627 0.00609987 13.53356640 0.00000000 13.53837800 0.00481160 coulomb-14 15.71594080 15.71874001 0.00279921 0.00000000 -15.71594080 15.71875847 0.00281767 15.71594080 0.00000000 0.00000000 -15.71594080 improper 0.00000000 0.00001014 0.00001014 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00000000 0.00010669 0.00010669 0.00011681 0.00011681 0.00011272 0.00011272 0.00000000 0.00000000 0.00012552 0.00012552 vdw (SR) 0.00000000 -1.50764499 -1.50764499 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 15.61288888 15.61288888 vdw total 15.61301440 15.61288548 -0.00012892 15.61288553 -0.00012887 15.61297879 -0.00003561 15.61301440 0.00000000 15.61288888 -0.00012552 vdw-14 17.12050960 17.12053047 0.00002087 0.00000000 -17.12050960 17.12062433 0.00011473 17.12050960 0.00000000 0.00000000 -17.12050960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.73301280 1.73285475 -0.00015805 1.73285473 -0.00015807 1.73302295 0.00001015 1.73301280 0.00000000 1.73288728 -0.00012552 bond 0.72843440 0.72827065 -0.00016375 0.72827064 -0.00016376 0.72819914 -0.00023526 0.72843440 0.00000000 0.72826704 -0.00016736 bonded 2.46144720 2.46124223 -0.00020497 2.46124218 -0.00020502 2.46133481 -0.00011239 2.46144720 0.00000000 2.46127984 -0.00016736 dihedral 0.00000000 0.00011683 0.00011683 0.00011681 0.00011681 0.00011272 0.00011272 0.00000000 0.00000000 0.00012552 0.00012552 nonbonded 29.14658080 29.15253896 0.00595816 29.15253882 0.00595802 29.15264506 0.00606426 29.14658080 0.00000000 29.15126688 0.00468608 potential 31.60802800 31.61378119 0.00575319 31.61378100 0.00575300 31.61392213 0.00589413 31.60802800 0.00000000 31.61250488 0.00447688 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 31.60802800 Difference in potential energy from amber=>gromacs conversion: 0.00575319 Difference in potential energy from amber=>lammps conversion: 0.00575300 Difference in potential energy from amber=>desmond conversion: 0.00589413 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00447688 ======================================================================= INFO 2017-03-18 22:41:51 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2489709.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2489709.inpcrd') INFO 2017-03-18 22:41:51 Beginning InterMol conversion INFO 2017-03-18 22:41:51 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:41:51 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:41:51 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2492140.inpcrd INFO 2017-03-18 22:41:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2492140/mobley_2492140_converted.input INFO 2017-03-18 22:41:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2492140/mobley_2492140_converted.cms WARNING 2017-03-18 22:42:07 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:42:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2492140/mobley_2492140_converted.inp INFO 2017-03-18 22:42:07 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2492140/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2492140/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2492140/mobley_2492140_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2492140/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 5.27949672 5.27949672 coulomb total 5.26681920 5.26718807 0.00036887 5.26718781 0.00036861 5.26718618 0.00036698 5.27949672 0.01267752 coulomb-14 5.26681920 5.26718807 0.00036887 0.00000000 -5.26681920 5.26718618 0.00036698 0.00000000 -5.26681920 proper 11.37002000 11.37022404 0.00020404 11.37022418 0.00020418 11.37024451 0.00022451 11.37022920 0.00020920 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.85593872 1.85593872 vdw total 1.85602240 1.85590656 -0.00011584 1.85590655 -0.00011585 1.85592534 -0.00009706 1.85593872 -0.00008368 vdw-14 1.85602240 1.85590656 -0.00011584 0.00000000 -1.85602240 1.85592534 -0.00009706 0.00000000 -1.85602240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.45512320 4.45504157 -0.00008163 4.45504161 -0.00008159 4.45505462 -0.00006858 4.45499768 -0.00012552 bond 0.80207280 0.80219297 0.00012017 0.80219296 0.00012016 0.80231912 0.00024632 0.80219832 0.00012552 bonded 16.62721600 16.62745859 0.00024259 16.62745876 0.00024276 16.62761825 0.00040225 16.62742520 0.00020920 dihedral 11.37002000 11.37022404 0.00020404 11.37022418 0.00020418 11.37024451 0.00022451 11.37022920 0.00020920 nonbonded 7.12284160 7.12309463 0.00025303 7.12309473 0.00025313 7.12311152 0.00026992 7.13543544 0.01259384 potential 23.75005760 23.75055322 0.00049562 23.75055299 0.00049539 23.75066039 0.00060279 23.76286064 0.01280304 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 23.75005760 Difference in potential energy from amber=>gromacs conversion: 0.00049562 Difference in potential energy from amber=>lammps conversion: 0.00049539 Difference in potential energy from amber=>desmond conversion: 0.00060279 Difference in potential energy from amber=>charmm conversion: 0.01280304 ======================================================================= INFO 2017-03-18 22:42:07 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2492140.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2492140.inpcrd') INFO 2017-03-18 22:42:07 Beginning InterMol conversion INFO 2017-03-18 22:42:07 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:42:07 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2493732.inpcrd INFO 2017-03-18 22:42:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2493732/mobley_2493732_converted.input INFO 2017-03-18 22:42:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2493732/mobley_2493732_converted.cms INFO 2017-03-18 22:42:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2493732/mobley_2493732_converted.rst7 WARNING 2017-03-18 22:42:23 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:42:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2493732/mobley_2493732_converted.inp INFO 2017-03-18 22:42:23 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2493732/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2493732/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2493732/mobley_2493732_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_2493732/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2493732/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -15.45921056 -15.45921056 coulomb total -15.44816480 -15.44705243 0.00111237 -15.44705227 0.00111253 -15.44704709 0.00111771 -15.44816480 0.00000000 -15.45921056 -0.01104576 coulomb-14 -15.44816480 -15.44705243 0.00111237 0.00000000 15.44816480 -15.44704709 0.00111771 -15.44816480 0.00000000 0.00000000 15.44816480 improper 0.00000000 0.00001211 0.00001211 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00000000 0.00008420 0.00008420 0.00009630 0.00009630 0.00009826 0.00009826 0.00000000 0.00000000 0.00008368 0.00008368 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.20129224 0.20129224 vdw total 0.20125040 0.20128809 0.00003769 0.20128809 0.00003769 0.20128222 0.00003182 0.20125040 0.00000000 0.20129224 0.00004184 vdw-14 0.20125040 0.20128809 0.00003769 0.00000000 -0.20125040 0.20128222 0.00003182 0.20125040 0.00000000 0.00000000 -0.20125040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.42967280 1.42983950 0.00016670 1.42983949 0.00016669 1.42993924 0.00026644 1.42967280 0.00000000 1.42984016 0.00016736 bond 2.97315040 2.97328901 0.00013861 2.97328902 0.00013862 2.97348082 0.00033042 2.97315040 0.00000000 2.97327592 0.00012552 bonded 4.40282320 4.40322482 0.00040162 4.40322481 0.00040161 4.40351832 0.00069512 4.40282320 0.00000000 4.40319976 0.00037656 dihedral 0.00000000 0.00009631 0.00009631 0.00009630 0.00009630 0.00009826 0.00009826 0.00000000 0.00000000 0.00008368 0.00008368 nonbonded -15.24691440 -15.24576435 0.00115005 -15.24576422 0.00115018 -15.24576487 0.00114953 -15.24691440 0.00000000 -15.25791832 -0.01100392 potential -10.84409120 -10.84253952 0.00155168 -10.84253935 0.00155185 -10.84226551 0.00182569 -10.84409120 0.00000000 -10.85467672 -0.01058552 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -10.84409120 Difference in potential energy from amber=>gromacs conversion: 0.00155168 Difference in potential energy from amber=>lammps conversion: 0.00155185 Difference in potential energy from amber=>desmond conversion: 0.00182569 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.01058552 ======================================================================= INFO 2017-03-18 22:42:23 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2493732.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2493732.inpcrd') INFO 2017-03-18 22:42:23 Beginning InterMol conversion INFO 2017-03-18 22:42:23 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:42:23 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:42:23 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2501588.inpcrd INFO 2017-03-18 22:42:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2501588/mobley_2501588_converted.input INFO 2017-03-18 22:42:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2501588/mobley_2501588_converted.cms WARNING 2017-03-18 22:42:39 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:42:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2501588/mobley_2501588_converted.inp INFO 2017-03-18 22:42:39 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2501588/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2501588/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2501588/mobley_2501588_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2501588/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 133.57053426 133.57053426 0.00000000 0.00000000 0.00000000 0.00000000 -86.48018384 -86.48018384 coulomb total -86.55022400 -86.53692431 0.01329969 -86.53692306 0.01330094 -86.53654316 0.01368084 -86.48018384 0.07004016 coulomb-14 -220.11396400 -220.10745857 0.00650543 0.00000000 220.11396400 -220.10722190 0.00674210 0.00000000 220.11396400 improper 0.00000000 0.00139683 0.00139683 0.00000000 0.00000000 0.00000000 0.00000000 0.00138072 0.00138072 proper 107.48737840 107.48589286 -0.00148554 107.48729054 -0.00008786 107.48727966 -0.00009874 107.49432384 0.00694544 vdw (SR) 0.00000000 -23.05129189 -23.05129189 0.00000000 0.00000000 0.00000000 0.00000000 16.70679568 16.70679568 vdw total 16.70671200 16.70671167 -0.00000033 16.70671158 -0.00000042 16.70648790 -0.00022410 16.70679568 0.00008368 vdw-14 39.75804160 39.75800355 -0.00003805 0.00000000 -39.75804160 39.75788319 -0.00015841 0.00000000 -39.75804160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 12.08046320 12.08031937 -0.00014383 12.08031927 -0.00014393 12.08114519 0.00068199 12.08033768 -0.00012552 bond 30.52771920 30.52768960 -0.00002960 30.52768949 -0.00002971 30.53108460 0.00336540 30.52767736 -0.00004184 bonded 150.09556080 150.09529866 -0.00026214 150.09529930 -0.00026150 150.09950945 0.00394865 150.10371960 0.00815880 dihedral 107.48737840 107.48728969 -0.00008871 107.48729054 -0.00008786 107.48727966 -0.00009874 107.49570456 0.00832616 nonbonded -69.84351200 -69.83021265 0.01329935 -69.83021106 0.01330094 -69.83005525 0.01345675 -69.77338816 0.07012384 potential 80.25204880 80.26508601 0.01303721 80.26508614 0.01303734 80.26902622 0.01697742 80.33028960 0.07824080 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 80.25204880 Difference in potential energy from amber=>gromacs conversion: 0.01303721 Difference in potential energy from amber=>lammps conversion: 0.01303734 Difference in potential energy from amber=>desmond conversion: 0.01697742 Difference in potential energy from amber=>charmm conversion: 0.07824080 ======================================================================= INFO 2017-03-18 22:42:39 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2501588.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2501588.inpcrd') INFO 2017-03-18 22:42:39 Beginning InterMol conversion INFO 2017-03-18 22:42:39 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:42:39 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:42:39 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2517158.inpcrd INFO 2017-03-18 22:42:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2517158/mobley_2517158_converted.input INFO 2017-03-18 22:42:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2517158/mobley_2517158_converted.cms WARNING 2017-03-18 22:42:55 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:42:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2517158/mobley_2517158_converted.inp INFO 2017-03-18 22:42:55 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2517158/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2517158/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2517158/mobley_2517158_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2517158/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 8.24192457 8.24192457 0.00000000 0.00000000 0.00000000 0.00000000 4.49064536 4.49064536 coulomb total 4.48608480 4.49851573 0.01243093 4.49851588 0.01243108 4.49845917 0.01237437 4.49064536 0.00456056 coulomb-14 -3.74635360 -3.74340884 0.00294476 0.00000000 3.74635360 -3.74342013 0.00293347 0.00000000 3.74635360 proper 13.89548240 13.89546439 -0.00001801 13.89546441 -0.00001799 13.89545771 -0.00002469 13.89548240 0.00000000 vdw (SR) 0.00000000 -3.20914482 -3.20914482 0.00000000 0.00000000 0.00000000 0.00000000 4.44646232 4.44646232 vdw total 4.44633680 4.44635159 0.00001479 4.44635186 0.00001506 4.44633900 0.00000220 4.44646232 0.00012552 vdw-14 7.65546480 7.65549641 0.00003161 0.00000000 -7.65546480 7.65549141 0.00002661 0.00000000 -7.65546480 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.34801280 4.34820623 0.00019343 4.34820610 0.00019330 4.34781795 -0.00019485 4.34822200 0.00020920 bond 1.31963360 1.31954609 -0.00008751 1.31954607 -0.00008753 1.31926309 -0.00037051 1.31954992 -0.00008368 bonded 19.56312880 19.56321670 0.00008790 19.56321658 0.00008778 19.56253876 -0.00059004 19.56325432 0.00012552 dihedral 13.89548240 13.89546439 -0.00001801 13.89546441 -0.00001799 13.89545771 -0.00002469 13.89548240 0.00000000 nonbonded 8.93242160 8.94486732 0.01244572 8.94486733 0.01244573 8.94479817 0.01237657 8.93710768 0.00468608 potential 28.49555040 28.50808402 0.01253362 28.50808399 0.01253359 28.50724414 0.01169374 28.50036200 0.00481160 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 28.49555040 Difference in potential energy from amber=>gromacs conversion: 0.01253362 Difference in potential energy from amber=>lammps conversion: 0.01253359 Difference in potential energy from amber=>desmond conversion: 0.01169374 Difference in potential energy from amber=>charmm conversion: 0.00481160 ======================================================================= INFO 2017-03-18 22:42:55 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2517158.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2517158.inpcrd') INFO 2017-03-18 22:42:55 Beginning InterMol conversion INFO 2017-03-18 22:42:55 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:42:56 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:42:56 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2518989.inpcrd INFO 2017-03-18 22:42:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2518989/mobley_2518989_converted.input INFO 2017-03-18 22:42:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2518989/mobley_2518989_converted.cms WARNING 2017-03-18 22:43:11 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:43:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2518989/mobley_2518989_converted.inp INFO 2017-03-18 22:43:11 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2518989/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2518989/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2518989/mobley_2518989_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2518989/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 396.40108172 396.40108172 0.00000000 0.00000000 0.00000000 0.00000000 -621.82047344 -621.82047344 coulomb total -621.80683360 -621.82901388 -0.02218028 -621.82900880 -0.02217520 -621.82825652 -0.02142292 -621.82047344 -0.01363984 coulomb-14 -1018.20861680 -1018.23009560 -0.02147880 0.00000000 1018.20861680 -1018.22994683 -0.02133003 0.00000000 1018.20861680 improper 0.00000000 0.00012123 0.00012123 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 82.42731040 82.42713696 -0.00017344 82.42725601 -0.00005439 82.42740370 0.00009330 82.42697568 -0.00033472 vdw (SR) 0.00000000 -36.88372448 -36.88372448 0.00000000 0.00000000 0.00000000 0.00000000 -14.16154296 -14.16154296 vdw total -14.16158480 -14.16170106 -0.00011626 -14.16170112 -0.00011632 -14.16189203 -0.00030723 -14.16154296 0.00004184 vdw-14 22.72204880 22.72202341 -0.00002539 0.00000000 -22.72204880 22.72179655 -0.00025225 0.00000000 -22.72204880 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 105.46023040 105.46004978 -0.00018062 105.46005049 -0.00017991 105.46001702 -0.00021338 105.45981200 -0.00041840 bond 17.59497520 17.59516633 0.00019113 17.59516641 0.00019121 17.59591664 0.00094144 17.59518440 0.00020920 bonded 205.48251600 205.48247430 -0.00004170 205.48247290 -0.00004310 205.48333736 0.00082136 205.48209760 -0.00041840 dihedral 82.42731040 82.42725818 -0.00005222 82.42725601 -0.00005439 82.42740370 0.00009330 82.42710120 -0.00020920 nonbonded -635.96841840 -635.99071495 -0.02229655 -635.99071912 -0.02230072 -635.99014855 -0.02173015 -635.98201640 -0.01359800 potential -430.48590240 -430.50824065 -0.02233825 -430.50824496 -0.02234256 -430.50728682 -0.02138442 -430.49991880 -0.01401640 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -430.48590240 Difference in potential energy from amber=>gromacs conversion: -0.02233825 Difference in potential energy from amber=>lammps conversion: -0.02234256 Difference in potential energy from amber=>desmond conversion: -0.02138442 Difference in potential energy from amber=>charmm conversion: -0.01401640 ======================================================================= INFO 2017-03-18 22:43:11 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2518989.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2518989.inpcrd') INFO 2017-03-18 22:43:12 Beginning InterMol conversion INFO 2017-03-18 22:43:12 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:43:12 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2523689.inpcrd INFO 2017-03-18 22:43:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2523689/mobley_2523689_converted.input INFO 2017-03-18 22:43:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2523689/mobley_2523689_converted.cms INFO 2017-03-18 22:43:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2523689/mobley_2523689_converted.rst7 WARNING 2017-03-18 22:43:27 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:43:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2523689/mobley_2523689_converted.inp INFO 2017-03-18 22:43:27 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2523689/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2523689/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2523689/mobley_2523689_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_2523689/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2523689/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 73.39902253 73.39902253 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 162.89441680 162.89441680 coulomb total 162.85634240 162.85949276 0.00315036 162.85949295 0.00315055 162.85968542 0.00334302 162.85634240 0.00000000 162.89441680 0.03807440 coulomb-14 89.45433840 89.46047023 0.00613183 0.00000000 -89.45433840 89.46023198 0.00589358 89.45433840 0.00000000 0.00000000 -89.45433840 improper 0.00000000 0.04490636 0.04490636 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.04489432 0.04489432 proper 5.09694880 5.05198978 -0.04495902 5.09690863 -0.00004017 5.09677228 -0.00017652 5.09694880 0.00000000 5.05201264 -0.04493616 vdw (SR) 0.00000000 2.00558590 2.00558590 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 47.02514752 47.02514752 vdw total 47.02523120 47.02514742 -0.00008378 47.02514752 -0.00008368 47.02573861 0.00050741 47.02481280 -0.00041840 47.02514752 -0.00008368 vdw-14 45.01942160 45.01956152 0.00013992 0.00000000 -45.01942160 45.02002577 0.00060417 45.01942160 0.00000000 0.00000000 -45.01942160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 46.30642000 46.30654315 0.00012315 46.30654134 0.00012134 46.30703881 0.00061881 46.30642000 0.00000000 46.30662920 0.00020920 bond 21.71788880 21.71808875 0.00019995 21.71808880 0.00020000 21.71891907 0.00103027 21.71788880 0.00000000 21.71809800 0.00020920 bonded 73.12125760 73.12152805 0.00027045 73.12153876 0.00028116 73.12273016 0.00147256 73.12125760 0.00000000 73.12163416 0.00037656 dihedral 5.09694880 5.09689615 -0.00005265 5.09690863 -0.00004017 5.09677228 -0.00017652 5.09694880 0.00000000 5.09690696 -0.00004184 nonbonded 209.88157360 209.88464018 0.00306658 209.88463629 0.00306269 209.88542402 0.00385042 209.88115520 -0.00041840 209.91956432 0.03799072 potential 283.00283120 283.00616823 0.00333703 283.00617840 0.00334720 283.00799007 0.00515887 283.00241280 -0.00041840 283.04119848 0.03836728 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 283.00283120 Difference in potential energy from amber=>gromacs conversion: 0.00333703 Difference in potential energy from amber=>lammps conversion: 0.00334720 Difference in potential energy from amber=>desmond conversion: 0.00515887 Difference in potential energy from amber=>amber conversion: -0.00041840 Difference in potential energy from amber=>charmm conversion: 0.03836728 ======================================================================= INFO 2017-03-18 22:43:27 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2523689.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2523689.inpcrd') INFO 2017-03-18 22:43:28 Beginning InterMol conversion INFO 2017-03-18 22:43:28 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:43:28 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:43:28 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_252413.inpcrd INFO 2017-03-18 22:43:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_252413/mobley_252413_converted.input INFO 2017-03-18 22:43:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_252413/mobley_252413_converted.cms WARNING 2017-03-18 22:43:44 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:43:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_252413/mobley_252413_converted.inp INFO 2017-03-18 22:43:44 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_252413/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_252413/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_252413/mobley_252413_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_252413/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 15.80535182 15.80535182 0.00000000 0.00000000 0.00000000 0.00000000 -13.03127720 -13.03127720 coulomb total -13.02060800 -13.03058788 -0.00997988 -13.03058768 -0.00997968 -13.03061763 -0.01000963 -13.03127720 -0.01066920 coulomb-14 -28.84031200 -28.83593969 0.00437231 0.00000000 28.84031200 -28.83591809 0.00439391 0.00000000 28.84031200 proper 7.44040720 7.44061287 0.00020567 7.44061305 0.00020585 7.44060519 0.00019799 7.44061640 0.00020920 vdw (SR) 0.00000000 6.16967553 6.16967553 0.00000000 0.00000000 0.00000000 0.00000000 19.53974024 19.53974024 vdw total 19.53969840 19.53948772 -0.00021068 19.53948794 -0.00021046 19.53947753 -0.00022087 19.53974024 0.00004184 vdw-14 13.36997200 13.36981218 -0.00015982 0.00000000 -13.36997200 13.36970577 -0.00026623 0.00000000 -13.36997200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.99316160 5.99332100 0.00015940 5.99332101 0.00015941 5.99313913 -0.00002247 5.99328712 0.00012552 bond 0.95855440 0.95843896 -0.00011544 0.95843896 -0.00011544 0.95850397 -0.00005043 0.95842888 -0.00012552 bonded 14.39212320 14.39237283 0.00024963 14.39237303 0.00024983 14.39224828 0.00012508 14.39233240 0.00020920 dihedral 7.44040720 7.44061287 0.00020567 7.44061305 0.00020585 7.44060519 0.00019799 7.44061640 0.00020920 nonbonded 6.51909040 6.50889984 -0.01019056 6.50890027 -0.01019013 6.50885989 -0.01023051 6.50846304 -0.01062736 potential 20.91121360 20.90127267 -0.00994093 20.90127325 -0.00994035 20.90104573 -0.01016787 20.90079544 -0.01041816 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 20.91121360 Difference in potential energy from amber=>gromacs conversion: -0.00994093 Difference in potential energy from amber=>lammps conversion: -0.00994035 Difference in potential energy from amber=>desmond conversion: -0.01016787 Difference in potential energy from amber=>charmm conversion: -0.01041816 ======================================================================= INFO 2017-03-18 22:43:44 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_252413.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_252413.inpcrd') INFO 2017-03-18 22:43:44 Beginning InterMol conversion INFO 2017-03-18 22:43:44 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:43:44 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2577969.inpcrd INFO 2017-03-18 22:43:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2577969/mobley_2577969_converted.input INFO 2017-03-18 22:43:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2577969/mobley_2577969_converted.cms INFO 2017-03-18 22:44:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2577969/mobley_2577969_converted.rst7 WARNING 2017-03-18 22:44:00 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:44:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2577969/mobley_2577969_converted.inp INFO 2017-03-18 22:44:00 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2577969/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2577969/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2577969/mobley_2577969_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_2577969/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2577969/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -2.92574884 -2.92574884 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 10.41933152 10.41933152 coulomb total 10.40853680 10.41490790 0.00637110 10.41490778 0.00637098 10.41492531 0.00638851 10.40853680 0.00000000 10.41933152 0.01079472 coulomb-14 13.34068400 13.34065675 -0.00002725 0.00000000 -13.34068400 13.34070551 0.00002151 13.34068400 0.00000000 0.00000000 -13.34068400 improper 0.00000000 0.00014140 0.00014140 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00125520 0.00120577 -0.00004943 0.00134704 0.00009184 0.00132025 0.00006505 0.00125520 0.00000000 0.00121336 -0.00004184 vdw (SR) 0.00000000 -9.87219209 -9.87219209 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 47.51279272 47.51279272 vdw total 47.51266720 47.51287363 0.00020643 47.51287222 0.00020502 47.51303602 0.00036882 47.51308560 0.00041840 47.51279272 0.00012552 vdw-14 57.38481520 57.38506572 0.00025052 0.00000000 -57.38481520 57.38523737 0.00042217 57.38523360 0.00041840 0.00000000 -57.38481520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.38446160 2.38434123 -0.00012037 2.38434123 -0.00012037 2.38439128 -0.00007032 2.38446160 0.00000000 2.38437792 -0.00008368 bond 12.15159120 12.15174500 0.00015380 12.15174517 0.00015397 12.15165463 0.00006343 12.15159120 0.00000000 12.15175856 0.00016736 bonded 14.53730800 14.53743339 0.00012539 14.53743343 0.00012543 14.53736615 0.00005815 14.53730800 0.00000000 14.53747536 0.00016736 dihedral 0.00125520 0.00134717 0.00009197 0.00134704 0.00009184 0.00132025 0.00006505 0.00125520 0.00000000 0.00133888 0.00008368 nonbonded 57.92120400 57.92778153 0.00657753 57.92778125 0.00657725 57.92796133 0.00675733 57.92162240 0.00041840 57.93212424 0.01092024 potential 72.45851200 72.46521493 0.00670293 72.46521477 0.00670277 72.46516414 0.00665214 72.45893040 0.00041840 72.46959960 0.01108760 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 72.45851200 Difference in potential energy from amber=>gromacs conversion: 0.00670293 Difference in potential energy from amber=>lammps conversion: 0.00670277 Difference in potential energy from amber=>desmond conversion: 0.00665214 Difference in potential energy from amber=>amber conversion: 0.00041840 Difference in potential energy from amber=>charmm conversion: 0.01108760 ======================================================================= INFO 2017-03-18 22:44:00 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2577969.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2577969.inpcrd') INFO 2017-03-18 22:44:00 Beginning InterMol conversion INFO 2017-03-18 22:44:00 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:44:00 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:44:00 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2607611.inpcrd INFO 2017-03-18 22:44:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2607611/mobley_2607611_converted.input INFO 2017-03-18 22:44:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2607611/mobley_2607611_converted.cms WARNING 2017-03-18 22:44:16 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:44:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2607611/mobley_2607611_converted.inp INFO 2017-03-18 22:44:16 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2607611/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2607611/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2607611/mobley_2607611_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2607611/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 4.83878120 4.83878120 0.00000000 0.00000000 0.00000000 0.00000000 -116.07194224 -116.07194224 coulomb total -116.02734080 -116.03475529 -0.00741449 -116.03475485 -0.00741405 -116.03464083 -0.00730003 -116.07194224 -0.04460144 coulomb-14 -120.87157600 -120.87353650 -0.00196050 0.00000000 120.87157600 -120.87339311 -0.00181711 0.00000000 120.87157600 improper 0.00000000 0.00001023 0.00001023 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 26.16380720 26.16381301 0.00000581 26.16382477 0.00001757 26.16384076 0.00003356 26.16380720 0.00000000 vdw (SR) 0.00000000 -4.47466635 -4.47466635 0.00000000 0.00000000 0.00000000 0.00000000 9.00714784 9.00714784 vdw total 9.00689680 9.00696206 0.00006526 9.00696207 0.00006527 9.00692613 0.00002933 9.00714784 0.00025104 vdw-14 13.48168480 13.48162841 -0.00005639 0.00000000 -13.48168480 13.48158773 -0.00009707 0.00000000 -13.48168480 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.65930240 4.65912335 -0.00017905 4.65912332 -0.00017908 4.65919981 -0.00010259 4.65913504 -0.00016736 bond 2.61918400 2.61917487 -0.00000913 2.61917488 -0.00000912 2.61862301 -0.00056099 2.61918400 0.00000000 bonded 33.44229360 33.44212147 -0.00017213 33.44212298 -0.00017062 33.44166357 -0.00063003 33.44212624 -0.00016736 dihedral 26.16380720 26.16382325 0.00001605 26.16382477 0.00001757 26.16384076 0.00003356 26.16380720 0.00000000 nonbonded -107.02044400 -107.02779323 -0.00734923 -107.02779110 -0.00734710 -107.02771470 -0.00727070 -107.06479440 -0.04435040 potential -73.57815040 -73.58567176 -0.00752136 -73.58566905 -0.00751865 -73.58615397 -0.00800357 -73.62266816 -0.04451776 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -73.57815040 Difference in potential energy from amber=>gromacs conversion: -0.00752136 Difference in potential energy from amber=>lammps conversion: -0.00751865 Difference in potential energy from amber=>desmond conversion: -0.00800357 Difference in potential energy from amber=>charmm conversion: -0.04451776 ======================================================================= INFO 2017-03-18 22:44:16 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2607611.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2607611.inpcrd') INFO 2017-03-18 22:44:16 Beginning InterMol conversion INFO 2017-03-18 22:44:16 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:44:16 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:44:16 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2609604.inpcrd INFO 2017-03-18 22:44:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2609604/mobley_2609604_converted.input INFO 2017-03-18 22:44:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2609604/mobley_2609604_converted.cms WARNING 2017-03-18 22:44:32 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:44:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2609604/mobley_2609604_converted.inp INFO 2017-03-18 22:44:32 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2609604/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2609604/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2609604/mobley_2609604_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2609604/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 1.40028391 1.40028391 0.00000000 0.00000000 0.00000000 0.00000000 -12.72559416 -12.72559416 coulomb total -12.73986160 -12.72648448 0.01337712 -12.72648452 0.01337708 -12.72652225 0.01333935 -12.72559416 0.01426744 coulomb-14 -14.11932640 -14.12676840 -0.00744200 0.00000000 14.11932640 -14.12675559 -0.00742919 0.00000000 14.11932640 proper 11.67294160 11.67303352 0.00009192 11.67303323 0.00009163 11.67304407 0.00010247 11.67302528 0.00008368 vdw (SR) 0.00000000 5.82223950 5.82223950 0.00000000 0.00000000 0.00000000 0.00000000 18.76159992 18.76159992 vdw total 18.76147440 18.76138872 -0.00008568 18.76138905 -0.00008535 18.76148578 0.00001138 18.76159992 0.00012552 vdw-14 12.93902000 12.93914922 0.00012922 0.00000000 -12.93902000 12.93915062 0.00013062 0.00000000 -12.93902000 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 10.18804000 10.18817754 0.00013754 10.18817765 0.00013765 10.18859517 0.00055517 10.18816552 0.00012552 bond 1.65686400 1.65687798 0.00001398 1.65687797 0.00001397 1.65699502 0.00013102 1.65686400 0.00000000 bonded 23.51784560 23.51808904 0.00024344 23.51808886 0.00024326 23.51863426 0.00078866 23.51805480 0.00020920 dihedral 11.67294160 11.67303352 0.00009192 11.67303323 0.00009163 11.67304407 0.00010247 11.67302528 0.00008368 nonbonded 6.02161280 6.03490424 0.01329144 6.03490453 0.01329173 6.03496353 0.01335073 6.03600576 0.01439296 potential 29.53945840 29.55299327 0.01353487 29.55299364 0.01353524 29.55353354 0.01407514 29.55410240 0.01464400 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 29.53945840 Difference in potential energy from amber=>gromacs conversion: 0.01353487 Difference in potential energy from amber=>lammps conversion: 0.01353524 Difference in potential energy from amber=>desmond conversion: 0.01407514 Difference in potential energy from amber=>charmm conversion: 0.01464400 ======================================================================= INFO 2017-03-18 22:44:32 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2609604.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2609604.inpcrd') INFO 2017-03-18 22:44:32 Beginning InterMol conversion INFO 2017-03-18 22:44:32 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:44:33 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:44:33 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2613240.inpcrd INFO 2017-03-18 22:44:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2613240/mobley_2613240_converted.input INFO 2017-03-18 22:44:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2613240/mobley_2613240_converted.cms WARNING 2017-03-18 22:44:48 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:44:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2613240/mobley_2613240_converted.inp INFO 2017-03-18 22:44:48 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2613240/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2613240/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2613240/mobley_2613240_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2613240/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -62.41508183 -62.41508183 0.00000000 0.00000000 0.00000000 0.00000000 18.03245424 18.03245424 coulomb total 17.98576080 18.00085256 0.01509176 18.00085249 0.01509169 18.00078722 0.01502642 18.03245424 0.04669344 coulomb-14 80.41396960 80.41593438 0.00196478 0.00000000 -80.41396960 80.41588420 0.00191460 0.00000000 -80.41396960 improper 0.00000000 0.00009340 0.00009340 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 15.06742080 15.06733408 -0.00008672 15.06742749 0.00000669 15.06741088 -0.00000992 15.06733712 -0.00008368 vdw (SR) 0.00000000 11.33335073 11.33335073 0.00000000 0.00000000 0.00000000 0.00000000 40.17305256 40.17305256 vdw total 40.17309440 40.17293771 -0.00015669 40.17293792 -0.00015648 40.17293064 -0.00016376 40.17305256 -0.00004184 vdw-14 28.83947520 28.83958698 0.00011178 0.00000000 -28.83947520 28.83961453 0.00013933 0.00000000 -28.83947520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.72927120 0.72906567 -0.00020553 0.72906568 -0.00020552 0.72906446 -0.00020674 0.72910384 -0.00016736 bond 1.67694720 1.67688115 -0.00006605 1.67688113 -0.00006607 1.67654898 -0.00039822 1.67686352 -0.00008368 bonded 17.47363920 17.47337430 -0.00026490 17.47337431 -0.00026489 17.47302432 -0.00061488 17.47338816 -0.00025104 dihedral 15.06742080 15.06742748 0.00000668 15.06742749 0.00000669 15.06741088 -0.00000992 15.06742080 -0.00000000 nonbonded 58.15885520 58.17379027 0.01493507 58.17379208 0.01493688 58.17371786 0.01486266 58.20550680 0.04665160 potential 75.63249440 75.64716457 0.01467017 75.64716350 0.01466910 75.64667398 0.01417958 75.67889496 0.04640056 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 75.63249440 Difference in potential energy from amber=>gromacs conversion: 0.01467017 Difference in potential energy from amber=>lammps conversion: 0.01466910 Difference in potential energy from amber=>desmond conversion: 0.01417958 Difference in potential energy from amber=>charmm conversion: 0.04640056 ======================================================================= INFO 2017-03-18 22:44:48 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2613240.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2613240.inpcrd') INFO 2017-03-18 22:44:49 Beginning InterMol conversion INFO 2017-03-18 22:44:49 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:44:49 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:44:49 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2636578.inpcrd INFO 2017-03-18 22:44:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2636578/mobley_2636578_converted.input INFO 2017-03-18 22:44:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2636578/mobley_2636578_converted.cms WARNING 2017-03-18 22:45:04 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:45:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2636578/mobley_2636578_converted.inp INFO 2017-03-18 22:45:04 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2636578/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2636578/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2636578/mobley_2636578_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2636578/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -5.18425441 -5.18425441 0.00000000 0.00000000 0.00000000 0.00000000 -55.29992800 -55.29992800 coulomb total -55.19742000 -55.19932276 -0.00190276 -55.19932372 -0.00190372 -55.19930778 -0.00188778 -55.29992800 -0.10250800 coulomb-14 -50.01344400 -50.01506835 -0.00162435 0.00000000 50.01344400 -50.01504689 -0.00160289 0.00000000 50.01344400 proper 6.51155920 6.51152287 -0.00003633 6.51152280 -0.00003640 6.51151732 -0.00004188 6.51151736 -0.00004184 vdw (SR) 0.00000000 -0.37904526 -0.37904526 0.00000000 0.00000000 0.00000000 0.00000000 25.41646112 25.41646112 vdw total 25.41654480 25.41626747 -0.00027733 25.41626782 -0.00027698 25.41649713 -0.00004767 25.41646112 -0.00008368 vdw-14 25.79561520 25.79531273 -0.00030247 0.00000000 -25.79561520 25.79546579 -0.00014941 0.00000000 -25.79561520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 7.96800960 7.96786359 -0.00014601 7.96786358 -0.00014602 7.96755325 -0.00045635 7.96800960 0.00000000 bond 3.70535040 3.70537967 0.00002927 3.70537969 0.00002929 3.70618584 0.00083544 3.70539224 0.00004184 bonded 18.18491920 18.18476613 -0.00015307 18.18476607 -0.00015313 18.18525641 0.00033721 18.18491920 -0.00000000 dihedral 6.51155920 6.51152287 -0.00003633 6.51152280 -0.00003640 6.51151732 -0.00004188 6.51151736 -0.00004184 nonbonded -29.78087520 -29.78305528 -0.00218008 -29.78305423 -0.00217903 -29.78281065 -0.00193545 -29.88346688 -0.10259168 potential -11.59595600 -11.59828915 -0.00233315 -11.59828816 -0.00233216 -11.59763433 -0.00167833 -11.69854768 -0.10259168 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -11.59595600 Difference in potential energy from amber=>gromacs conversion: -0.00233315 Difference in potential energy from amber=>lammps conversion: -0.00233216 Difference in potential energy from amber=>desmond conversion: -0.00167833 Difference in potential energy from amber=>charmm conversion: -0.10259168 ======================================================================= INFO 2017-03-18 22:45:04 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2636578.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2636578.inpcrd') INFO 2017-03-18 22:45:05 Beginning InterMol conversion INFO 2017-03-18 22:45:05 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:45:05 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:45:05 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2659552.inpcrd INFO 2017-03-18 22:45:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2659552/mobley_2659552_converted.input INFO 2017-03-18 22:45:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2659552/mobley_2659552_converted.cms WARNING 2017-03-18 22:45:20 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:45:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2659552/mobley_2659552_converted.inp INFO 2017-03-18 22:45:20 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2659552/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2659552/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2659552/mobley_2659552_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2659552/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -104.98645585 -104.98645585 0.00000000 0.00000000 0.00000000 0.00000000 1.82434952 1.82434952 coulomb total 1.84639920 1.83706577 -0.00933343 1.83706574 -0.00933346 1.83702871 -0.00937049 1.82434952 -0.02204968 coulomb-14 106.83216400 106.82352162 -0.00864238 0.00000000 -106.83216400 106.82345417 -0.00870983 0.00000000 -106.83216400 improper 0.00000000 0.01259444 0.01259444 0.00000000 0.00000000 0.00000000 0.00000000 0.01259384 0.01259384 proper 33.48915440 33.47664782 -0.01250658 33.48924268 0.00008828 33.48926197 0.00010757 33.47664424 -0.01251016 vdw (SR) 0.00000000 -5.10679493 -5.10679493 0.00000000 0.00000000 0.00000000 0.00000000 21.22547384 21.22547384 vdw total 21.22585040 21.22540378 -0.00044662 21.22540397 -0.00044643 21.22528276 -0.00056764 21.22547384 -0.00037656 vdw-14 26.33242240 26.33219871 -0.00022369 0.00000000 -26.33242240 26.33212998 -0.00029242 0.00000000 -26.33242240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.86638640 5.86655984 0.00017344 5.86656004 0.00017364 5.86643585 0.00004945 5.86655376 0.00016736 bond 12.88672000 12.88652995 -0.00019005 12.88653005 -0.00018995 12.88521811 -0.00150189 12.88651080 -0.00020920 bonded 52.24226080 52.24233205 0.00007125 52.24233276 0.00007196 52.24091594 -0.00134486 52.24230264 0.00004184 dihedral 33.48915440 33.48924226 0.00008786 33.48924268 0.00008828 33.48926197 0.00010757 33.48923808 0.00008368 nonbonded 23.07224960 23.06246955 -0.00978005 23.06246950 -0.00978010 23.06231147 -0.00993813 23.04982336 -0.02242624 potential 75.31451040 75.30480160 -0.00970880 75.30480352 -0.00970688 75.30310816 -0.01140224 75.29212600 -0.02238440 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 75.31451040 Difference in potential energy from amber=>gromacs conversion: -0.00970880 Difference in potential energy from amber=>lammps conversion: -0.00970688 Difference in potential energy from amber=>desmond conversion: -0.01140224 Difference in potential energy from amber=>charmm conversion: -0.02238440 ======================================================================= INFO 2017-03-18 22:45:20 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2659552.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2659552.inpcrd') INFO 2017-03-18 22:45:21 Beginning InterMol conversion INFO 2017-03-18 22:45:21 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:45:21 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2661134.inpcrd INFO 2017-03-18 22:45:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2661134/mobley_2661134_converted.input INFO 2017-03-18 22:45:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2661134/mobley_2661134_converted.cms INFO 2017-03-18 22:45:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2661134/mobley_2661134_converted.rst7 WARNING 2017-03-18 22:45:36 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:45:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2661134/mobley_2661134_converted.inp INFO 2017-03-18 22:45:37 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2661134/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2661134/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2661134/mobley_2661134_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_2661134/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2661134/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 26.28975231 26.28975231 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -45.23201064 -45.23201064 coulomb total -45.21941680 -45.22783081 -0.00841401 -45.22783082 -0.00841402 -45.22841370 -0.00899690 -45.21941680 0.00000000 -45.23201064 -0.01259384 coulomb-14 -71.51502000 -71.51758312 -0.00256312 0.00000000 71.51502000 -71.51754379 -0.00252379 -71.51502000 0.00000000 0.00000000 71.51502000 improper 0.00000000 0.00006662 0.00006662 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00083680 0.00058328 -0.00025352 0.00064987 -0.00018693 0.00064591 -0.00019089 0.00083680 0.00000000 0.00058576 -0.00025104 vdw (SR) 0.00000000 -2.70775892 -2.70775892 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 14.01916144 14.01916144 vdw total 14.01891040 14.01914842 0.00023802 14.01914847 0.00023807 14.01922405 0.00031365 14.01891040 0.00000000 14.01916144 0.00025104 vdw-14 16.72679520 16.72690734 0.00011214 0.00000000 -16.72679520 16.72699034 0.00019514 16.72679520 0.00000000 0.00000000 -16.72679520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.48074160 0.20319141 -0.27755019 0.20319141 -0.27755019 0.20318165 -0.27755995 0.48074160 0.00000000 0.20321688 -0.27752472 bond 2.41458640 2.41442114 -0.00016526 2.41442113 -0.00016527 2.41337132 -0.00121508 2.41458640 0.00000000 2.41441904 -0.00016736 bonded 2.89616480 2.61826244 -0.27790236 2.61826241 -0.27790239 2.61719888 -0.27896592 2.89616480 0.00000000 2.61830536 -0.27785944 dihedral 0.00083680 0.00064990 -0.00018690 0.00064987 -0.00018693 0.00064591 -0.00019089 0.00083680 0.00000000 0.00066944 -0.00016736 nonbonded -31.20050640 -31.20868239 -0.00817599 -31.20868194 -0.00817554 -31.20918965 -0.00868325 -31.20050640 0.00000000 -31.21284920 -0.01234280 potential -28.30434160 -28.59041995 -0.28607835 -28.59041925 -0.28607765 -28.59204319 -0.28770159 -28.30434160 0.00000000 -28.59458568 -0.29024408 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -28.30434160 Difference in potential energy from amber=>gromacs conversion: -0.28607835 Difference in potential energy from amber=>lammps conversion: -0.28607765 Difference in potential energy from amber=>desmond conversion: -0.28770159 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.29024408 ======================================================================= INFO 2017-03-18 22:45:37 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2661134.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2661134.inpcrd') INFO 2017-03-18 22:45:37 Beginning InterMol conversion INFO 2017-03-18 22:45:37 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:45:37 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2681549.inpcrd INFO 2017-03-18 22:45:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2681549/mobley_2681549_converted.input INFO 2017-03-18 22:45:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2681549/mobley_2681549_converted.cms INFO 2017-03-18 22:45:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2681549/mobley_2681549_converted.rst7 WARNING 2017-03-18 22:45:53 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:45:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2681549/mobley_2681549_converted.inp INFO 2017-03-18 22:45:53 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2681549/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2681549/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2681549/mobley_2681549_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_2681549/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2681549/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 35.45099760 35.45099760 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -44.32617464 -44.32617464 coulomb total -44.31818320 -44.31261804 0.00556516 -44.31261848 0.00556472 -44.31259827 0.00558493 -44.31818320 0.00000000 -44.32617464 -0.00799144 coulomb-14 -79.76293920 -79.76361564 -0.00067644 0.00000000 79.76293920 -79.76359483 -0.00065563 -79.76293920 0.00000000 0.00000000 79.76293920 improper 0.00000000 0.00002704 0.00002704 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00026803 -0.00015037 0.00029506 -0.00012334 0.00029926 -0.00011914 0.00041840 0.00000000 0.00025104 -0.00016736 vdw (SR) 0.00000000 -2.48190618 -2.48190618 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 13.42787856 13.42787856 vdw total 13.42771120 13.42787549 0.00016429 13.42787563 0.00016443 13.42792756 0.00021636 13.42771120 0.00000000 13.42787856 0.00016736 vdw-14 15.90966000 15.90978167 0.00012167 0.00000000 -15.90966000 15.90982736 0.00016736 15.90966000 0.00000000 0.00000000 -15.90966000 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.16945200 0.16927237 -0.00017963 0.16927237 -0.00017963 0.16922444 -0.00022756 0.16945200 0.00000000 0.16928464 -0.00016736 bond 0.98031120 0.98023339 -0.00007781 0.98023338 -0.00007782 0.97989311 -0.00041809 0.98031120 0.00000000 0.98022752 -0.00008368 bonded 1.15018160 1.14980083 -0.00038077 1.14980081 -0.00038079 1.14941681 -0.00076479 1.15018160 0.00000000 1.14980504 -0.00037656 dihedral 0.00041840 0.00029507 -0.00012333 0.00029506 -0.00012334 0.00029926 -0.00011914 0.00041840 0.00000000 0.00029288 -0.00012552 nonbonded -30.89047200 -30.88474255 0.00572945 -30.88474201 0.00572999 -30.88467071 0.00580129 -30.89047200 0.00000000 -30.89829608 -0.00782408 potential -29.74029040 -29.73494172 0.00534868 -29.73494116 0.00534924 -29.73532742 0.00496298 -29.74029040 0.00000000 -29.74849104 -0.00820064 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -29.74029040 Difference in potential energy from amber=>gromacs conversion: 0.00534868 Difference in potential energy from amber=>lammps conversion: 0.00534924 Difference in potential energy from amber=>desmond conversion: 0.00496298 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.00820064 ======================================================================= INFO 2017-03-18 22:45:53 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2681549.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2681549.inpcrd') INFO 2017-03-18 22:45:53 Beginning InterMol conversion INFO 2017-03-18 22:45:53 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:45:53 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:45:53 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2689721.inpcrd INFO 2017-03-18 22:45:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2689721/mobley_2689721_converted.input INFO 2017-03-18 22:45:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2689721/mobley_2689721_converted.cms WARNING 2017-03-18 22:46:09 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:46:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2689721/mobley_2689721_converted.inp INFO 2017-03-18 22:46:09 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2689721/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2689721/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2689721/mobley_2689721_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2689721/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 5.88917798 5.88917798 0.00000000 0.00000000 0.00000000 0.00000000 2.42479536 2.42479536 coulomb total 2.38906400 2.42049367 0.03142967 2.42049366 0.03142966 2.42049839 0.03143439 2.42479536 0.03573136 coulomb-14 -3.47690400 -3.46868431 0.00821969 0.00000000 3.47690400 -3.46868194 0.00822206 0.00000000 3.47690400 proper 11.90264320 11.90243659 -0.00020661 11.90243651 -0.00020669 11.90235919 -0.00028401 11.90243400 -0.00020920 vdw (SR) 0.00000000 -2.36041778 -2.36041778 0.00000000 0.00000000 0.00000000 0.00000000 10.27607136 10.27607136 vdw total 10.27590400 10.27601347 0.00010947 10.27601404 0.00011004 10.27616061 0.00025661 10.27607136 0.00016736 vdw-14 12.63651680 12.63643125 -0.00008555 0.00000000 -12.63651680 12.63657295 0.00005615 0.00000000 -12.63651680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.49494320 1.49511353 0.00017033 1.49511353 0.00017033 1.49529485 0.00035165 1.49502688 0.00008368 bond 0.95353360 0.95370231 0.00016871 0.95370230 0.00016870 0.95372600 0.00019240 0.95370096 0.00016736 bonded 14.35112000 14.35125244 0.00013244 14.35125234 0.00013234 14.35138004 0.00026004 14.35116184 0.00004184 dihedral 11.90264320 11.90243659 -0.00020661 11.90243651 -0.00020669 11.90235919 -0.00028401 11.90243400 -0.00020920 nonbonded 12.66496800 12.69650714 0.03153914 12.69650741 0.03153941 12.69665900 0.03169100 12.70086672 0.03589872 potential 27.01608800 27.04775958 0.03167158 27.04776004 0.03167204 27.04799376 0.03190576 27.05207040 0.03598240 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 27.01608800 Difference in potential energy from amber=>gromacs conversion: 0.03167158 Difference in potential energy from amber=>lammps conversion: 0.03167204 Difference in potential energy from amber=>desmond conversion: 0.03190576 Difference in potential energy from amber=>charmm conversion: 0.03598240 ======================================================================= INFO 2017-03-18 22:46:09 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2689721.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2689721.inpcrd') INFO 2017-03-18 22:46:09 Beginning InterMol conversion INFO 2017-03-18 22:46:09 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:46:09 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:46:09 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2693089.inpcrd INFO 2017-03-18 22:46:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2693089/mobley_2693089_converted.input INFO 2017-03-18 22:46:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2693089/mobley_2693089_converted.cms WARNING 2017-03-18 22:46:25 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:46:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2693089/mobley_2693089_converted.inp INFO 2017-03-18 22:46:25 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2693089/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2693089/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2693089/mobley_2693089_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2693089/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 28.23793151 28.23793151 0.00000000 0.00000000 0.00000000 0.00000000 224.51498808 224.51498808 coulomb total 224.50298000 224.50833175 0.00535175 224.50832715 0.00534715 224.50851342 0.00553342 224.51498808 0.01200808 coulomb-14 196.26098000 196.27040024 0.00942024 0.00000000 -196.26098000 196.27066722 0.00968722 0.00000000 -196.26098000 improper 0.00000000 0.00005807 0.00005807 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.11171280 0.11185581 0.00014301 0.11191385 0.00020105 0.11191981 0.00020701 0.11183832 0.00012552 vdw (SR) 0.00000000 -2.86941151 -2.86941151 0.00000000 0.00000000 0.00000000 0.00000000 29.19356712 29.19356712 vdw total 29.19344160 29.19356484 0.00012324 29.19356503 0.00012343 29.19373317 0.00029157 29.19356712 0.00012552 vdw-14 32.06282880 32.06297635 0.00014755 0.00000000 -32.06282880 32.06313452 0.00030572 0.00000000 -32.06282880 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.84051760 2.84063855 0.00012095 2.84063856 0.00012096 2.84073011 0.00021251 2.84060128 0.00008368 bond 1.12131200 1.12111738 -0.00019462 1.12111736 -0.00019464 1.12109228 -0.00021972 1.12110280 -0.00020920 bonded 4.07354240 4.07366981 0.00012741 4.07366977 0.00012737 4.07374219 0.00019979 4.07358424 0.00004184 dihedral 0.11171280 0.11191388 0.00020108 0.11191385 0.00020105 0.11191981 0.00020701 0.11188016 0.00016736 nonbonded 253.69642160 253.70189659 0.00547499 253.70189427 0.00547267 253.70224659 0.00582499 253.70855520 0.01213360 potential 257.76996400 257.77556640 0.00560240 257.77556219 0.00559819 257.77588478 0.00592078 257.78222312 0.01225912 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 257.76996400 Difference in potential energy from amber=>gromacs conversion: 0.00560240 Difference in potential energy from amber=>lammps conversion: 0.00559819 Difference in potential energy from amber=>desmond conversion: 0.00592078 Difference in potential energy from amber=>charmm conversion: 0.01225912 ======================================================================= INFO 2017-03-18 22:46:25 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2693089.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2693089.inpcrd') INFO 2017-03-18 22:46:25 Beginning InterMol conversion INFO 2017-03-18 22:46:25 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:46:25 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:46:25 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2725215.inpcrd INFO 2017-03-18 22:46:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2725215/mobley_2725215_converted.input INFO 2017-03-18 22:46:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2725215/mobley_2725215_converted.cms WARNING 2017-03-18 22:46:41 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:46:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2725215/mobley_2725215_converted.inp INFO 2017-03-18 22:46:41 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2725215/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2725215/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2725215/mobley_2725215_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2725215/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 247.83508573 247.83508573 0.00000000 0.00000000 0.00000000 0.00000000 -420.49061928 -420.49061928 coulomb total -420.35392800 -420.36840290 -0.01447490 -420.36840464 -0.01447664 -420.36769336 -0.01376536 -420.49061928 -0.13669128 coulomb-14 -668.18061600 -668.20348863 -0.02287263 0.00000000 668.18061600 -668.20311755 -0.02250155 0.00000000 668.18061600 improper 0.00000000 0.00143863 0.00143863 0.00000000 0.00000000 0.00000000 0.00000000 0.00142256 0.00142256 proper 104.66610720 104.66449378 -0.00161342 104.66593147 -0.00017573 104.66588754 -0.00021966 104.66447544 -0.00163176 vdw (SR) 0.00000000 -19.36197631 -19.36197631 0.00000000 0.00000000 0.00000000 0.00000000 15.83794624 15.83794624 vdw total 15.83769520 15.83766545 -0.00002975 15.83766549 -0.00002971 15.83718329 -0.00051191 15.83794624 0.00025104 vdw-14 35.19957360 35.19964176 0.00006816 0.00000000 -35.19957360 35.19950410 -0.00006950 0.00000000 -35.19957360 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 12.91935520 12.91927092 -0.00008428 12.91927110 -0.00008410 12.92026187 0.00090667 12.91927152 -0.00008368 bond 28.63487760 28.63481491 -0.00006269 28.63481484 -0.00006276 28.63726963 0.00239203 28.63483576 -0.00004184 bonded 146.22034000 146.22001824 -0.00032176 146.22001741 -0.00032259 146.22341905 0.00307905 146.22000528 -0.00033472 dihedral 104.66610720 104.66593241 -0.00017479 104.66593147 -0.00017573 104.66588754 -0.00021966 104.66589800 -0.00020920 nonbonded -404.51623280 -404.53073746 -0.01450466 -404.53073454 -0.01450174 -404.53051007 -0.01427727 -404.65267304 -0.13644024 potential -258.29589280 -258.31071922 -0.01482642 -258.31071253 -0.01481973 -258.30750842 -0.01161562 -258.43266776 -0.13677496 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -258.29589280 Difference in potential energy from amber=>gromacs conversion: -0.01482642 Difference in potential energy from amber=>lammps conversion: -0.01481973 Difference in potential energy from amber=>desmond conversion: -0.01161562 Difference in potential energy from amber=>charmm conversion: -0.13677496 ======================================================================= INFO 2017-03-18 22:46:41 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2725215.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2725215.inpcrd') INFO 2017-03-18 22:46:41 Beginning InterMol conversion INFO 2017-03-18 22:46:41 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:46:42 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:46:42 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2725802.inpcrd INFO 2017-03-18 22:46:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2725802/mobley_2725802_converted.input INFO 2017-03-18 22:46:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2725802/mobley_2725802_converted.cms WARNING 2017-03-18 22:46:57 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:46:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2725802/mobley_2725802_converted.inp INFO 2017-03-18 22:46:57 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2725802/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2725802/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2725802/mobley_2725802_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2725802/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 24.76866708 24.76866708 0.00000000 0.00000000 0.00000000 0.00000000 -120.75413112 -120.75413112 coulomb total -120.74605600 -120.75169404 -0.00563804 -120.75169185 -0.00563585 -120.75176628 -0.00571028 -120.75413112 -0.00807512 coulomb-14 -145.51449920 -145.52036113 -0.00586193 0.00000000 145.51449920 -145.52045136 -0.00595216 0.00000000 145.51449920 improper 0.00000000 0.00316014 0.00316014 0.00000000 0.00000000 0.00000000 0.00000000 0.00317984 0.00317984 proper 27.77506560 27.77198809 -0.00307751 27.77514175 0.00007615 27.77495468 -0.00011092 27.77468904 -0.00037656 vdw (SR) 0.00000000 2.27924508 2.27924508 0.00000000 0.00000000 0.00000000 0.00000000 10.04084688 10.04084688 vdw total 10.04118160 10.04074734 -0.00043426 10.04074772 -0.00043388 10.04101734 -0.00016426 10.04084688 -0.00033472 vdw-14 7.76173840 7.76150225 -0.00023615 0.00000000 -7.76173840 7.76161129 -0.00012711 0.00000000 -7.76173840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 28.58969040 28.58969701 0.00000661 28.58969709 0.00000669 28.58934765 -0.00034275 28.58956488 -0.00012552 bond 4.29780480 4.29782443 0.00001963 4.29782446 0.00001966 4.29784995 0.00004515 4.29780480 0.00000000 bonded 60.66256080 60.66266968 0.00010888 60.66266331 0.00010251 60.66215227 -0.00040853 60.66523856 0.00267776 dihedral 27.77506560 27.77514823 0.00008263 27.77514175 0.00007615 27.77495468 -0.00011092 27.77786888 0.00280328 nonbonded -110.70487440 -110.71094671 -0.00607231 -110.71094538 -0.00607098 -110.71074895 -0.00587455 -110.71328424 -0.00840984 potential -50.04231360 -50.04827703 -0.00596343 -50.04827998 -0.00596638 -50.04865905 -0.00634545 -50.04804568 -0.00573208 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -50.04231360 Difference in potential energy from amber=>gromacs conversion: -0.00596343 Difference in potential energy from amber=>lammps conversion: -0.00596638 Difference in potential energy from amber=>desmond conversion: -0.00634545 Difference in potential energy from amber=>charmm conversion: -0.00573208 ======================================================================= INFO 2017-03-18 22:46:57 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2725802.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2725802.inpcrd') INFO 2017-03-18 22:46:58 Beginning InterMol conversion INFO 2017-03-18 22:46:58 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:46:58 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:46:58 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2727678.inpcrd INFO 2017-03-18 22:46:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2727678/mobley_2727678_converted.input INFO 2017-03-18 22:46:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2727678/mobley_2727678_converted.cms WARNING 2017-03-18 22:47:13 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:47:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2727678/mobley_2727678_converted.inp INFO 2017-03-18 22:47:13 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2727678/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2727678/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2727678/mobley_2727678_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2727678/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 238.89645208 238.89645208 0.00000000 0.00000000 0.00000000 0.00000000 -659.11183784 -659.11183784 coulomb total -659.06953760 -659.09478543 -0.02524783 -659.09476712 -0.02522952 -659.09508929 -0.02555169 -659.11183784 -0.04230024 coulomb-14 -897.96045680 -897.99123752 -0.03078072 0.00000000 897.96045680 -897.99148116 -0.03102436 0.00000000 897.96045680 improper 0.00000000 0.00017616 0.00017616 0.00000000 0.00000000 0.00000000 0.00000000 0.00016736 0.00016736 proper 50.20841840 50.20819847 -0.00021993 50.20837238 -0.00004602 50.20836652 -0.00005188 50.20820920 -0.00020920 vdw (SR) 0.00000000 -2.08689180 -2.08689180 0.00000000 0.00000000 0.00000000 0.00000000 13.51026152 13.51026152 vdw total 13.51013600 13.51028123 0.00014523 13.51028118 0.00014518 13.51076011 0.00062411 13.51026152 0.00012552 vdw-14 15.59711520 15.59717303 0.00005783 0.00000000 -15.59711520 15.59765640 0.00054120 0.00000000 -15.59711520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 12.15075440 12.15085561 0.00010121 12.15085565 0.00010125 12.15129091 0.00053651 12.15083808 0.00008368 bond 28.96499520 28.96514326 0.00014806 28.96514331 0.00014811 28.96392912 -0.00106608 28.96516256 0.00016736 bonded 91.32416800 91.32437350 0.00020550 91.32437134 0.00020334 91.32358655 -0.00058145 91.32437720 0.00020920 dihedral 50.20841840 50.20837463 -0.00004377 50.20837238 -0.00004602 50.20836652 -0.00005188 50.20837656 -0.00004184 nonbonded -645.55940160 -645.58450420 -0.02510260 -645.58450560 -0.02510400 -645.58432918 -0.02492758 -645.60157632 -0.04217472 potential -554.23523360 -554.26013070 -0.02489710 -554.26012840 -0.02489480 -554.26079366 -0.02556006 -554.27724096 -0.04200736 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -554.23523360 Difference in potential energy from amber=>gromacs conversion: -0.02489710 Difference in potential energy from amber=>lammps conversion: -0.02489480 Difference in potential energy from amber=>desmond conversion: -0.02556006 Difference in potential energy from amber=>charmm conversion: -0.04200736 ======================================================================= INFO 2017-03-18 22:47:13 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2727678.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2727678.inpcrd') INFO 2017-03-18 22:47:14 Beginning InterMol conversion INFO 2017-03-18 22:47:14 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:47:14 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2751110.inpcrd INFO 2017-03-18 22:47:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2751110/mobley_2751110_converted.input INFO 2017-03-18 22:47:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2751110/mobley_2751110_converted.cms INFO 2017-03-18 22:47:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2751110/mobley_2751110_converted.rst7 WARNING 2017-03-18 22:47:29 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:47:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2751110/mobley_2751110_converted.inp INFO 2017-03-18 22:47:29 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2751110/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2751110/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2751110/mobley_2751110_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_2751110/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2751110/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 41.45627775 41.45627775 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -85.34703112 -85.34703112 coulomb total -85.32975120 -85.33266967 -0.00291847 -85.33266745 -0.00291625 -85.33303564 -0.00328444 -85.32975120 0.00000000 -85.34703112 -0.01727992 coulomb-14 -126.78440480 -126.78894742 -0.00454262 0.00000000 126.78440480 -126.78889256 -0.00448776 -126.78440480 0.00000000 0.00000000 126.78440480 improper 0.00000000 0.00007195 0.00007195 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00083680 0.00086784 0.00003104 0.00093975 0.00010295 0.00094143 0.00010463 0.00083680 0.00000000 0.00087864 0.00004184 vdw (SR) 0.00000000 1.68355655 1.68355655 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 26.01025440 26.01025440 vdw total 26.01025440 26.01018354 -0.00007086 26.01018369 -0.00007071 26.01020948 -0.00004492 26.01025440 0.00000000 26.01025440 0.00000000 vdw-14 24.32661280 24.32662698 0.00001418 0.00000000 -24.32661280 24.32669995 0.00008715 24.32661280 0.00000000 0.00000000 -24.32661280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.32925680 1.32924561 -0.00001119 1.32924563 -0.00001117 1.32954454 0.00028774 1.32925680 0.00000000 1.32925680 0.00000000 bond 11.92691040 11.92691487 0.00000447 11.92691500 0.00000460 11.92678287 -0.00012753 11.92691040 0.00000000 11.92691040 0.00000000 bonded 13.25700400 13.25710027 0.00009627 13.25710038 0.00009638 13.25726884 0.00026484 13.25700400 0.00000000 13.25712952 0.00012552 dihedral 0.00083680 0.00093979 0.00010299 0.00093975 0.00010295 0.00094143 0.00010463 0.00083680 0.00000000 0.00096232 0.00012552 nonbonded -59.31949680 -59.32248613 -0.00298933 -59.32248418 -0.00298738 -59.32282616 -0.00332936 -59.31949680 0.00000000 -59.33677672 -0.01727992 potential -46.06249280 -46.06538586 -0.00289306 -46.06538394 -0.00289114 -46.06561448 -0.00312168 -46.06249280 0.00000000 -46.07968904 -0.01719624 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -46.06249280 Difference in potential energy from amber=>gromacs conversion: -0.00289306 Difference in potential energy from amber=>lammps conversion: -0.00289114 Difference in potential energy from amber=>desmond conversion: -0.00312168 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.01719624 ======================================================================= INFO 2017-03-18 22:47:29 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2751110.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2751110.inpcrd') INFO 2017-03-18 22:47:30 Beginning InterMol conversion INFO 2017-03-18 22:47:30 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:47:30 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:47:30 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2763835.inpcrd INFO 2017-03-18 22:47:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2763835/mobley_2763835_converted.input INFO 2017-03-18 22:47:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2763835/mobley_2763835_converted.cms WARNING 2017-03-18 22:47:45 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:47:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2763835/mobley_2763835_converted.inp INFO 2017-03-18 22:47:46 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2763835/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2763835/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2763835/mobley_2763835_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2763835/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 11.17464211 11.17464211 0.00000000 0.00000000 0.00000000 0.00000000 -44.61754840 -44.61754840 coulomb total -44.60353200 -44.61043750 -0.00690550 -44.61043560 -0.00690360 -44.61048409 -0.00695209 -44.61754840 -0.01401640 coulomb-14 -55.78359840 -55.78507962 -0.00148122 0.00000000 55.78359840 -55.78507159 -0.00147319 0.00000000 55.78359840 improper 0.00000000 0.00010929 0.00010929 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 11.72607840 11.72583494 -0.00024346 11.72593489 -0.00014351 11.72572477 -0.00035363 11.72540896 -0.00066944 vdw (SR) 0.00000000 3.97853236 3.97853236 0.00000000 0.00000000 0.00000000 0.00000000 28.02995488 28.02995488 vdw total 28.02987120 28.02992249 0.00005129 28.02992266 0.00005146 28.02993376 0.00006256 28.02995488 0.00008368 vdw-14 24.05130560 24.05139013 0.00008453 0.00000000 -24.05130560 24.05142284 0.00011724 0.00000000 -24.05130560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.52843920 0.52864194 0.00020274 0.52864196 0.00020276 0.52861738 0.00017818 0.52864840 0.00020920 bond 1.84556240 1.84547360 -0.00008880 1.84547362 -0.00008878 1.84577873 0.00021633 1.84547872 -0.00008368 bonded 14.10008000 14.10005977 -0.00002023 14.10005046 -0.00002954 14.10012088 0.00004088 14.09966160 -0.00041840 dihedral 11.72607840 11.72594423 -0.00013417 11.72593489 -0.00014351 11.72572477 -0.00035363 11.72553448 -0.00054392 nonbonded -16.57366080 -16.58051501 -0.00685421 -16.58051419 -0.00685339 -16.58055033 -0.00688953 -16.58759352 -0.01393272 potential -2.47358080 -2.48045525 -0.00687445 -2.48046373 -0.00688293 -2.48048799 -0.00690719 -2.48793192 -0.01435112 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -2.47358080 Difference in potential energy from amber=>gromacs conversion: -0.00687445 Difference in potential energy from amber=>lammps conversion: -0.00688293 Difference in potential energy from amber=>desmond conversion: -0.00690719 Difference in potential energy from amber=>charmm conversion: -0.01435112 ======================================================================= INFO 2017-03-18 22:47:46 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2763835.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2763835.inpcrd') INFO 2017-03-18 22:47:46 Beginning InterMol conversion INFO 2017-03-18 22:47:46 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:47:46 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:47:46 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2771569.inpcrd INFO 2017-03-18 22:47:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2771569/mobley_2771569_converted.input INFO 2017-03-18 22:47:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2771569/mobley_2771569_converted.cms WARNING 2017-03-18 22:48:02 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:48:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2771569/mobley_2771569_converted.inp INFO 2017-03-18 22:48:02 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2771569/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2771569/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2771569/mobley_2771569_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2771569/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -64.95124825 -64.95124825 0.00000000 0.00000000 0.00000000 0.00000000 235.25380984 235.25380984 coulomb total 235.21025440 235.23229603 0.02204163 235.23229153 0.02203713 235.23218986 0.02193546 235.25380984 0.04355544 coulomb-14 300.17103840 300.18354428 0.01250588 0.00000000 -300.17103840 300.18348789 0.01244949 0.00000000 -300.17103840 proper 12.24029200 12.24041910 0.00012710 12.24041919 0.00012719 12.24038673 0.00009473 12.24054304 0.00025104 vdw (SR) 0.00000000 -2.95544221 -2.95544221 0.00000000 0.00000000 0.00000000 0.00000000 13.72046568 13.72046568 vdw total 13.72017280 13.72044354 0.00027074 13.72044392 0.00027112 13.72036826 0.00019546 13.72046568 0.00029288 vdw-14 16.67575040 16.67588575 0.00013535 0.00000000 -16.67575040 16.67580747 0.00005707 0.00000000 -16.67575040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.40663680 2.40681586 0.00017906 2.40681588 0.00017908 2.40679617 0.00015937 2.40672048 0.00008368 bond 0.43471760 0.43477322 0.00005562 0.43477321 0.00005561 0.43480152 0.00008392 0.43475944 0.00004184 bonded 15.08164640 15.08200817 0.00036177 15.08200827 0.00036187 15.08198442 0.00033802 15.08202296 0.00037656 dihedral 12.24029200 12.24041910 0.00012710 12.24041919 0.00012719 12.24038673 0.00009473 12.24054304 0.00025104 nonbonded 248.93042720 248.95273957 0.02231237 248.95273629 0.02230909 248.95255812 0.02213092 248.97427552 0.04384832 potential 264.01207360 264.03474775 0.02267415 264.03474670 0.02267310 264.03446888 0.02239528 264.05629848 0.04422488 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 264.01207360 Difference in potential energy from amber=>gromacs conversion: 0.02267415 Difference in potential energy from amber=>lammps conversion: 0.02267310 Difference in potential energy from amber=>desmond conversion: 0.02239528 Difference in potential energy from amber=>charmm conversion: 0.04422488 ======================================================================= INFO 2017-03-18 22:48:02 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2771569.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2771569.inpcrd') INFO 2017-03-18 22:48:02 Beginning InterMol conversion INFO 2017-03-18 22:48:02 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:48:02 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:48:02 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2782339.inpcrd INFO 2017-03-18 22:48:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2782339/mobley_2782339_converted.input INFO 2017-03-18 22:48:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2782339/mobley_2782339_converted.cms WARNING 2017-03-18 22:48:18 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:48:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2782339/mobley_2782339_converted.inp INFO 2017-03-18 22:48:18 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2782339/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2782339/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2782339/mobley_2782339_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2782339/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 68.81009646 68.81009646 0.00000000 0.00000000 0.00000000 0.00000000 -295.77411464 -295.77411464 coulomb total -295.79666640 -295.80654678 -0.00988038 -295.80654482 -0.00987842 -295.80676156 -0.01009516 -295.77411464 0.02255176 coulomb-14 -364.60422000 -364.61664324 -0.01242324 0.00000000 364.60422000 -364.61697576 -0.01275576 0.00000000 364.60422000 improper 0.00000000 0.00011587 0.00011587 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 33.47283680 33.47268106 -0.00015574 33.47279705 -0.00003975 33.47278931 -0.00004749 33.47266944 -0.00016736 vdw (SR) 0.00000000 -3.81126919 -3.81126919 0.00000000 0.00000000 0.00000000 0.00000000 11.34374448 11.34374448 vdw total 11.34366080 11.34376778 0.00010698 11.34376791 0.00010711 11.34395929 0.00029849 11.34374448 0.00008368 vdw-14 15.15486640 15.15503698 0.00017058 0.00000000 -15.15486640 15.15523568 0.00036928 0.00000000 -15.15486640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 90.84761040 90.84775599 0.00014559 90.84775684 0.00014644 90.84849113 0.00088073 90.84769408 0.00008368 bond 7.20066400 7.20059723 -0.00006677 7.20059706 -0.00006694 7.19932106 -0.00134294 7.20058032 -0.00008368 bonded 131.52111120 131.52115015 0.00003895 131.52115095 0.00003975 131.52060151 -0.00050969 131.52106936 -0.00004184 dihedral 33.47283680 33.47279693 -0.00003987 33.47279705 -0.00003975 33.47278931 -0.00004749 33.47279496 -0.00004184 nonbonded -284.45300560 -284.46277899 -0.00977339 -284.46277524 -0.00976964 -284.46280227 -0.00979667 -284.43037016 0.02263544 potential -152.93189440 -152.94162884 -0.00973444 -152.94162638 -0.00973198 -152.94227072 -0.01037632 -152.90925896 0.02263544 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -152.93189440 Difference in potential energy from amber=>gromacs conversion: -0.00973444 Difference in potential energy from amber=>lammps conversion: -0.00973198 Difference in potential energy from amber=>desmond conversion: -0.01037632 Difference in potential energy from amber=>charmm conversion: 0.02263544 ======================================================================= INFO 2017-03-18 22:48:18 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2782339.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2782339.inpcrd') INFO 2017-03-18 22:48:18 Beginning InterMol conversion INFO 2017-03-18 22:48:18 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:48:18 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:48:18 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2784376.inpcrd INFO 2017-03-18 22:48:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2784376/mobley_2784376_converted.input INFO 2017-03-18 22:48:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2784376/mobley_2784376_converted.cms WARNING 2017-03-18 22:48:34 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:48:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2784376/mobley_2784376_converted.inp INFO 2017-03-18 22:48:34 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2784376/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2784376/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2784376/mobley_2784376_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2784376/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 23.35195000 23.35195000 coulomb total 23.32370800 23.34736803 0.02366003 23.34736768 0.02365968 23.34735835 0.02365035 23.35195000 0.02824200 coulomb-14 23.32370800 23.34736803 0.02366003 0.00000000 -23.32370800 23.34735835 0.02365035 0.00000000 -23.32370800 proper 26.87759760 26.87740388 -0.00019372 26.87740388 -0.00019372 26.87739961 -0.00019799 26.88525432 0.00765672 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.22744224 0.22744224 vdw total 0.22760960 0.22743447 -0.00017513 0.22743447 -0.00017513 0.22743028 -0.00017932 0.22744224 -0.00016736 vdw-14 0.22760960 0.22743447 -0.00017513 0.00000000 -0.22760960 0.22743028 -0.00017932 0.00000000 -0.22760960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.02719600 0.02712123 -0.00007477 0.02712123 -0.00007477 0.02712525 -0.00007075 0.02711232 -0.00008368 bond 0.10083440 0.10063649 -0.00019791 0.10063648 -0.00019792 0.10061640 -0.00021800 0.10062520 -0.00020920 bonded 27.00562800 27.00516160 -0.00046640 27.00516159 -0.00046641 27.00514126 -0.00048674 27.01299184 0.00736384 dihedral 26.87759760 26.87740388 -0.00019372 26.87740388 -0.00019372 26.87739961 -0.00019799 26.88525432 0.00765672 nonbonded 23.55131760 23.57480250 0.02348490 23.57480239 0.02348479 23.57478863 0.02347103 23.57939224 0.02807464 potential 50.55694560 50.57996410 0.02301850 50.57996178 0.02301618 50.57991953 0.02297393 50.59238408 0.03543848 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 50.55694560 Difference in potential energy from amber=>gromacs conversion: 0.02301850 Difference in potential energy from amber=>lammps conversion: 0.02301618 Difference in potential energy from amber=>desmond conversion: 0.02297393 Difference in potential energy from amber=>charmm conversion: 0.03543848 ======================================================================= INFO 2017-03-18 22:48:34 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2784376.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2784376.inpcrd') INFO 2017-03-18 22:48:34 Beginning InterMol conversion INFO 2017-03-18 22:48:34 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:48:34 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2789243.inpcrd INFO 2017-03-18 22:48:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2789243/mobley_2789243_converted.input INFO 2017-03-18 22:48:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2789243/mobley_2789243_converted.cms INFO 2017-03-18 22:48:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2789243/mobley_2789243_converted.rst7 WARNING 2017-03-18 22:48:50 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:48:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2789243/mobley_2789243_converted.inp INFO 2017-03-18 22:48:50 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2789243/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2789243/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2789243/mobley_2789243_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_2789243/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2789243/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -25.10015596 -25.10015596 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -23.62629488 -23.62629488 coulomb total -23.61156720 -23.60307708 0.00849012 -23.60307661 0.00849059 -23.60319869 0.00836851 -23.61156720 0.00000000 -23.62629488 -0.01472768 coulomb-14 1.49159600 1.49707887 0.00548287 0.00000000 -1.49159600 1.49693990 0.00534390 1.49159600 0.00000000 0.00000000 -1.49159600 improper 0.00000000 0.00006998 0.00006998 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00083680 0.00064211 -0.00019469 0.00071210 -0.00012470 0.00071075 -0.00012605 0.00083680 0.00000000 0.00062760 -0.00020920 vdw (SR) 0.00000000 -0.98670718 -0.98670718 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 18.11985800 18.11985800 vdw total 18.12006720 18.11991842 -0.00014878 18.11991825 -0.00014895 18.12030417 0.00023697 18.12006720 0.00000000 18.11985800 -0.00020920 vdw-14 19.10665440 19.10662560 -0.00002880 0.00000000 -19.10665440 19.10701205 0.00035765 19.10665440 0.00000000 0.00000000 -19.10665440 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.88698400 1.88718211 0.00019811 1.88718211 0.00019811 1.88717597 0.00019197 1.88698400 0.00000000 1.88719320 0.00020920 bond 0.82759520 0.82764316 0.00004796 0.82764315 0.00004795 0.82727365 -0.00032155 0.82759520 0.00000000 0.82763704 0.00004184 bonded 2.71541600 2.71553736 0.00012136 2.71553736 0.00012136 2.71516037 -0.00025563 2.71541600 0.00000000 2.71554152 0.00012552 dihedral 0.00083680 0.00071209 -0.00012471 0.00071210 -0.00012470 0.00071075 -0.00012605 0.00083680 0.00000000 0.00071128 -0.00012552 nonbonded -5.49150000 -5.48315866 0.00834134 -5.48315836 0.00834164 -5.48289452 0.00860548 -5.49150000 0.00000000 -5.50643688 -0.01493688 potential -2.77608400 -2.76762130 0.00846270 -2.76762102 0.00846298 -2.76777658 0.00830742 -2.77608400 0.00000000 -2.79089536 -0.01481136 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -2.77608400 Difference in potential energy from amber=>gromacs conversion: 0.00846270 Difference in potential energy from amber=>lammps conversion: 0.00846298 Difference in potential energy from amber=>desmond conversion: 0.00830742 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.01481136 ======================================================================= INFO 2017-03-18 22:48:50 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2789243.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2789243.inpcrd') INFO 2017-03-18 22:48:50 Beginning InterMol conversion INFO 2017-03-18 22:48:50 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:48:50 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:48:50 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2792521.inpcrd INFO 2017-03-18 22:48:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2792521/mobley_2792521_converted.input INFO 2017-03-18 22:48:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2792521/mobley_2792521_converted.cms WARNING 2017-03-18 22:49:06 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:49:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2792521/mobley_2792521_converted.inp INFO 2017-03-18 22:49:06 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2792521/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2792521/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2792521/mobley_2792521_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2792521/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -2.43409018 -2.43409018 0.00000000 0.00000000 0.00000000 0.00000000 -3.51732144 -3.51732144 coulomb total -3.52083600 -3.50930014 0.01153586 -3.50930008 0.01153592 -3.50932454 0.01151146 -3.51732144 0.00351456 coulomb-14 -1.07905360 -1.07520996 0.00384364 0.00000000 1.07905360 -1.07513213 0.00392147 0.00000000 1.07905360 improper 0.00000000 0.00113964 0.00113964 0.00000000 0.00000000 0.00000000 0.00000000 0.00112968 0.00112968 proper 0.05188160 0.05081212 -0.00106948 0.05195134 0.00006974 0.05195181 0.00007021 0.05079376 -0.00108784 vdw (SR) 0.00000000 -1.65859658 -1.65859658 0.00000000 0.00000000 0.00000000 0.00000000 3.41498080 3.41498080 vdw total 3.41498080 3.41491576 -0.00006504 3.41491578 -0.00006502 3.41492207 -0.00005873 3.41498080 0.00000000 vdw-14 5.07351840 5.07351234 -0.00000606 0.00000000 -5.07351840 5.07352568 0.00000728 0.00000000 -5.07351840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.43804080 1.43818280 0.00014200 1.43818280 0.00014200 1.43850685 0.00046605 1.43816632 0.00012552 bond 0.97068800 0.97050507 -0.00018293 0.97050508 -0.00018292 0.97102646 0.00033846 0.97052064 -0.00016736 bonded 2.46061040 2.46063962 0.00002922 2.46063922 0.00002882 2.46148511 0.00087471 2.46061040 -0.00000000 dihedral 0.05188160 0.05195176 0.00007016 0.05195134 0.00006974 0.05195181 0.00007021 0.05192344 0.00004184 nonbonded -0.10585520 -0.09438439 0.01147081 -0.09438432 0.01147088 -0.09440247 0.01145273 -0.10234064 0.00351456 potential 2.35475520 2.36625523 0.01150003 2.36625488 0.01149968 2.36703980 0.01228460 2.35831160 0.00355640 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 2.35475520 Difference in potential energy from amber=>gromacs conversion: 0.01150003 Difference in potential energy from amber=>lammps conversion: 0.01149968 Difference in potential energy from amber=>desmond conversion: 0.01228460 Difference in potential energy from amber=>charmm conversion: 0.00355640 ======================================================================= INFO 2017-03-18 22:49:06 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2792521.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2792521.inpcrd') INFO 2017-03-18 22:49:06 Beginning InterMol conversion INFO 2017-03-18 22:49:06 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:49:06 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:49:06 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2802855.inpcrd INFO 2017-03-18 22:49:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2802855/mobley_2802855_converted.input INFO 2017-03-18 22:49:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2802855/mobley_2802855_converted.cms WARNING 2017-03-18 22:49:22 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:49:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2802855/mobley_2802855_converted.inp INFO 2017-03-18 22:49:22 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2802855/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2802855/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2802855/mobley_2802855_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2802855/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 6.26818832 6.26818832 0.00000000 0.00000000 0.00000000 0.00000000 4.09032024 4.09032024 coulomb total 4.09278880 4.08762191 -0.00516689 4.08762185 -0.00516695 4.08759674 -0.00519206 4.09032024 -0.00246856 coulomb-14 -2.17819040 -2.18056641 -0.00237601 0.00000000 2.17819040 -2.18057533 -0.00238493 0.00000000 2.17819040 proper 8.73284480 8.73301938 0.00017458 8.73301927 0.00017447 8.73302392 0.00017912 8.73301216 0.00016736 vdw (SR) 0.00000000 -1.16317828 -1.16317828 0.00000000 0.00000000 0.00000000 0.00000000 2.00254608 2.00254608 vdw total 2.00246240 2.00248639 0.00002399 2.00248642 0.00002402 2.00256382 0.00010142 2.00254608 0.00008368 vdw-14 3.16561440 3.16566467 0.00005027 0.00000000 -3.16561440 3.16574217 0.00012777 0.00000000 -3.16561440 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.39575840 2.39584784 0.00008944 2.39584785 0.00008945 2.39587875 0.00012035 2.39588392 0.00012552 bond 1.12507760 1.12513047 0.00005287 1.12513049 0.00005289 1.12488788 -0.00018972 1.12511944 0.00004184 bonded 12.25368080 12.25399770 0.00031690 12.25399761 0.00031681 12.25379055 0.00010975 12.25401552 0.00033472 dihedral 8.73284480 8.73301938 0.00017458 8.73301927 0.00017447 8.73302392 0.00017912 8.73301216 0.00016736 nonbonded 6.09525120 6.09010830 -0.00514290 6.09010823 -0.00514297 6.09016056 -0.00509064 6.09286632 -0.00238488 potential 18.34893200 18.34410600 -0.00482600 18.34410617 -0.00482583 18.34391045 -0.00502155 18.34688184 -0.00205016 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 18.34893200 Difference in potential energy from amber=>gromacs conversion: -0.00482600 Difference in potential energy from amber=>lammps conversion: -0.00482583 Difference in potential energy from amber=>desmond conversion: -0.00502155 Difference in potential energy from amber=>charmm conversion: -0.00205016 ======================================================================= INFO 2017-03-18 22:49:22 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2802855.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2802855.inpcrd') INFO 2017-03-18 22:49:22 Beginning InterMol conversion INFO 2017-03-18 22:49:22 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:49:22 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_282648.inpcrd INFO 2017-03-18 22:49:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_282648/mobley_282648_converted.input INFO 2017-03-18 22:49:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_282648/mobley_282648_converted.cms INFO 2017-03-18 22:49:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_282648/mobley_282648_converted.rst7 WARNING 2017-03-18 22:49:38 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:49:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_282648/mobley_282648_converted.inp INFO 2017-03-18 22:49:38 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_282648/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_282648/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_282648/mobley_282648_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_282648/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_282648/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -7.62754947 -7.62754947 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 4.02981960 4.02981960 coulomb total 4.01622160 3.99273653 -0.02348507 3.99273647 -0.02348513 3.99270932 -0.02351228 4.01622160 0.00000000 4.02981960 0.01359800 coulomb-14 11.62189680 11.62028599 -0.00161081 0.00000000 -11.62189680 11.62026010 -0.00163670 11.62189680 0.00000000 0.00000000 -11.62189680 improper 0.00000000 0.00006683 0.00006683 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00083680 0.00060733 -0.00022947 0.00067409 -0.00016271 0.00066436 -0.00017244 0.00083680 0.00000000 0.00062760 -0.00020920 vdw (SR) 0.00000000 -3.34813106 -3.34813106 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 26.95161256 26.95161256 vdw total 26.95165440 26.95164480 -0.00000960 26.95164478 -0.00000962 26.95179256 0.00013816 26.95165440 0.00000000 26.95161256 -0.00004184 vdw-14 30.29969120 30.29977585 0.00008465 0.00000000 -30.29969120 30.29992078 0.00022958 30.29969120 0.00000000 0.00000000 -30.29969120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.14599760 1.14583656 -0.00016104 1.14583656 -0.00016104 1.14554177 -0.00045583 1.14599760 0.00000000 1.14583024 -0.00016736 bond 4.67980400 4.67997495 0.00017095 4.67997513 0.00017113 4.67969543 -0.00010857 4.67980400 0.00000000 4.67997136 0.00016736 bonded 5.82663840 5.82648567 -0.00015273 5.82648578 -0.00015262 5.82590156 -0.00073684 5.82663840 0.00000000 5.82651288 -0.00012552 dihedral 0.00083680 0.00067416 -0.00016264 0.00067409 -0.00016271 0.00066436 -0.00017244 0.00083680 0.00000000 0.00071128 -0.00012552 nonbonded 30.96787600 30.94438132 -0.02349468 30.94438117 -0.02349483 30.94450188 -0.02337412 30.96787600 0.00000000 30.98143216 0.01355616 potential 36.79451440 36.77086700 -0.02364740 36.77086685 -0.02364755 36.77033477 -0.02417963 36.79451440 0.00000000 36.80794504 0.01343064 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 36.79451440 Difference in potential energy from amber=>gromacs conversion: -0.02364740 Difference in potential energy from amber=>lammps conversion: -0.02364755 Difference in potential energy from amber=>desmond conversion: -0.02417963 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.01343064 ======================================================================= INFO 2017-03-18 22:49:38 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_282648.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_282648.inpcrd') INFO 2017-03-18 22:49:38 Beginning InterMol conversion INFO 2017-03-18 22:49:38 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:49:38 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2837389.inpcrd INFO 2017-03-18 22:49:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2837389/mobley_2837389_converted.input INFO 2017-03-18 22:49:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2837389/mobley_2837389_converted.cms INFO 2017-03-18 22:49:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2837389/mobley_2837389_converted.rst7 WARNING 2017-03-18 22:49:54 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:49:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2837389/mobley_2837389_converted.inp INFO 2017-03-18 22:49:54 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2837389/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2837389/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2837389/mobley_2837389_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_2837389/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2837389/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 53.00729215 53.00729215 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 6.31637560 6.31637560 coulomb total 6.33499440 6.32148449 -0.01350991 6.32148426 -0.01351014 6.32141230 -0.01358210 6.33541280 0.00041840 6.31637560 -0.01861880 coulomb-14 -46.67628560 -46.68580765 -0.00952205 0.00000000 46.67628560 -46.68584688 -0.00956128 -46.67586720 0.00041840 0.00000000 46.67628560 improper 0.00000000 0.00010701 0.00010701 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00083680 0.00082246 -0.00001434 0.00092976 0.00009296 0.00092971 0.00009291 0.00083680 0.00000000 0.00083680 0.00000000 vdw (SR) 0.00000000 -0.03419533 -0.03419533 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.86156928 -0.86156928 vdw total -0.86190400 -0.86158921 0.00031479 -0.86158920 0.00031480 -0.86158970 0.00031430 -0.86190400 0.00000000 -0.86156928 0.00033472 vdw-14 -0.82759520 -0.82739389 0.00020131 0.00000000 0.82759520 -0.82739442 0.00020078 -0.82759520 0.00000000 0.00000000 0.82759520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 14.80424720 14.80422726 -0.00001994 14.80422712 -0.00002008 14.80436038 0.00011318 14.80424720 0.00000000 14.80424720 0.00000000 bond 0.50919280 0.50928220 0.00008940 0.50928221 0.00008941 0.50895952 -0.00023328 0.50919280 0.00000000 0.50927648 0.00008368 bonded 15.31427680 15.31443893 0.00016213 15.31443909 0.00016229 15.31424960 -0.00002720 15.31427680 0.00000000 15.31448600 0.00020920 dihedral 0.00083680 0.00092948 0.00009268 0.00092976 0.00009296 0.00092971 0.00009291 0.00083680 0.00000000 0.00096232 0.00012552 nonbonded 5.47309040 5.45989528 -0.01319512 5.45989532 -0.01319508 5.45982260 -0.01326780 5.47350880 0.00041840 5.45480632 -0.01828408 potential 20.78736720 20.77433421 -0.01303299 20.77433446 -0.01303274 20.77405923 -0.01330797 20.78778560 0.00041840 20.76920864 -0.01815856 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 20.78736720 Difference in potential energy from amber=>gromacs conversion: -0.01303299 Difference in potential energy from amber=>lammps conversion: -0.01303274 Difference in potential energy from amber=>desmond conversion: -0.01330797 Difference in potential energy from amber=>amber conversion: 0.00041840 Difference in potential energy from amber=>charmm conversion: -0.01815856 ======================================================================= INFO 2017-03-18 22:49:54 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2837389.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2837389.inpcrd') INFO 2017-03-18 22:49:54 Beginning InterMol conversion INFO 2017-03-18 22:49:54 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:49:55 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2844990.inpcrd INFO 2017-03-18 22:49:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2844990/mobley_2844990_converted.input INFO 2017-03-18 22:49:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2844990/mobley_2844990_converted.cms INFO 2017-03-18 22:50:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2844990/mobley_2844990_converted.rst7 WARNING 2017-03-18 22:50:10 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:50:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2844990/mobley_2844990_converted.inp INFO 2017-03-18 22:50:10 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2844990/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2844990/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2844990/mobley_2844990_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_2844990/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2844990/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -12.03749688 -12.03749688 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -16.60290696 -16.60290696 coulomb total -16.64269680 -16.64522542 -0.00252862 -16.64522519 -0.00252839 -16.64525703 -0.00256023 -16.64269680 0.00000000 -16.60290696 0.03978984 coulomb-14 -4.60867600 -4.60772854 0.00094746 0.00000000 4.60867600 -4.60777288 0.00090312 -4.60867600 0.00000000 0.00000000 4.60867600 improper 0.00000000 0.00027547 0.00027547 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00029288 0.00029288 proper 0.00251040 0.00236051 -0.00014989 0.00263586 0.00012546 0.00263451 0.00012411 0.00251040 0.00000000 0.00234304 -0.00016736 vdw (SR) 0.00000000 -10.77662497 -10.77662497 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 43.69049952 43.69049952 vdw total 43.69058320 43.69048581 -0.00009739 43.69048697 -0.00009623 43.69047609 -0.00010711 43.69058320 0.00000000 43.69049952 -0.00008368 vdw-14 54.46731200 54.46711079 -0.00020121 0.00000000 -54.46731200 54.46709945 -0.00021255 54.46731200 0.00000000 0.00000000 -54.46731200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 8.48975440 8.48970744 -0.00004696 8.48970754 -0.00004686 8.49033229 0.00057789 8.48975440 0.00000000 8.48971256 -0.00004184 bond 1.88028960 1.88048117 0.00019157 1.88048119 0.00019159 1.88076497 0.00047537 1.88028960 0.00000000 1.88049880 0.00020920 bonded 10.37255440 10.37282459 0.00027019 10.37282459 0.00027019 10.37373177 0.00117737 10.37255440 0.00000000 10.37284728 0.00029288 dihedral 0.00251040 0.00263598 0.00012558 0.00263586 0.00012546 0.00263451 0.00012411 0.00251040 0.00000000 0.00263592 0.00012552 nonbonded 27.04788640 27.04526040 -0.00262600 27.04526052 -0.00262588 27.04521906 -0.00266734 27.04788640 0.00000000 27.08759256 0.03970616 potential 37.42044080 37.41808499 -0.00235581 37.41808521 -0.00235559 37.41870394 -0.00173686 37.42044080 0.00000000 37.46048168 0.04004088 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 37.42044080 Difference in potential energy from amber=>gromacs conversion: -0.00235581 Difference in potential energy from amber=>lammps conversion: -0.00235559 Difference in potential energy from amber=>desmond conversion: -0.00173686 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.04004088 ======================================================================= INFO 2017-03-18 22:50:10 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2844990.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2844990.inpcrd') INFO 2017-03-18 22:50:11 Beginning InterMol conversion INFO 2017-03-18 22:50:11 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:50:11 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2845466.inpcrd INFO 2017-03-18 22:50:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2845466/mobley_2845466_converted.input INFO 2017-03-18 22:50:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2845466/mobley_2845466_converted.cms INFO 2017-03-18 22:50:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2845466/mobley_2845466_converted.rst7 WARNING 2017-03-18 22:50:26 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:50:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2845466/mobley_2845466_converted.inp INFO 2017-03-18 22:50:26 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2845466/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2845466/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2845466/mobley_2845466_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_2845466/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2845466/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -31.63139594 -31.63139594 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -39.95703264 -39.95703264 coulomb total -40.07393360 -40.06900451 0.00492909 -40.06900401 0.00492959 -40.06903690 0.00489670 -40.07393360 0.00000000 -39.95703264 0.11690096 coulomb-14 -8.43368880 -8.43760857 -0.00391977 0.00000000 8.43368880 -8.43766352 -0.00397472 -8.43368880 0.00000000 0.00000000 8.43368880 improper 0.00000000 0.00019534 0.00019534 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00020920 0.00020920 proper 0.00209200 0.00186588 -0.00022612 0.00206121 -0.00003079 0.00205743 -0.00003457 0.00209200 0.00000000 0.00188280 -0.00020920 vdw (SR) 0.00000000 -9.88857668 -9.88857668 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 40.77818448 40.77818448 vdw total 40.77810080 40.77818020 0.00007940 40.77818030 0.00007950 40.77824845 0.00014765 40.77810080 0.00000000 40.77818448 0.00008368 vdw-14 50.66656640 50.66675688 0.00019048 0.00000000 -50.66656640 50.66682874 0.00026234 50.66656640 0.00000000 0.00000000 -50.66656640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 10.00436240 10.00450404 0.00014164 10.00450424 0.00014184 10.00484327 0.00048087 10.00436240 0.00000000 10.00452976 0.00016736 bond 1.51167920 1.51168975 0.00001055 1.51168974 0.00001054 1.51190349 0.00022429 1.51167920 0.00000000 1.51167920 0.00000000 bonded 11.51813360 11.51825501 0.00012141 11.51825519 0.00012159 11.51880419 0.00067059 11.51813360 0.00000000 11.51830096 0.00016736 dihedral 0.00209200 0.00206122 -0.00003078 0.00206121 -0.00003079 0.00205743 -0.00003457 0.00209200 0.00000000 0.00209200 0.00000000 nonbonded 0.70416720 0.70917569 0.00500849 0.70917616 0.00500896 0.70921156 0.00504436 0.70416720 0.00000000 0.82115184 0.11698464 potential 12.22230080 12.22743070 0.00512990 12.22743122 0.00513042 12.22776276 0.00546196 12.22230080 0.00000000 12.33941096 0.11711016 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 12.22230080 Difference in potential energy from amber=>gromacs conversion: 0.00512990 Difference in potential energy from amber=>lammps conversion: 0.00513042 Difference in potential energy from amber=>desmond conversion: 0.00546196 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.11711016 ======================================================================= INFO 2017-03-18 22:50:26 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2845466.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2845466.inpcrd') INFO 2017-03-18 22:50:27 Beginning InterMol conversion INFO 2017-03-18 22:50:27 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:50:27 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2850833.inpcrd INFO 2017-03-18 22:50:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2850833/mobley_2850833_converted.input INFO 2017-03-18 22:50:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2850833/mobley_2850833_converted.cms INFO 2017-03-18 22:50:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2850833/mobley_2850833_converted.rst7 WARNING 2017-03-18 22:50:43 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:50:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2850833/mobley_2850833_converted.inp INFO 2017-03-18 22:50:43 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2850833/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2850833/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2850833/mobley_2850833_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_2850833/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2850833/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 167.76433933 167.76433933 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -106.06578072 -106.06578072 coulomb total -106.07737040 -106.09275407 -0.01538367 -106.09275078 -0.01538038 -106.09326709 -0.01589669 -106.07737040 0.00000000 -106.06578072 0.01158968 coulomb-14 -273.84363680 -273.85709340 -0.01345660 0.00000000 273.84363680 -273.85698083 -0.01334403 -273.84363680 0.00000000 0.00000000 273.84363680 improper 0.00000000 0.00009619 0.00009619 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00041840 0.00020376 -0.00021464 0.00030006 -0.00011834 0.00030126 -0.00011714 0.00041840 0.00000000 0.00020920 -0.00020920 vdw (SR) 0.00000000 0.60453399 0.60453399 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 21.82131728 21.82131728 vdw total 21.82123360 21.82125201 0.00001841 21.82125201 0.00001841 21.82126210 0.00002850 21.82123360 0.00000000 21.82131728 0.00008368 vdw-14 21.21664560 21.21671802 0.00007242 0.00000000 -21.21664560 21.21673815 0.00009255 21.21664560 0.00000000 0.00000000 -21.21664560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.75688560 0.75685387 -0.00003173 0.75685389 -0.00003171 0.75689832 0.00001272 0.75688560 0.00000000 0.75684376 -0.00004184 bond 3.20034160 3.20015048 -0.00019112 3.20015047 -0.00019113 3.19965743 -0.00068417 3.20034160 0.00000000 3.20013240 -0.00020920 bonded 3.95764560 3.95730430 -0.00034130 3.95730442 -0.00034118 3.95685701 -0.00078859 3.95764560 0.00000000 3.95726904 -0.00037656 dihedral 0.00041840 0.00029995 -0.00011845 0.00030006 -0.00011834 0.00030126 -0.00011714 0.00041840 0.00000000 0.00029288 -0.00012552 nonbonded -84.25613680 -84.27150206 -0.01536526 -84.27150045 -0.01536365 -84.27200499 -0.01586819 -84.25613680 0.00000000 -84.24446344 0.01167336 potential -80.29849120 -80.31419776 -0.01570656 -80.31419794 -0.01570674 -80.31520963 -0.01671843 -80.29849120 0.00000000 -80.28715256 0.01133864 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -80.29849120 Difference in potential energy from amber=>gromacs conversion: -0.01570656 Difference in potential energy from amber=>lammps conversion: -0.01570674 Difference in potential energy from amber=>desmond conversion: -0.01671843 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.01133864 ======================================================================= INFO 2017-03-18 22:50:43 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2850833.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2850833.inpcrd') INFO 2017-03-18 22:50:43 Beginning InterMol conversion INFO 2017-03-18 22:50:43 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:50:43 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2859600.inpcrd INFO 2017-03-18 22:50:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2859600/mobley_2859600_converted.input INFO 2017-03-18 22:50:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2859600/mobley_2859600_converted.cms INFO 2017-03-18 22:50:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2859600/mobley_2859600_converted.rst7 WARNING 2017-03-18 22:50:59 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:50:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2859600/mobley_2859600_converted.inp INFO 2017-03-18 22:50:59 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2859600/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2859600/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2859600/mobley_2859600_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_2859600/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2859600/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -9.18385848 -9.18385848 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -1.13285984 -1.13285984 coulomb total -1.14181360 -1.13359648 0.00821712 -1.13359648 0.00821712 -1.13364593 0.00816767 -1.14181360 0.00000000 -1.13285984 0.00895376 coulomb-14 8.04917920 8.05026201 0.00108281 0.00000000 -8.04917920 8.05023804 0.00105884 8.04917920 0.00000000 0.00000000 -8.04917920 improper 0.00000000 0.00958648 0.00958648 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00958136 0.00958136 proper 5.63919520 5.62963300 -0.00956220 5.63923578 0.00004058 5.63918064 -0.00001456 5.63919520 0.00000000 5.62965568 -0.00953952 vdw (SR) 0.00000000 -0.13133409 -0.13133409 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 18.58005616 18.58005616 vdw total 18.57988880 18.58005144 0.00016264 18.58005156 0.00016276 18.58008262 0.00019382 18.57988880 0.00000000 18.58005616 0.00016736 vdw-14 18.71126640 18.71138553 0.00011913 0.00000000 -18.71126640 18.71145882 0.00019242 18.71126640 0.00000000 0.00000000 -18.71126640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.45391600 2.45390229 -0.00001371 2.45390228 -0.00001372 2.45379777 -0.00011823 2.45391600 0.00000000 2.45391600 0.00000000 bond 1.20624720 1.20614126 -0.00010594 1.20614126 -0.00010594 1.20619508 -0.00005212 1.20624720 0.00000000 1.20612168 -0.00012552 bonded 9.29935840 9.29926304 -0.00009536 9.29927932 -0.00007908 9.29917348 -0.00018492 9.29935840 0.00000000 9.29927472 -0.00008368 dihedral 5.63919520 5.63921948 0.00002428 5.63923578 0.00004058 5.63918064 -0.00001456 5.63919520 0.00000000 5.63923704 0.00004184 nonbonded 17.43807520 17.44645496 0.00837976 17.44645492 0.00837972 17.44643669 0.00836149 17.43807520 0.00000000 17.44719632 0.00912112 potential 26.73743360 26.74571800 0.00828440 26.74573424 0.00830064 26.74556299 0.00812939 26.73743360 0.00000000 26.74647104 0.00903744 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 26.73743360 Difference in potential energy from amber=>gromacs conversion: 0.00828440 Difference in potential energy from amber=>lammps conversion: 0.00830064 Difference in potential energy from amber=>desmond conversion: 0.00812939 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00903744 ======================================================================= INFO 2017-03-18 22:50:59 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2859600.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2859600.inpcrd') INFO 2017-03-18 22:50:59 Beginning InterMol conversion INFO 2017-03-18 22:50:59 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:50:59 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:50:59 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2864987.inpcrd INFO 2017-03-18 22:50:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2864987/mobley_2864987_converted.input INFO 2017-03-18 22:50:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2864987/mobley_2864987_converted.cms WARNING 2017-03-18 22:51:15 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:51:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2864987/mobley_2864987_converted.inp INFO 2017-03-18 22:51:15 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2864987/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2864987/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2864987/mobley_2864987_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2864987/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 25.00794259 25.00794259 0.00000000 0.00000000 0.00000000 0.00000000 -37.29450240 -37.29450240 coulomb total -37.28571600 -37.28678783 -0.00107183 -37.28678752 -0.00107152 -37.28689877 -0.00118277 -37.29450240 -0.00878640 coulomb-14 -62.29264720 -62.29473042 -0.00208322 0.00000000 62.29264720 -62.29483585 -0.00218865 0.00000000 62.29264720 proper 9.65625360 9.65624472 -0.00000888 9.65624481 -0.00000879 9.65623900 -0.00001460 9.65625360 0.00000000 vdw (SR) 0.00000000 -0.50705737 -0.50705737 0.00000000 0.00000000 0.00000000 0.00000000 6.24482920 6.24482920 vdw total 6.24462000 6.24468584 0.00006584 6.24468611 0.00006611 6.24467828 0.00005828 6.24482920 0.00020920 vdw-14 6.75172080 6.75174321 0.00002241 0.00000000 -6.75172080 6.75173005 0.00000925 0.00000000 -6.75172080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.85685920 1.85667162 -0.00018758 1.85667163 -0.00018757 1.85663607 -0.00022313 1.85665000 -0.00020920 bond 0.74098640 0.74097144 -0.00001496 0.74097146 -0.00001494 0.74120311 0.00021671 0.74098640 0.00000000 bonded 12.25409920 12.25388778 -0.00021142 12.25388791 -0.00021129 12.25407818 -0.00002102 12.25389000 -0.00020920 dihedral 9.65625360 9.65624472 -0.00000888 9.65624481 -0.00000879 9.65623900 -0.00001460 9.65625360 0.00000000 nonbonded -31.04109600 -31.04210199 -0.00100599 -31.04210142 -0.00100542 -31.04222049 -0.00112449 -31.04967320 -0.00857720 potential -18.78699680 -18.78821421 -0.00121741 -18.78821351 -0.00121671 -18.78818568 -0.00118888 -18.79582504 -0.00882824 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -18.78699680 Difference in potential energy from amber=>gromacs conversion: -0.00121741 Difference in potential energy from amber=>lammps conversion: -0.00121671 Difference in potential energy from amber=>desmond conversion: -0.00118888 Difference in potential energy from amber=>charmm conversion: -0.00882824 ======================================================================= INFO 2017-03-18 22:51:15 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2864987.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2864987.inpcrd') INFO 2017-03-18 22:51:15 Beginning InterMol conversion INFO 2017-03-18 22:51:15 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:51:15 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:51:15 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2881590.inpcrd INFO 2017-03-18 22:51:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2881590/mobley_2881590_converted.input INFO 2017-03-18 22:51:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2881590/mobley_2881590_converted.cms WARNING 2017-03-18 22:51:31 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:51:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2881590/mobley_2881590_converted.inp INFO 2017-03-18 22:51:31 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2881590/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2881590/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2881590/mobley_2881590_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2881590/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -24.93872357 -24.93872357 0.00000000 0.00000000 0.00000000 0.00000000 -8.99543264 -8.99543264 coulomb total -8.98430320 -8.99515218 -0.01084898 -8.99515189 -0.01084869 -8.99512085 -0.01081765 -8.99543264 -0.01112944 coulomb-14 15.95108160 15.94357139 -0.00751021 0.00000000 -15.95108160 15.94356902 -0.00751258 0.00000000 -15.95108160 proper 1.70288800 1.70299961 0.00011161 1.70299963 0.00011163 1.70301222 0.00012422 1.70301352 0.00012552 vdw (SR) 0.00000000 -0.58687076 -0.58687076 0.00000000 0.00000000 0.00000000 0.00000000 16.89018040 16.89018040 vdw total 16.88997120 16.89003753 0.00006633 16.89003773 0.00006653 16.89030585 0.00033465 16.89018040 0.00020920 vdw-14 17.47698640 17.47690829 -0.00007811 0.00000000 -17.47698640 17.47715389 0.00016749 0.00000000 -17.47698640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.76683120 4.76683814 0.00000694 4.76683831 0.00000711 4.76677769 -0.00005351 4.76691488 0.00008368 bond 1.81376400 1.81383836 0.00007436 1.81383835 0.00007435 1.81393422 0.00017022 1.81384768 0.00008368 bonded 8.28348320 8.28367611 0.00019291 8.28367629 0.00019309 8.28372413 0.00024093 8.28377608 0.00029288 dihedral 1.70288800 1.70299961 0.00011161 1.70299963 0.00011163 1.70301222 0.00012422 1.70301352 0.00012552 nonbonded 7.90566800 7.89488534 -0.01078266 7.89488583 -0.01078217 7.89518500 -0.01048300 7.89474776 -0.01092024 potential 16.18915120 16.17856146 -0.01058974 16.17856191 -0.01058929 16.17885199 -0.01029921 16.17852384 -0.01062736 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 16.18915120 Difference in potential energy from amber=>gromacs conversion: -0.01058974 Difference in potential energy from amber=>lammps conversion: -0.01058929 Difference in potential energy from amber=>desmond conversion: -0.01029921 Difference in potential energy from amber=>charmm conversion: -0.01062736 ======================================================================= INFO 2017-03-18 22:51:31 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2881590.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2881590.inpcrd') INFO 2017-03-18 22:51:31 Beginning InterMol conversion INFO 2017-03-18 22:51:31 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:51:31 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:51:31 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2913224.inpcrd INFO 2017-03-18 22:51:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2913224/mobley_2913224_converted.input INFO 2017-03-18 22:51:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2913224/mobley_2913224_converted.cms WARNING 2017-03-18 22:51:47 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:51:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2913224/mobley_2913224_converted.inp INFO 2017-03-18 22:51:47 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2913224/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2913224/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2913224/mobley_2913224_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2913224/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 235.00849429 235.00849429 0.00000000 0.00000000 0.00000000 0.00000000 -278.33779672 -278.33779672 coulomb total -278.31549600 -278.32798522 -0.01248922 -278.32798106 -0.01248506 -278.32802415 -0.01252815 -278.33779672 -0.02230072 coulomb-14 -513.31738720 -513.33647950 -0.01909230 0.00000000 513.31738720 -513.33673402 -0.01934682 0.00000000 513.31738720 improper 0.00000000 0.00013860 0.00013860 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 50.42222080 50.42200308 -0.00021772 50.42212038 -0.00010042 50.42213796 -0.00008284 50.42196976 -0.00025104 vdw (SR) 0.00000000 -4.59667338 -4.59667338 0.00000000 0.00000000 0.00000000 0.00000000 28.06840584 28.06840584 vdw total 28.06836400 28.06821724 -0.00014676 28.06821714 -0.00014686 28.06815568 -0.00020832 28.06840584 0.00004184 vdw-14 32.66490640 32.66489062 -0.00001578 0.00000000 -32.66490640 32.66487828 -0.00002812 0.00000000 -32.66490640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 11.04366800 11.04370726 0.00003926 11.04370733 0.00003933 11.04318525 -0.00048275 11.04370984 0.00004184 bond 13.59716320 13.59718514 0.00002194 13.59718496 0.00002176 13.59625305 -0.00091015 13.59720504 0.00004184 bonded 75.06305200 75.06303408 -0.00001792 75.06301267 -0.00003933 75.06157626 -0.00147574 75.06301016 -0.00004184 dihedral 50.42222080 50.42214168 -0.00007912 50.42212038 -0.00010042 50.42213796 -0.00008284 50.42209528 -0.00012552 nonbonded -250.24713200 -250.25976798 -0.01263598 -250.25976350 -0.01263150 -250.25986847 -0.01273647 -250.26939088 -0.02225888 potential -175.18408000 -175.19673389 -0.01265389 -175.19675334 -0.01267334 -175.19841982 -0.01433982 -175.20638072 -0.02230072 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -175.18408000 Difference in potential energy from amber=>gromacs conversion: -0.01265389 Difference in potential energy from amber=>lammps conversion: -0.01267334 Difference in potential energy from amber=>desmond conversion: -0.01433982 Difference in potential energy from amber=>charmm conversion: -0.02230072 ======================================================================= INFO 2017-03-18 22:51:47 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2913224.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2913224.inpcrd') INFO 2017-03-18 22:51:47 Beginning InterMol conversion INFO 2017-03-18 22:51:47 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:51:47 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:51:47 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2923700.inpcrd INFO 2017-03-18 22:51:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2923700/mobley_2923700_converted.input INFO 2017-03-18 22:51:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2923700/mobley_2923700_converted.cms WARNING 2017-03-18 22:52:03 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:52:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2923700/mobley_2923700_converted.inp INFO 2017-03-18 22:52:03 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2923700/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2923700/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2923700/mobley_2923700_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2923700/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 23.18971438 23.18971438 0.00000000 0.00000000 0.00000000 0.00000000 -74.93401744 -74.93401744 coulomb total -74.92832720 -74.93845189 -0.01012469 -74.93845248 -0.01012528 -74.93900519 -0.01067799 -74.93401744 -0.00569024 coulomb-14 -98.12693360 -98.12816627 -0.00123267 0.00000000 98.12693360 -98.12815951 -0.00122591 0.00000000 98.12693360 improper 0.00000000 0.00007364 0.00007364 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.02050160 0.02041381 -0.00008779 0.02048739 -0.00001421 0.02048954 -0.00001206 0.02041792 -0.00008368 vdw (SR) 0.00000000 -3.62937720 -3.62937720 0.00000000 0.00000000 0.00000000 0.00000000 15.68974896 15.68974896 vdw total 15.69000000 15.68972566 -0.00027434 15.68972553 -0.00027447 15.68977244 -0.00022756 15.68974896 -0.00025104 vdw-14 19.31920160 19.31910286 -0.00009874 0.00000000 -19.31920160 19.31915558 -0.00004602 0.00000000 -19.31920160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.72341360 0.72344650 0.00003290 0.72344649 0.00003289 0.72335225 -0.00006135 0.72341360 0.00000000 bond 1.71878720 1.71870896 -0.00007824 1.71870896 -0.00007824 1.71876580 -0.00002140 1.71870352 -0.00008368 bonded 2.46270240 2.46264291 -0.00005949 2.46264284 -0.00005956 2.46260759 -0.00009481 2.46261872 -0.00008368 dihedral 0.02050160 0.02048745 -0.00001415 0.02048739 -0.00001421 0.02048954 -0.00001206 0.02050160 -0.00000000 nonbonded -59.23832720 -59.24872623 -0.01039903 -59.24872444 -0.01039724 -59.24923274 -0.01090554 -59.24426848 -0.00594128 potential -56.77562480 -56.78608332 -0.01045852 -56.78608062 -0.01045582 -56.78669525 -0.01107045 -56.78164976 -0.00602496 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -56.77562480 Difference in potential energy from amber=>gromacs conversion: -0.01045852 Difference in potential energy from amber=>lammps conversion: -0.01045582 Difference in potential energy from amber=>desmond conversion: -0.01107045 Difference in potential energy from amber=>charmm conversion: -0.00602496 ======================================================================= INFO 2017-03-18 22:52:03 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2923700.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2923700.inpcrd') INFO 2017-03-18 22:52:03 Beginning InterMol conversion INFO 2017-03-18 22:52:03 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:52:04 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:52:04 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2925352.inpcrd INFO 2017-03-18 22:52:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2925352/mobley_2925352_converted.input INFO 2017-03-18 22:52:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2925352/mobley_2925352_converted.cms WARNING 2017-03-18 22:52:19 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:52:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2925352/mobley_2925352_converted.inp INFO 2017-03-18 22:52:19 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2925352/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2925352/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2925352/mobley_2925352_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2925352/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 30.69379902 30.69379902 0.00000000 0.00000000 0.00000000 0.00000000 -74.09328448 -74.09328448 coulomb total -74.10282400 -74.09705131 0.00577269 -74.09705008 0.00577392 -74.09759998 0.00522402 -74.09328448 0.00953952 coulomb-14 -104.78451440 -104.79085033 -0.00633593 0.00000000 104.78451440 -104.79083642 -0.00632202 0.00000000 104.78451440 improper 0.00000000 0.00007364 0.00007364 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00125520 0.00098321 -0.00027199 0.00105680 -0.00019840 0.00105839 -0.00019681 0.00096232 -0.00029288 vdw (SR) 0.00000000 -1.83639725 -1.83639725 0.00000000 0.00000000 0.00000000 0.00000000 16.11639144 16.11639144 vdw total 16.11634960 16.11636840 0.00001880 16.11636843 0.00001883 16.11638838 0.00003878 16.11639144 0.00004184 vdw-14 17.95270720 17.95276565 0.00005845 0.00000000 -17.95270720 17.95279678 0.00008958 0.00000000 -17.95270720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.37572320 0.37583607 0.00011287 0.37583608 0.00011288 0.37582574 0.00010254 0.37584872 0.00012552 bond 1.39201680 1.39198367 -0.00003313 1.39198366 -0.00003314 1.39208827 0.00007147 1.39197496 -0.00004184 bonded 1.76899520 1.76887660 -0.00011860 1.76887654 -0.00011866 1.76897240 -0.00002280 1.76886968 -0.00012552 dihedral 0.00125520 0.00105685 -0.00019835 0.00105680 -0.00019840 0.00105839 -0.00019681 0.00104600 -0.00020920 nonbonded -57.98647440 -57.98068291 0.00579149 -57.98068374 0.00579066 -57.98121161 0.00526279 -57.97689304 0.00958136 potential -56.21747920 -56.21180631 0.00567289 -56.21180570 0.00567350 -56.21229271 0.00518649 -56.20802336 0.00945584 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -56.21747920 Difference in potential energy from amber=>gromacs conversion: 0.00567289 Difference in potential energy from amber=>lammps conversion: 0.00567350 Difference in potential energy from amber=>desmond conversion: 0.00518649 Difference in potential energy from amber=>charmm conversion: 0.00945584 ======================================================================= INFO 2017-03-18 22:52:19 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2925352.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2925352.inpcrd') INFO 2017-03-18 22:52:19 Beginning InterMol conversion INFO 2017-03-18 22:52:19 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:52:20 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:52:20 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2929847.inpcrd INFO 2017-03-18 22:52:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2929847/mobley_2929847_converted.input INFO 2017-03-18 22:52:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2929847/mobley_2929847_converted.cms WARNING 2017-03-18 22:52:35 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:52:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2929847/mobley_2929847_converted.inp INFO 2017-03-18 22:52:35 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2929847/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2929847/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2929847/mobley_2929847_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2929847/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 72.53399363 72.53399363 0.00000000 0.00000000 0.00000000 0.00000000 -125.03298240 -125.03298240 coulomb total -125.04051360 -125.04130965 -0.00079605 -125.04130856 -0.00079496 -125.04161650 -0.00110290 -125.03298240 0.00753120 coulomb-14 -197.56555120 -197.57530329 -0.00975209 0.00000000 197.56555120 -197.57516478 -0.00961358 0.00000000 197.56555120 improper 0.00000000 0.01041098 0.01041098 0.00000000 0.00000000 0.00000000 0.00000000 0.01041816 0.01041816 proper 4.42499840 4.41476671 -0.01023169 4.42517789 0.00017949 4.42518229 0.00018389 4.41474760 -0.01025080 vdw (SR) 0.00000000 0.14271151 0.14271151 0.00000000 0.00000000 0.00000000 0.00000000 10.52409888 10.52409888 vdw total 10.52401520 10.52395268 -0.00006252 10.52395286 -0.00006234 10.52396335 -0.00005185 10.52409888 0.00008368 vdw-14 10.38134080 10.38124117 -0.00009963 0.00000000 -10.38134080 10.38124800 -0.00009280 0.00000000 -10.38134080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.80867120 4.80862400 -0.00004720 4.80862392 -0.00004728 4.80850413 -0.00016707 4.80867120 0.00000000 bond 5.77768560 5.77767004 -0.00001556 5.77767012 -0.00001548 5.77725448 -0.00043112 5.77768560 0.00000000 bonded 15.01135520 15.01147173 0.00011653 15.01147193 0.00011673 15.01094090 -0.00041430 15.01152256 0.00016736 dihedral 4.42499840 4.42517769 0.00017929 4.42517789 0.00017949 4.42518229 0.00018389 4.42516576 0.00016736 nonbonded -114.51649840 -114.51735697 -0.00085857 -114.51735612 -0.00085772 -114.51765315 -0.00115475 -114.50888352 0.00761488 potential -99.50514320 -99.50588525 -0.00074205 -99.50588377 -0.00074057 -99.50675739 -0.00161419 -99.49736096 0.00778224 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -99.50514320 Difference in potential energy from amber=>gromacs conversion: -0.00074205 Difference in potential energy from amber=>lammps conversion: -0.00074057 Difference in potential energy from amber=>desmond conversion: -0.00161419 Difference in potential energy from amber=>charmm conversion: 0.00778224 ======================================================================= INFO 2017-03-18 22:52:35 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2929847.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2929847.inpcrd') INFO 2017-03-18 22:52:36 Beginning InterMol conversion INFO 2017-03-18 22:52:36 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:52:36 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:52:36 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2958326.inpcrd INFO 2017-03-18 22:52:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2958326/mobley_2958326_converted.input INFO 2017-03-18 22:52:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2958326/mobley_2958326_converted.cms WARNING 2017-03-18 22:52:51 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:52:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2958326/mobley_2958326_converted.inp INFO 2017-03-18 22:52:51 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2958326/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2958326/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2958326/mobley_2958326_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2958326/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -5.31313420 -5.31313420 0.00000000 0.00000000 0.00000000 0.00000000 -11.73423720 -11.73423720 coulomb total -11.72607840 -11.72668764 -0.00060924 -11.72668759 -0.00060919 -11.72668830 -0.00060990 -11.73423720 -0.00815880 coulomb-14 -6.41323520 -6.41355344 -0.00031824 0.00000000 6.41323520 -6.41349503 -0.00025983 0.00000000 6.41323520 proper 0.20752640 0.20741777 -0.00010863 0.20741775 -0.00010865 0.20741613 -0.00011027 0.20744272 -0.00008368 vdw (SR) 0.00000000 -2.78083207 -2.78083207 0.00000000 0.00000000 0.00000000 0.00000000 3.56778048 3.56778048 vdw total 3.56811520 3.56768672 -0.00042848 3.56768676 -0.00042844 3.56770609 -0.00040911 3.56778048 -0.00033472 vdw-14 6.34880160 6.34851879 -0.00028281 0.00000000 -6.34880160 6.34854223 -0.00025937 0.00000000 -6.34880160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.96136320 5.96120427 -0.00015893 5.96120421 -0.00015899 5.96122069 -0.00014251 5.96115400 -0.00020920 bond 3.03549200 3.03534116 -0.00015084 3.03534117 -0.00015083 3.03553637 0.00004437 3.03532464 -0.00016736 bonded 9.20438160 9.20396321 -0.00041839 9.20396312 -0.00041848 9.20417319 -0.00020841 9.20392136 -0.00046024 dihedral 0.20752640 0.20741777 -0.00010863 0.20741775 -0.00010865 0.20741613 -0.00011027 0.20744272 -0.00008368 nonbonded -8.15796320 -8.15900093 -0.00103773 -8.15900083 -0.00103763 -8.15898221 -0.00101901 -8.16645672 -0.00849352 potential 1.04641840 1.04496228 -0.00145612 1.04496241 -0.00145599 1.04513283 -0.00128557 1.03746464 -0.00895376 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 1.04641840 Difference in potential energy from amber=>gromacs conversion: -0.00145612 Difference in potential energy from amber=>lammps conversion: -0.00145599 Difference in potential energy from amber=>desmond conversion: -0.00128557 Difference in potential energy from amber=>charmm conversion: -0.00895376 ======================================================================= INFO 2017-03-18 22:52:51 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2958326.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2958326.inpcrd') INFO 2017-03-18 22:52:52 Beginning InterMol conversion INFO 2017-03-18 22:52:52 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:52:52 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2960202.inpcrd INFO 2017-03-18 22:52:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2960202/mobley_2960202_converted.input INFO 2017-03-18 22:52:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2960202/mobley_2960202_converted.cms INFO 2017-03-18 22:53:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2960202/mobley_2960202_converted.rst7 WARNING 2017-03-18 22:53:07 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:53:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2960202/mobley_2960202_converted.inp INFO 2017-03-18 22:53:07 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2960202/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2960202/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2960202/mobley_2960202_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_2960202/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2960202/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -10.32254444 -10.32254444 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -7.83671568 -7.83671568 coulomb total -7.84123440 -7.84031228 0.00092212 -7.84031225 0.00092215 -7.84034301 0.00089139 -7.84123440 0.00000000 -7.83671568 0.00451872 coulomb-14 2.48864320 2.48223216 -0.00641104 0.00000000 -2.48864320 2.48218251 -0.00646069 2.48864320 0.00000000 0.00000000 -2.48864320 improper 0.00000000 0.00008670 0.00008670 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00125520 0.00129784 0.00004264 0.00138451 0.00012931 0.00138260 0.00012740 0.00125520 0.00000000 0.00129704 0.00004184 vdw (SR) 0.00000000 -13.35125941 -13.35125941 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 48.61941888 48.61941888 vdw total 48.61933520 48.61931342 -0.00002178 48.61931428 -0.00002092 48.61926763 -0.00006757 48.61933520 0.00000000 48.61941888 0.00008368 vdw-14 61.97047920 61.97057283 0.00009363 0.00000000 -61.97047920 61.97052564 0.00004644 61.97047920 0.00000000 0.00000000 -61.97047920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 9.15752080 9.15745448 -0.00006632 9.15745427 -0.00006653 9.15794828 0.00042748 9.15752080 0.00000000 9.15747896 -0.00004184 bond 2.25433920 2.25433059 -0.00000861 2.25433058 -0.00000862 2.25481317 0.00047397 2.25433920 0.00000000 2.25433920 0.00000000 bonded 11.41311520 11.41316961 0.00005441 11.41316937 0.00005417 11.41414405 0.00102885 11.41311520 0.00000000 11.41319888 0.00008368 dihedral 0.00125520 0.00138454 0.00012934 0.00138451 0.00012931 0.00138260 0.00012740 0.00125520 0.00000000 0.00138072 0.00012552 nonbonded 40.77810080 40.77900114 0.00090034 40.77900120 0.00090040 40.77892462 0.00082382 40.77810080 0.00000000 40.78270320 0.00460240 potential 52.19121600 52.19217075 0.00095475 52.19216995 0.00095395 52.19274149 0.00152549 52.19121600 0.00000000 52.19590208 0.00468608 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 52.19121600 Difference in potential energy from amber=>gromacs conversion: 0.00095475 Difference in potential energy from amber=>lammps conversion: 0.00095395 Difference in potential energy from amber=>desmond conversion: 0.00152549 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00468608 ======================================================================= INFO 2017-03-18 22:53:07 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2960202.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2960202.inpcrd') INFO 2017-03-18 22:53:08 Beginning InterMol conversion INFO 2017-03-18 22:53:08 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:53:08 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_296847.inpcrd INFO 2017-03-18 22:53:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_296847/mobley_296847_converted.input INFO 2017-03-18 22:53:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_296847/mobley_296847_converted.cms INFO 2017-03-18 22:53:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_296847/mobley_296847_converted.rst7 WARNING 2017-03-18 22:53:23 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:53:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_296847/mobley_296847_converted.inp INFO 2017-03-18 22:53:24 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_296847/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_296847/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_296847/mobley_296847_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_296847/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_296847/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 15.47398617 15.47398617 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -67.75251616 -67.75251616 coulomb total -67.72850000 -67.74410218 -0.01560218 -67.74410214 -0.01560214 -67.74423456 -0.01573456 -67.72850000 0.00000000 -67.75251616 -0.02401616 coulomb-14 -83.20804480 -83.21808835 -0.01004355 0.00000000 83.20804480 -83.21823870 -0.01019390 -83.20804480 0.00000000 0.00000000 83.20804480 improper 0.00000000 0.00004056 0.00004056 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00083680 0.00075565 -0.00008115 0.00079624 -0.00004056 0.00080103 -0.00003577 0.00083680 0.00000000 0.00075312 -0.00008368 vdw (SR) 0.00000000 -0.60320880 -0.60320880 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 18.68486536 18.68486536 vdw total 18.68490720 18.68492366 0.00001646 18.68492352 0.00001632 18.68532031 0.00041311 18.68490720 0.00000000 18.68486536 -0.00004184 vdw-14 19.28824000 19.28813246 -0.00010754 0.00000000 -19.28824000 19.28853020 0.00029020 19.28824000 0.00000000 0.00000000 -19.28824000 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.44013280 1.44001263 -0.00012017 1.44001264 -0.00012016 1.44000431 -0.00012849 1.44013280 0.00000000 1.44000728 -0.00012552 bond 0.56525840 0.56516812 -0.00009028 0.56516811 -0.00009029 0.56498326 -0.00027514 0.56525840 0.00000000 0.56517472 -0.00008368 bonded 2.00622800 2.00597696 -0.00025104 2.00597699 -0.00025101 2.00578860 -0.00043940 2.00622800 0.00000000 2.00597696 -0.00025104 dihedral 0.00083680 0.00079621 -0.00004059 0.00079624 -0.00004056 0.00080103 -0.00003577 0.00083680 0.00000000 0.00079496 -0.00004184 nonbonded -49.04359280 -49.05917853 -0.01558573 -49.05917820 -0.01558540 -49.05891425 -0.01532145 -49.04359280 0.00000000 -49.06765080 -0.02405800 potential -47.03736480 -47.05320156 -0.01583676 -47.05320124 -0.01583644 -47.05315229 -0.01578749 -47.03736480 0.00000000 -47.06163200 -0.02426720 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -47.03736480 Difference in potential energy from amber=>gromacs conversion: -0.01583676 Difference in potential energy from amber=>lammps conversion: -0.01583644 Difference in potential energy from amber=>desmond conversion: -0.01578749 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.02426720 ======================================================================= INFO 2017-03-18 22:53:24 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_296847.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_296847.inpcrd') INFO 2017-03-18 22:53:24 Beginning InterMol conversion INFO 2017-03-18 22:53:24 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:53:24 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:53:24 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2972345.inpcrd INFO 2017-03-18 22:53:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2972345/mobley_2972345_converted.input INFO 2017-03-18 22:53:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2972345/mobley_2972345_converted.cms WARNING 2017-03-18 22:53:40 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:53:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2972345/mobley_2972345_converted.inp INFO 2017-03-18 22:53:40 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2972345/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2972345/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2972345/mobley_2972345_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2972345/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 19.36656974 19.36656974 0.00000000 0.00000000 0.00000000 0.00000000 1.53766184 1.53766184 coulomb total 1.51837360 1.50464269 -0.01373091 1.50464267 -0.01373093 1.50457669 -0.01379691 1.53766184 0.01928824 coulomb-14 -17.86358800 -17.86192705 0.00166095 0.00000000 17.86358800 -17.86192854 0.00165946 0.00000000 17.86358800 improper 0.00000000 0.05215820 0.05215820 0.00000000 0.00000000 0.00000000 0.00000000 0.05217448 0.05217448 proper 0.44936160 0.39732307 -0.05203853 0.44948294 0.00012134 0.44941771 0.00005611 0.39731264 -0.05204896 vdw (SR) 0.00000000 -7.96164128 -7.96164128 0.00000000 0.00000000 0.00000000 0.00000000 33.26853208 33.26853208 vdw total 33.26823920 33.26856392 0.00032472 33.26856388 0.00032468 33.26852907 0.00028987 33.26853208 0.00029288 vdw-14 41.22997280 41.23020520 0.00023240 0.00000000 -41.22997280 41.23017853 0.00020573 0.00000000 -41.22997280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.70451360 3.70456940 0.00005580 3.70456941 0.00005581 3.70469901 0.00018541 3.70447176 -0.00004184 bond 3.97480000 3.97465354 -0.00014646 3.97465356 -0.00014644 3.97491510 0.00011510 3.97463264 -0.00016736 bonded 8.12867520 8.12870421 0.00002901 8.12870591 0.00003071 8.12903182 0.00035662 8.12859152 -0.00008368 dihedral 0.44936160 0.44948127 0.00011967 0.44948294 0.00012134 0.44941771 0.00005611 0.44948712 0.00012552 nonbonded 34.78661280 34.77320661 -0.01340619 34.77320685 -0.01340595 34.77310576 -0.01350704 34.80619392 0.01958112 potential 42.91528800 42.90191082 -0.01337718 42.90191175 -0.01337625 42.90199418 -0.01329382 42.93478544 0.01949744 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 42.91528800 Difference in potential energy from amber=>gromacs conversion: -0.01337718 Difference in potential energy from amber=>lammps conversion: -0.01337625 Difference in potential energy from amber=>desmond conversion: -0.01329382 Difference in potential energy from amber=>charmm conversion: 0.01949744 ======================================================================= INFO 2017-03-18 22:53:40 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2972345.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2972345.inpcrd') INFO 2017-03-18 22:53:40 Beginning InterMol conversion INFO 2017-03-18 22:53:40 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:53:40 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2972906.inpcrd INFO 2017-03-18 22:53:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2972906/mobley_2972906_converted.input INFO 2017-03-18 22:53:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2972906/mobley_2972906_converted.cms INFO 2017-03-18 22:53:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2972906/mobley_2972906_converted.rst7 WARNING 2017-03-18 22:53:56 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:53:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2972906/mobley_2972906_converted.inp INFO 2017-03-18 22:53:56 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2972906/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2972906/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2972906/mobley_2972906_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_2972906/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2972906/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 25.25041980 25.25041980 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 3.91593112 3.91593112 coulomb total 3.92542880 3.91632740 -0.00910140 3.91632734 -0.00910146 3.91628948 -0.00913932 3.92542880 0.00000000 3.91593112 -0.00949768 coulomb-14 -21.32752160 -21.33409240 -0.00657080 0.00000000 21.32752160 -21.33411048 -0.00658888 -21.32752160 0.00000000 0.00000000 21.32752160 improper 0.00000000 0.00002248 0.00002248 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00000000 0.00012762 0.00012762 0.00015011 0.00015011 0.00014664 0.00014664 0.00000000 0.00000000 0.00012552 0.00012552 vdw (SR) 0.00000000 -0.02653931 -0.02653931 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.75320368 -0.75320368 vdw total -0.75312000 -0.75320857 -0.00008857 -0.75320858 -0.00008858 -0.75320959 -0.00008959 -0.75312000 0.00000000 -0.75320368 -0.00008368 vdw-14 -0.72676080 -0.72666926 0.00009154 0.00000000 0.72676080 -0.72667037 0.00009043 -0.72676080 0.00000000 0.00000000 0.72676080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.80911360 3.80902340 -0.00009020 3.80902339 -0.00009021 3.80920193 0.00008833 3.80911360 0.00000000 3.80907176 -0.00004184 bond 1.58992000 1.59003167 0.00011167 1.59003167 0.00011167 1.59045124 0.00053124 1.58992000 0.00000000 1.59004552 0.00012552 bonded 5.39903360 5.39920517 0.00017157 5.39920518 0.00017158 5.39979981 0.00076621 5.39903360 0.00000000 5.39928464 0.00025104 dihedral 0.00000000 0.00015010 0.00015010 0.00015011 0.00015011 0.00014664 0.00014664 0.00000000 0.00000000 0.00016736 0.00016736 nonbonded 3.17230880 3.16311883 -0.00918997 3.16311877 -0.00919003 3.16307989 -0.00922891 3.17230880 0.00000000 3.16272744 -0.00958136 potential 8.57134240 8.56232400 -0.00901840 8.56232379 -0.00901861 8.56285599 -0.00848641 8.57134240 0.00000000 8.56197024 -0.00937216 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 8.57134240 Difference in potential energy from amber=>gromacs conversion: -0.00901840 Difference in potential energy from amber=>lammps conversion: -0.00901861 Difference in potential energy from amber=>desmond conversion: -0.00848641 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.00937216 ======================================================================= INFO 2017-03-18 22:53:56 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2972906.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2972906.inpcrd') INFO 2017-03-18 22:53:56 Beginning InterMol conversion INFO 2017-03-18 22:53:56 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:53:56 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:53:56 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_299266.inpcrd INFO 2017-03-18 22:53:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_299266/mobley_299266_converted.input INFO 2017-03-18 22:53:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_299266/mobley_299266_converted.cms WARNING 2017-03-18 22:54:12 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:54:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_299266/mobley_299266_converted.inp INFO 2017-03-18 22:54:12 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_299266/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_299266/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_299266/mobley_299266_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_299266/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 28.31903620 28.31903620 0.00000000 0.00000000 0.00000000 0.00000000 -10.49292808 -10.49292808 coulomb total -10.47924640 -10.48986585 -0.01061945 -10.48986581 -0.01061941 -10.48988895 -0.01064255 -10.49292808 -0.01368168 coulomb-14 -38.81454960 -38.80890205 0.00564755 0.00000000 38.81454960 -38.80892978 0.00561982 0.00000000 38.81454960 improper 0.00000000 0.00000822 0.00000822 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 38.42920320 38.42914071 -0.00006249 38.42914881 -0.00005439 38.42884392 -0.00035928 38.42916136 -0.00004184 vdw (SR) 0.00000000 0.56866907 0.56866907 0.00000000 0.00000000 0.00000000 0.00000000 4.39165192 4.39165192 vdw total 4.39152640 4.39158508 0.00005868 4.39158498 0.00005858 4.39164656 0.00012016 4.39165192 0.00012552 vdw-14 3.82292080 3.82291600 -0.00000480 0.00000000 -3.82292080 3.82296702 0.00004622 0.00000000 -3.82292080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.83470800 0.83485135 0.00014335 0.83485134 0.00014334 0.83501869 0.00031069 0.83483352 0.00012552 bond 1.02800880 1.02814552 0.00013672 1.02814553 0.00013673 1.02872032 0.00071152 1.02813432 0.00012552 bonded 40.29192000 40.29214580 0.00022580 40.29214568 0.00022568 40.29258293 0.00066293 40.29212920 0.00020920 dihedral 38.42920320 38.42914893 -0.00005427 38.42914881 -0.00005439 38.42884392 -0.00035928 38.42916136 -0.00004184 nonbonded -6.08772000 -6.09828077 -0.01056077 -6.09828042 -0.01056042 -6.09824238 -0.01052238 -6.10127616 -0.01355616 potential 34.20420000 34.19386503 -0.01033497 34.19386510 -0.01033490 34.19432325 -0.00987675 34.19085304 -0.01334696 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 34.20420000 Difference in potential energy from amber=>gromacs conversion: -0.01033497 Difference in potential energy from amber=>lammps conversion: -0.01033490 Difference in potential energy from amber=>desmond conversion: -0.00987675 Difference in potential energy from amber=>charmm conversion: -0.01334696 ======================================================================= INFO 2017-03-18 22:54:12 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_299266.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_299266.inpcrd') INFO 2017-03-18 22:54:12 Beginning InterMol conversion INFO 2017-03-18 22:54:12 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:54:12 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:54:12 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3006808.inpcrd INFO 2017-03-18 22:54:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3006808/mobley_3006808_converted.input INFO 2017-03-18 22:54:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3006808/mobley_3006808_converted.cms WARNING 2017-03-18 22:54:28 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:54:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3006808/mobley_3006808_converted.inp INFO 2017-03-18 22:54:28 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3006808/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3006808/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3006808/mobley_3006808_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3006808/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -105.94218713 -105.94218713 0.00000000 0.00000000 0.00000000 0.00000000 135.93673744 135.93673744 coulomb total 135.90887200 135.91330132 0.00442932 135.91329867 0.00442667 135.91353632 0.00466432 135.93673744 0.02786544 coulomb-14 241.84733360 241.85548845 0.00815485 0.00000000 -241.84733360 241.85584846 0.00851486 0.00000000 -241.84733360 proper 4.76808640 4.76799246 -0.00009394 4.76799226 -0.00009414 4.76798996 -0.00009644 4.76800272 -0.00008368 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 3.48937232 3.48937232 vdw total 3.48945600 3.48940519 -0.00005081 3.48940525 -0.00005075 3.48945509 -0.00000091 3.48937232 -0.00008368 vdw-14 3.48945600 3.48940519 -0.00005081 0.00000000 -3.48945600 3.48945509 -0.00000091 0.00000000 -3.48945600 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.14432400 1.14439533 0.00007133 1.14439534 0.00007134 1.14448692 0.00016292 1.14444952 0.00012552 bond 1.19536880 1.19533898 -0.00002982 1.19533897 -0.00002983 1.19540469 0.00003589 1.19532696 -0.00004184 bonded 7.10777920 7.10772677 -0.00005243 7.10772657 -0.00005263 7.10788156 0.00010236 7.10777920 0.00000000 dihedral 4.76808640 4.76799246 -0.00009394 4.76799226 -0.00009414 4.76798996 -0.00009644 4.76800272 -0.00008368 nonbonded 139.39832800 139.40270652 0.00437852 139.40270446 0.00437646 139.40299142 0.00466342 139.42610976 0.02778176 potential 146.50610720 146.51043329 0.00432609 146.51043346 0.00432626 146.51086483 0.00475763 146.53388896 0.02778176 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 146.50610720 Difference in potential energy from amber=>gromacs conversion: 0.00432609 Difference in potential energy from amber=>lammps conversion: 0.00432626 Difference in potential energy from amber=>desmond conversion: 0.00475763 Difference in potential energy from amber=>charmm conversion: 0.02778176 ======================================================================= INFO 2017-03-18 22:54:28 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3006808.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3006808.inpcrd') INFO 2017-03-18 22:54:28 Beginning InterMol conversion INFO 2017-03-18 22:54:28 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:54:28 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:54:28 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_303222.inpcrd INFO 2017-03-18 22:54:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_303222/mobley_303222_converted.input INFO 2017-03-18 22:54:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_303222/mobley_303222_converted.cms WARNING 2017-03-18 22:54:44 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:54:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_303222/mobley_303222_converted.inp INFO 2017-03-18 22:54:44 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_303222/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_303222/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_303222/mobley_303222_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_303222/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 10.83881385 10.83881385 0.00000000 0.00000000 0.00000000 0.00000000 11.50231808 11.50231808 coulomb total 11.50934720 11.50361419 -0.00573301 11.50361386 -0.00573334 11.50357623 -0.00577097 11.50231808 -0.00702912 coulomb-14 0.66692960 0.66480034 -0.00212926 0.00000000 -0.66692960 0.66477285 -0.00215675 0.00000000 -0.66692960 improper 0.00000000 0.00001898 0.00001898 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 19.26188080 19.26199166 0.00011086 19.26200381 0.00012301 19.26206791 0.00018711 19.26196448 0.00008368 vdw (SR) 0.00000000 -0.10679068 -0.10679068 0.00000000 0.00000000 0.00000000 0.00000000 0.81349512 0.81349512 vdw total 0.81336960 0.81346314 0.00009354 0.81346315 0.00009355 0.81345693 0.00008733 0.81349512 0.00012552 vdw-14 0.92006160 0.92025381 0.00019221 0.00000000 -0.92006160 0.92024778 0.00018618 0.00000000 -0.92006160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.60040400 0.60054269 0.00013869 0.60054270 0.00013870 0.60059248 0.00018848 0.60052952 0.00012552 bond 0.87487440 0.87472827 -0.00014613 0.87472825 -0.00014615 0.87511308 0.00023868 0.87474888 -0.00012552 bonded 20.73715920 20.73728160 0.00012240 20.73727476 0.00011556 20.73777347 0.00061427 20.73724288 0.00008368 dihedral 19.26188080 19.26201064 0.00012984 19.26200381 0.00012301 19.26206791 0.00018711 19.26196448 0.00008368 nonbonded 12.32271680 12.31707733 -0.00563947 12.31707719 -0.00563961 12.31703316 -0.00568364 12.31581320 -0.00690360 potential 33.05987600 33.05435893 -0.00551707 33.05435228 -0.00552372 33.05479646 -0.00507954 33.05305608 -0.00681992 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 33.05987600 Difference in potential energy from amber=>gromacs conversion: -0.00551707 Difference in potential energy from amber=>lammps conversion: -0.00552372 Difference in potential energy from amber=>desmond conversion: -0.00507954 Difference in potential energy from amber=>charmm conversion: -0.00681992 ======================================================================= INFO 2017-03-18 22:54:44 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_303222.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_303222.inpcrd') INFO 2017-03-18 22:54:44 Beginning InterMol conversion INFO 2017-03-18 22:54:44 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:54:44 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:54:44 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3034976.inpcrd INFO 2017-03-18 22:54:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3034976/mobley_3034976_converted.input INFO 2017-03-18 22:54:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3034976/mobley_3034976_converted.cms WARNING 2017-03-18 22:55:00 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:55:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3034976/mobley_3034976_converted.inp INFO 2017-03-18 22:55:00 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3034976/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3034976/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3034976/mobley_3034976_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3034976/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 50.87869273 50.87869273 0.00000000 0.00000000 0.00000000 0.00000000 -165.10992848 -165.10992848 coulomb total -165.06172880 -165.06469690 -0.00296810 -165.06469526 -0.00296646 -165.06546093 -0.00373213 -165.10992848 -0.04819968 coulomb-14 -215.94879200 -215.94338963 0.00540237 0.00000000 215.94879200 -215.94331724 0.00547476 0.00000000 215.94879200 improper 0.00000000 0.00001877 0.00001877 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 11.07797680 11.07775422 -0.00022258 11.07777137 -0.00020543 11.07773254 -0.00024426 11.07776760 -0.00020920 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 2.03367504 2.03367504 vdw total 2.03384240 2.03363025 -0.00021215 2.03363027 -0.00021213 2.03360723 -0.00023517 2.03367504 -0.00016736 vdw-14 2.03384240 2.03363025 -0.00021215 0.00000000 -2.03384240 2.03360723 -0.00023517 0.00000000 -2.03384240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.39031920 2.39026642 -0.00005278 2.39026644 -0.00005276 2.38980013 -0.00051907 2.39031920 0.00000000 bond 5.17477120 5.17470088 -0.00007032 5.17470091 -0.00007029 5.17471727 -0.00005393 5.17468752 -0.00008368 bonded 18.64306720 18.64274030 -0.00032690 18.64273871 -0.00032849 18.64224994 -0.00081726 18.64277432 -0.00029288 dihedral 11.07797680 11.07777299 -0.00020381 11.07777137 -0.00020543 11.07773254 -0.00024426 11.07776760 -0.00020920 nonbonded -163.02788640 -163.03106665 -0.00318025 -163.03106624 -0.00317984 -163.03185370 -0.00396730 -163.07625344 -0.04836704 potential -144.38481920 -144.38832634 -0.00350714 -144.38832539 -0.00350619 -144.38961867 -0.00479947 -144.43343728 -0.04861808 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -144.38481920 Difference in potential energy from amber=>gromacs conversion: -0.00350714 Difference in potential energy from amber=>lammps conversion: -0.00350619 Difference in potential energy from amber=>desmond conversion: -0.00479947 Difference in potential energy from amber=>charmm conversion: -0.04861808 ======================================================================= INFO 2017-03-18 22:55:00 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3034976.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3034976.inpcrd') INFO 2017-03-18 22:55:00 Beginning InterMol conversion INFO 2017-03-18 22:55:00 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:55:00 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:55:00 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3040612.inpcrd INFO 2017-03-18 22:55:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3040612/mobley_3040612_converted.input INFO 2017-03-18 22:55:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3040612/mobley_3040612_converted.cms WARNING 2017-03-18 22:55:16 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:55:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3040612/mobley_3040612_converted.inp INFO 2017-03-18 22:55:16 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3040612/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3040612/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3040612/mobley_3040612_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3040612/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -7.25516421 -7.25516421 0.00000000 0.00000000 0.00000000 0.00000000 -12.22753080 -12.22753080 coulomb total -12.23150560 -12.23197507 -0.00046947 -12.23197504 -0.00046944 -12.23200278 -0.00049718 -12.22753080 0.00397480 coulomb-14 -4.97644960 -4.97681086 -0.00036126 0.00000000 4.97644960 -4.97680562 -0.00035602 0.00000000 4.97644960 improper 0.00000000 0.00002862 0.00002862 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.02092000 0.02075823 -0.00016177 0.02078680 -0.00013320 0.02078581 -0.00013419 0.02075264 -0.00016736 vdw (SR) 0.00000000 6.24949898 6.24949898 0.00000000 0.00000000 0.00000000 0.00000000 29.70054240 29.70054240 vdw total 29.70054240 29.70044150 -0.00010090 29.70044157 -0.00010083 29.70073750 0.00019510 29.70054240 0.00000000 vdw-14 23.45090160 23.45094252 0.00004092 0.00000000 -23.45090160 23.45100808 0.00010648 0.00000000 -23.45090160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.30038720 1.30038648 -0.00000072 1.30038649 -0.00000071 1.30038603 -0.00000117 1.30034536 -0.00004184 bond 2.19785520 2.19780682 -0.00004838 2.19780683 -0.00004837 2.19765292 -0.00020228 2.19781336 -0.00004184 bonded 3.51916240 3.51898015 -0.00018225 3.51898012 -0.00018228 3.51882476 -0.00033764 3.51895320 -0.00020920 dihedral 0.02092000 0.02078685 -0.00013315 0.02078680 -0.00013320 0.02078581 -0.00013419 0.02079448 -0.00012552 nonbonded 17.46903680 17.46846643 -0.00057037 17.46846694 -0.00056986 17.46873472 -0.00030208 17.47301160 0.00397480 potential 20.98819920 20.98744658 -0.00075262 20.98744692 -0.00075228 20.98748955 -0.00070965 20.99196480 0.00376560 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 20.98819920 Difference in potential energy from amber=>gromacs conversion: -0.00075262 Difference in potential energy from amber=>lammps conversion: -0.00075228 Difference in potential energy from amber=>desmond conversion: -0.00070965 Difference in potential energy from amber=>charmm conversion: 0.00376560 ======================================================================= INFO 2017-03-18 22:55:16 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3040612.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3040612.inpcrd') INFO 2017-03-18 22:55:16 Beginning InterMol conversion INFO 2017-03-18 22:55:16 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:55:16 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:55:16 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3047364.inpcrd INFO 2017-03-18 22:55:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3047364/mobley_3047364_converted.input INFO 2017-03-18 22:55:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3047364/mobley_3047364_converted.cms WARNING 2017-03-18 22:55:32 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:55:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3047364/mobley_3047364_converted.inp INFO 2017-03-18 22:55:32 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3047364/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3047364/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3047364/mobley_3047364_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3047364/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 1030.91661768 1030.91661768 0.00000000 0.00000000 0.00000000 0.00000000 -1866.10584000 -1866.10584000 coulomb total -1866.05605040 -1866.11959005 -0.06353965 -1866.11956352 -0.06351312 -1866.11980619 -0.06375579 -1866.10584000 -0.04978960 coulomb-14 -2896.93716640 -2897.03620773 -0.09904133 0.00000000 2896.93716640 -2897.03658242 -0.09941602 0.00000000 2896.93716640 improper 0.00000000 0.00011802 0.00011802 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 1.71627680 1.71611189 -0.00016491 1.71622596 -0.00005084 1.71624625 -0.00003055 1.71610944 -0.00016736 vdw (SR) 0.00000000 -9.14258807 -9.14258807 0.00000000 0.00000000 0.00000000 0.00000000 36.95061944 36.95061944 vdw total 36.95057760 36.95075509 0.00017749 36.95075542 0.00017782 36.95055354 -0.00002406 36.95061944 0.00004184 vdw-14 46.09303600 46.09334316 0.00030716 0.00000000 -46.09303600 46.09323307 0.00019707 0.00000000 -46.09303600 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 12.93107040 12.93091163 -0.00015877 12.93091183 -0.00015857 12.93148913 0.00041873 12.93090304 -0.00016736 bond 9.80311200 9.80325494 0.00014294 9.80325509 0.00014309 9.80376295 0.00065095 9.80323752 0.00012552 bonded 24.45045920 24.45039648 -0.00006272 24.45039288 -0.00006632 24.45149833 0.00103913 24.45037552 -0.00008368 dihedral 1.71627680 1.71622991 -0.00004689 1.71622596 -0.00005084 1.71624625 -0.00003055 1.71623496 -0.00004184 nonbonded -1829.10547280 -1829.16883496 -0.06336216 -1829.16881856 -0.06334576 -1829.16925265 -0.06377985 -1829.15522056 -0.04974776 potential -1804.65501360 -1804.71843848 -0.06342488 -1804.71840120 -0.06338760 -1804.71812087 -0.06310727 -1804.70484504 -0.04983144 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -1804.65501360 Difference in potential energy from amber=>gromacs conversion: -0.06342488 Difference in potential energy from amber=>lammps conversion: -0.06338760 Difference in potential energy from amber=>desmond conversion: -0.06310727 Difference in potential energy from amber=>charmm conversion: -0.04983144 ======================================================================= INFO 2017-03-18 22:55:32 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3047364.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3047364.inpcrd') INFO 2017-03-18 22:55:32 Beginning InterMol conversion INFO 2017-03-18 22:55:32 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:55:32 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3053621.inpcrd INFO 2017-03-18 22:55:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3053621/mobley_3053621_converted.input INFO 2017-03-18 22:55:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3053621/mobley_3053621_converted.cms INFO 2017-03-18 22:55:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3053621/mobley_3053621_converted.rst7 WARNING 2017-03-18 22:55:48 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:55:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3053621/mobley_3053621_converted.inp INFO 2017-03-18 22:55:48 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3053621/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3053621/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3053621/mobley_3053621_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_3053621/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3053621/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 10.64360980 10.64360980 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 9.94951016 9.94951016 coulomb total 9.95499120 9.94627066 -0.00872054 9.94627049 -0.00872071 9.94625769 -0.00873351 9.95499120 0.00000000 9.94951016 -0.00548104 coulomb-14 -0.69412560 -0.69733914 -0.00321354 0.00000000 0.69412560 -0.69733865 -0.00321305 -0.69412560 0.00000000 0.00000000 0.69412560 improper 0.00000000 0.00003282 0.00003282 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00031805 -0.00010035 0.00035084 -0.00006756 0.00034715 -0.00007125 0.00041840 0.00000000 0.00033472 -0.00008368 vdw (SR) 0.00000000 -0.69412071 -0.69412071 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 14.83822128 14.83822128 vdw total 14.83813760 14.83824860 0.00011100 14.83824848 0.00011088 14.83831621 0.00017861 14.83813760 0.00000000 14.83822128 0.00008368 vdw-14 15.53226320 15.53236931 0.00010611 0.00000000 -15.53226320 15.53243654 0.00017334 15.53226320 0.00000000 0.00000000 -15.53226320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.00209200 0.00199167 -0.00010033 0.00199167 -0.00010033 0.00197967 -0.00011233 0.00209200 0.00000000 0.00200832 -0.00008368 bond 0.73094480 0.73090974 -0.00003506 0.73090974 -0.00003506 0.73079815 -0.00014665 0.73094480 0.00000000 0.73090296 -0.00004184 bonded 0.73345520 0.73325228 -0.00020292 0.73325225 -0.00020295 0.73312497 -0.00033023 0.73345520 0.00000000 0.73328784 -0.00016736 dihedral 0.00041840 0.00035087 -0.00006753 0.00035084 -0.00006756 0.00034715 -0.00007125 0.00041840 0.00000000 0.00037656 -0.00004184 nonbonded 24.79312880 24.78451926 -0.00860954 24.78451896 -0.00860984 24.78457391 -0.00855489 24.79312880 0.00000000 24.78773144 -0.00539736 potential 25.52658400 25.51777154 -0.00881246 25.51777124 -0.00881276 25.51767505 -0.00890895 25.52658400 0.00000000 25.52101928 -0.00556472 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 25.52658400 Difference in potential energy from amber=>gromacs conversion: -0.00881246 Difference in potential energy from amber=>lammps conversion: -0.00881276 Difference in potential energy from amber=>desmond conversion: -0.00890895 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.00556472 ======================================================================= INFO 2017-03-18 22:55:48 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3053621.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3053621.inpcrd') INFO 2017-03-18 22:55:48 Beginning InterMol conversion INFO 2017-03-18 22:55:48 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:55:49 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:55:49 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3060426.inpcrd INFO 2017-03-18 22:55:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3060426/mobley_3060426_converted.input INFO 2017-03-18 22:55:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3060426/mobley_3060426_converted.cms WARNING 2017-03-18 22:56:04 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:56:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3060426/mobley_3060426_converted.inp INFO 2017-03-18 22:56:04 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3060426/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3060426/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3060426/mobley_3060426_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3060426/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 21.78158484 21.78158484 0.00000000 0.00000000 0.00000000 0.00000000 -18.26504280 -18.26504280 coulomb total -18.28073280 -18.26591517 0.01481763 -18.26591516 0.01481764 -18.26596223 0.01477057 -18.26504280 0.01569000 coulomb-14 -40.03711440 -40.04750001 -0.01038561 0.00000000 40.03711440 -40.04748532 -0.01037092 0.00000000 40.03711440 proper 11.22483520 11.22465167 -0.00018353 11.22464943 -0.00018577 11.22463140 -0.00020380 11.22466784 -0.00016736 vdw (SR) 0.00000000 10.43443391 10.43443391 0.00000000 0.00000000 0.00000000 0.00000000 28.50994336 28.50994336 vdw total 28.50977600 28.50960990 -0.00016610 28.50961031 -0.00016569 28.50945638 -0.00031962 28.50994336 0.00016736 vdw-14 18.07529840 18.07517598 -0.00012242 0.00000000 -18.07529840 18.07511029 -0.00018811 0.00000000 -18.07529840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 8.00022640 8.00040381 0.00017741 8.00040380 0.00017740 7.99960277 -0.00062363 8.00035192 0.00012552 bond 1.09411600 1.09404803 -0.00006797 1.09404801 -0.00006799 1.09406752 -0.00004848 1.09403232 -0.00008368 bonded 20.31917760 20.31910350 -0.00007410 20.31910124 -0.00007636 20.31830170 -0.00087590 20.31905208 -0.00012552 dihedral 11.22483520 11.22465167 -0.00018353 11.22464943 -0.00018577 11.22463140 -0.00020380 11.22466784 -0.00016736 nonbonded 10.22904320 10.24369473 0.01465153 10.24369557 0.01465237 10.24349415 0.01445095 10.24490056 0.01585736 potential 30.54822080 30.56279823 0.01457743 30.56279660 0.01457580 30.56169520 0.01347440 30.56395264 0.01573184 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 30.54822080 Difference in potential energy from amber=>gromacs conversion: 0.01457743 Difference in potential energy from amber=>lammps conversion: 0.01457580 Difference in potential energy from amber=>desmond conversion: 0.01347440 Difference in potential energy from amber=>charmm conversion: 0.01573184 ======================================================================= INFO 2017-03-18 22:56:04 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3060426.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3060426.inpcrd') INFO 2017-03-18 22:56:05 Beginning InterMol conversion INFO 2017-03-18 22:56:05 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:56:05 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:56:05 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3083321.inpcrd INFO 2017-03-18 22:56:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3083321/mobley_3083321_converted.input INFO 2017-03-18 22:56:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3083321/mobley_3083321_converted.cms WARNING 2017-03-18 22:56:20 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:56:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3083321/mobley_3083321_converted.inp INFO 2017-03-18 22:56:20 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3083321/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3083321/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3083321/mobley_3083321_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3083321/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -12.59356994 -12.59356994 0.00000000 0.00000000 0.00000000 0.00000000 -14.26367440 -14.26367440 coulomb total -14.26869520 -14.25417966 0.01451554 -14.25417965 0.01451555 -14.25418558 0.01450962 -14.26367440 0.00502080 coulomb-14 -1.67443680 -1.66060972 0.01382708 0.00000000 1.67443680 -1.66063059 0.01380621 0.00000000 1.67443680 proper 21.60617600 21.60596160 -0.00021440 21.60598228 -0.00019372 21.60590772 -0.00026828 21.60584128 -0.00033472 vdw (SR) 0.00000000 -0.92141987 -0.92141987 0.00000000 0.00000000 0.00000000 0.00000000 5.46585208 5.46585208 vdw total 5.46597760 5.46579068 -0.00018692 5.46579058 -0.00018702 5.46577807 -0.00019953 5.46585208 -0.00012552 vdw-14 6.38729440 6.38721055 -0.00008385 0.00000000 -6.38729440 6.38718616 -0.00010824 0.00000000 -6.38729440 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.92171120 1.92191013 0.00019893 1.92191015 0.00019895 1.92179404 0.00008284 1.92196224 0.00025104 bond 1.19536880 1.19521015 -0.00015865 1.19521014 -0.00015866 1.19492170 -0.00044710 1.19520144 -0.00016736 bonded 24.72325600 24.72308188 -0.00017412 24.72310257 -0.00015343 24.72262346 -0.00063254 24.72300496 -0.00025104 dihedral 21.60617600 21.60596160 -0.00021440 21.60598228 -0.00019372 21.60590772 -0.00026828 21.60584128 -0.00033472 nonbonded -8.80271760 -8.78838898 0.01432862 -8.78838866 0.01432894 -8.78840750 0.01431010 -8.79782232 0.00489528 potential 15.92053840 15.93469290 0.01415450 15.93471379 0.01417539 15.93419468 0.01365628 15.92518264 0.00464424 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 15.92053840 Difference in potential energy from amber=>gromacs conversion: 0.01415450 Difference in potential energy from amber=>lammps conversion: 0.01417539 Difference in potential energy from amber=>desmond conversion: 0.01365628 Difference in potential energy from amber=>charmm conversion: 0.00464424 ======================================================================= INFO 2017-03-18 22:56:20 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3083321.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3083321.inpcrd') INFO 2017-03-18 22:56:21 Beginning InterMol conversion INFO 2017-03-18 22:56:21 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:56:21 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:56:21 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3105103.inpcrd INFO 2017-03-18 22:56:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3105103/mobley_3105103_converted.input INFO 2017-03-18 22:56:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3105103/mobley_3105103_converted.cms WARNING 2017-03-18 22:56:37 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:56:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3105103/mobley_3105103_converted.inp INFO 2017-03-18 22:56:37 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3105103/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3105103/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3105103/mobley_3105103_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3105103/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 630.51917583 630.51917583 0.00000000 0.00000000 0.00000000 0.00000000 -623.45428360 -623.45428360 coulomb total -623.51516080 -623.53624357 -0.02108277 -623.53624816 -0.02108736 -623.53550341 -0.02034261 -623.45428360 0.06087720 coulomb-14 -1254.01258080 -1254.05541940 -0.04283860 0.00000000 1254.01258080 -1254.05495635 -0.04237555 0.00000000 1254.01258080 improper 0.00000000 0.00175712 0.00175712 0.00000000 0.00000000 0.00000000 0.00000000 0.00175728 0.00175728 proper 46.86791280 46.86602644 -0.00188636 46.86778310 -0.00012970 46.86782619 -0.00008661 46.86603000 -0.00188280 vdw (SR) 0.00000000 345.41303877 345.41303877 0.00000000 0.00000000 0.00000000 0.00000000 397.57782192 397.57782192 vdw total 397.57790560 397.57541946 -0.00248614 397.57542449 -0.00248111 397.57275133 -0.00515427 397.57782192 -0.00008368 vdw-14 52.16234640 52.16238069 0.00003429 0.00000000 -52.16234640 52.16201921 -0.00032719 0.00000000 -52.16234640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 18.76147440 18.76166018 0.00018578 18.76166017 0.00018577 18.76149411 0.00001971 18.76155808 0.00008368 bond 23.95800240 23.95791836 -0.00008404 23.95791830 -0.00008410 23.95993122 0.00192882 23.95791872 -0.00008368 bonded 89.58738960 89.58736210 -0.00002750 89.58736157 -0.00002803 89.58925152 0.00186192 89.58726408 -0.00012552 dihedral 46.86791280 46.86778355 -0.00012925 46.86778310 -0.00012970 46.86782619 -0.00008661 46.86778728 -0.00012552 nonbonded -225.93725520 -225.96082411 -0.02356891 -225.96081112 -0.02355592 -225.96275208 -0.02549688 -225.87646168 0.06079352 potential -136.34986560 -136.37346202 -0.02359642 -136.37345081 -0.02358521 -136.37367298 -0.02380738 -136.28919760 0.06066800 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -136.34986560 Difference in potential energy from amber=>gromacs conversion: -0.02359642 Difference in potential energy from amber=>lammps conversion: -0.02358521 Difference in potential energy from amber=>desmond conversion: -0.02380738 Difference in potential energy from amber=>charmm conversion: 0.06066800 ======================================================================= INFO 2017-03-18 22:56:37 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3105103.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3105103.inpcrd') INFO 2017-03-18 22:56:37 Beginning InterMol conversion INFO 2017-03-18 22:56:37 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:56:37 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:56:37 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_313406.inpcrd INFO 2017-03-18 22:56:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_313406/mobley_313406_converted.input INFO 2017-03-18 22:56:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_313406/mobley_313406_converted.cms WARNING 2017-03-18 22:56:53 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:56:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_313406/mobley_313406_converted.inp INFO 2017-03-18 22:56:53 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_313406/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_313406/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_313406/mobley_313406_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_313406/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -1.60638953 -1.60638953 0.00000000 0.00000000 0.00000000 0.00000000 -6.70214040 -6.70214040 coulomb total -6.71029920 -6.70461344 0.00568576 -6.70461356 0.00568564 -6.70466115 0.00563805 -6.70214040 0.00815880 coulomb-14 -5.10071440 -5.09822391 0.00249049 0.00000000 5.10071440 -5.09826429 0.00245011 0.00000000 5.10071440 proper 3.24301840 3.24314189 0.00012349 3.24314187 0.00012347 3.24314044 0.00012204 3.24314392 0.00012552 vdw (SR) 0.00000000 -0.44584826 -0.44584826 0.00000000 0.00000000 0.00000000 0.00000000 1.57017152 1.57017152 vdw total 1.56983680 1.57013813 0.00030133 1.57013817 0.00030137 1.57015537 0.00031857 1.57017152 0.00033472 vdw-14 2.01585120 2.01598639 0.00013519 0.00000000 -2.01585120 2.01600514 0.00015394 0.00000000 -2.01585120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.03302960 1.03318694 0.00015734 1.03318696 0.00015736 1.03323191 0.00020231 1.03315512 0.00012552 bond 0.75939600 0.75931163 -0.00008437 0.75931165 -0.00008435 0.75916110 -0.00023490 0.75931232 -0.00008368 bonded 5.03544400 5.03564046 0.00019646 5.03564048 0.00019648 5.03553345 0.00008945 5.03561136 0.00016736 dihedral 3.24301840 3.24314189 0.00012349 3.24314187 0.00012347 3.24314044 0.00012204 3.24314392 0.00012552 nonbonded -5.14046240 -5.13447531 0.00598709 -5.13447510 0.00598730 -5.13450578 0.00595662 -5.13196888 0.00849352 potential -0.10501840 -0.09883485 0.00618355 -0.09883476 0.00618364 -0.09898952 0.00602888 -0.09631568 0.00870272 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -0.10501840 Difference in potential energy from amber=>gromacs conversion: 0.00618355 Difference in potential energy from amber=>lammps conversion: 0.00618364 Difference in potential energy from amber=>desmond conversion: 0.00602888 Difference in potential energy from amber=>charmm conversion: 0.00870272 ======================================================================= INFO 2017-03-18 22:56:53 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_313406.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_313406.inpcrd') INFO 2017-03-18 22:56:53 Beginning InterMol conversion INFO 2017-03-18 22:56:53 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:56:53 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:56:53 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3144334.inpcrd INFO 2017-03-18 22:56:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3144334/mobley_3144334_converted.input INFO 2017-03-18 22:56:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3144334/mobley_3144334_converted.cms WARNING 2017-03-18 22:57:09 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:57:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3144334/mobley_3144334_converted.inp INFO 2017-03-18 22:57:09 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3144334/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3144334/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3144334/mobley_3144334_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3144334/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 11.38092035 11.38092035 0.00000000 0.00000000 0.00000000 0.00000000 -79.60139496 -79.60139496 coulomb total -79.62235680 -79.61368228 0.00867452 -79.61368337 0.00867343 -79.61429775 0.00805905 -79.60139496 0.02096184 coulomb-14 -90.98359040 -90.99460263 -0.01101223 0.00000000 90.98359040 -90.99465666 -0.01106626 0.00000000 90.98359040 improper 0.00000000 0.00002692 0.00002692 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00037627 -0.00004213 0.00040317 -0.00001523 0.00040376 -0.00001464 0.00037656 -0.00004184 vdw (SR) 0.00000000 -0.88556290 -0.88556290 0.00000000 0.00000000 0.00000000 0.00000000 21.35651672 21.35651672 vdw total 21.35680960 21.35642805 -0.00038155 21.35642802 -0.00038158 21.35637922 -0.00043038 21.35651672 -0.00029288 vdw-14 22.24214400 22.24199095 -0.00015305 0.00000000 -22.24214400 22.24197359 -0.00017041 0.00000000 -22.24214400 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.82885040 0.82888137 0.00003097 0.82888136 0.00003096 0.82897282 0.00012242 0.82889224 0.00004184 bond 2.06396720 2.06409083 0.00012363 2.06409084 0.00012364 2.06374369 -0.00022351 2.06409272 0.00012552 bonded 2.89323600 2.89337539 0.00013939 2.89337537 0.00013937 2.89312027 -0.00011573 2.89340336 0.00016736 dihedral 0.00041840 0.00040320 -0.00001520 0.00040317 -0.00001523 0.00040376 -0.00001464 0.00041840 0.00000000 nonbonded -58.26554720 -58.25725423 0.00829297 -58.25725451 0.00829269 -58.25791853 0.00762867 -58.24487824 0.02066896 potential -55.37231120 -55.36387884 0.00843236 -55.36387626 0.00843494 -55.36485531 0.00745589 -55.35151672 0.02079448 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -55.37231120 Difference in potential energy from amber=>gromacs conversion: 0.00843236 Difference in potential energy from amber=>lammps conversion: 0.00843494 Difference in potential energy from amber=>desmond conversion: 0.00745589 Difference in potential energy from amber=>charmm conversion: 0.02079448 ======================================================================= INFO 2017-03-18 22:57:09 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3144334.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3144334.inpcrd') INFO 2017-03-18 22:57:09 Beginning InterMol conversion INFO 2017-03-18 22:57:09 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:57:09 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:57:09 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3151666.inpcrd INFO 2017-03-18 22:57:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3151666/mobley_3151666_converted.input INFO 2017-03-18 22:57:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3151666/mobley_3151666_converted.cms WARNING 2017-03-18 22:57:25 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:57:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3151666/mobley_3151666_converted.inp INFO 2017-03-18 22:57:25 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3151666/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3151666/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3151666/mobley_3151666_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3151666/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 15.59511339 15.59511339 0.00000000 0.00000000 0.00000000 0.00000000 -5.80881456 -5.80881456 coulomb total -5.82412800 -5.81083445 0.01329355 -5.81083418 0.01329382 -5.81089012 0.01323788 -5.80881456 0.01531344 coulomb-14 -21.40785440 -21.40594784 0.00190656 0.00000000 21.40785440 -21.40593545 0.00191895 0.00000000 21.40785440 proper 15.11093440 15.11082182 -0.00011258 15.11082185 -0.00011255 15.11083637 -0.00009803 15.11080888 -0.00012552 vdw (SR) 0.00000000 -5.00428822 -5.00428822 0.00000000 0.00000000 0.00000000 0.00000000 7.93905632 7.93905632 vdw total 7.93914000 7.93883982 -0.00030018 7.93884001 -0.00029999 7.93887988 -0.00026012 7.93905632 -0.00008368 vdw-14 12.94320400 12.94312804 -0.00007596 0.00000000 -12.94320400 12.94316572 -0.00003828 0.00000000 -12.94320400 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.03044720 4.03057734 0.00013014 4.03057732 0.00013012 4.03077726 0.00033006 4.03048904 0.00004184 bond 1.23302480 1.23313433 0.00010953 1.23313434 0.00010954 1.23283312 -0.00019168 1.23315032 0.00012552 bonded 20.37440640 20.37453349 0.00012709 20.37453351 0.00012711 20.37444675 0.00004035 20.37444824 0.00004184 dihedral 15.11093440 15.11082182 -0.00011258 15.11082185 -0.00011255 15.11083637 -0.00009803 15.11080888 -0.00012552 nonbonded 2.11501200 2.12800537 0.01299337 2.12800554 0.01299354 2.12798976 0.01297776 2.13024176 0.01522976 potential 22.48941840 22.50253886 0.01312046 22.50253901 0.01312061 22.50229474 0.01287634 22.50464816 0.01522976 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 22.48941840 Difference in potential energy from amber=>gromacs conversion: 0.01312046 Difference in potential energy from amber=>lammps conversion: 0.01312061 Difference in potential energy from amber=>desmond conversion: 0.01287634 Difference in potential energy from amber=>charmm conversion: 0.01522976 ======================================================================= INFO 2017-03-18 22:57:25 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3151666.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3151666.inpcrd') INFO 2017-03-18 22:57:25 Beginning InterMol conversion INFO 2017-03-18 22:57:25 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:57:25 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:57:25 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3167746.inpcrd INFO 2017-03-18 22:57:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3167746/mobley_3167746_converted.input INFO 2017-03-18 22:57:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3167746/mobley_3167746_converted.cms WARNING 2017-03-18 22:57:41 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:57:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3167746/mobley_3167746_converted.inp INFO 2017-03-18 22:57:41 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3167746/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3167746/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3167746/mobley_3167746_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3167746/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 7.21719390 7.21719390 0.00000000 0.00000000 0.00000000 0.00000000 3.65409640 3.65409640 coulomb total 3.64384560 3.64953947 0.00569387 3.64953944 0.00569384 3.64949973 0.00565413 3.65409640 0.01025080 coulomb-14 -3.56853360 -3.56765443 0.00087917 0.00000000 3.56853360 -3.56764659 0.00088701 0.00000000 3.56853360 proper 8.54958560 8.54953949 -0.00004611 8.54953958 -0.00004602 8.54954305 -0.00004255 8.54954376 -0.00004184 vdw (SR) 0.00000000 -3.20623757 -3.20623757 0.00000000 0.00000000 0.00000000 0.00000000 6.49001160 6.49001160 vdw total 6.49022080 6.48986074 -0.00036006 6.48986098 -0.00035982 6.48986091 -0.00035989 6.49001160 -0.00020920 vdw-14 9.69642000 9.69609831 -0.00032169 0.00000000 -9.69642000 9.69610633 -0.00031367 0.00000000 -9.69642000 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.20661760 3.20657715 -0.00004045 3.20657714 -0.00004046 3.20678113 0.00016353 3.20653392 -0.00008368 bond 1.11168880 1.11173774 0.00004894 1.11173775 0.00004895 1.11198124 0.00029244 1.11173064 0.00004184 bonded 12.86789200 12.86785438 -0.00003762 12.86785447 -0.00003753 12.86830543 0.00041343 12.86780832 -0.00008368 dihedral 8.54958560 8.54953949 -0.00004611 8.54953958 -0.00004602 8.54954305 -0.00004255 8.54954376 -0.00004184 nonbonded 10.13406640 10.13940021 0.00533381 10.13940016 0.00533376 10.13936064 0.00529424 10.14410800 0.01004160 potential 23.00195840 23.00725459 0.00529619 23.00725451 0.00529611 23.00758362 0.00562522 23.01191632 0.00995792 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 23.00195840 Difference in potential energy from amber=>gromacs conversion: 0.00529619 Difference in potential energy from amber=>lammps conversion: 0.00529611 Difference in potential energy from amber=>desmond conversion: 0.00562522 Difference in potential energy from amber=>charmm conversion: 0.00995792 ======================================================================= INFO 2017-03-18 22:57:41 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3167746.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3167746.inpcrd') INFO 2017-03-18 22:57:41 Beginning InterMol conversion INFO 2017-03-18 22:57:41 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:57:42 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3169935.inpcrd INFO 2017-03-18 22:57:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3169935/mobley_3169935_converted.input INFO 2017-03-18 22:57:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3169935/mobley_3169935_converted.cms INFO 2017-03-18 22:57:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3169935/mobley_3169935_converted.rst7 WARNING 2017-03-18 22:57:57 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:57:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3169935/mobley_3169935_converted.inp INFO 2017-03-18 22:57:57 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3169935/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3169935/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3169935/mobley_3169935_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_3169935/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3169935/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -34.50628565 -34.50628565 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -69.22520048 -69.22520048 coulomb total -69.22804560 -69.22210941 0.00593619 -69.22210850 0.00593710 -69.22232101 0.00572459 -69.22804560 0.00000000 -69.22520048 0.00284512 coulomb-14 -34.71130080 -34.71582376 -0.00452296 0.00000000 34.71130080 -34.71579525 -0.00449445 -34.71130080 0.00000000 0.00000000 34.71130080 improper 0.00000000 0.11498584 0.11498584 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.11497632 0.11497632 proper 0.22007840 0.10492978 -0.11514862 0.21991419 -0.00016421 0.21991690 -0.00016150 0.22007840 0.00000000 0.10493472 -0.11514368 vdw (SR) 0.00000000 -1.88917768 -1.88917768 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 16.13082624 16.13082624 vdw total 16.13099360 16.13085642 -0.00013718 16.13085636 -0.00013724 16.13090197 -0.00009163 16.13099360 0.00000000 16.13082624 -0.00016736 vdw-14 18.02006960 18.02003410 -0.00003550 0.00000000 -18.02006960 18.02007692 0.00000732 18.02006960 0.00000000 0.00000000 -18.02006960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.23504480 4.23508653 0.00004173 4.23508664 0.00004184 4.23499535 -0.00004945 4.23504480 0.00000000 4.23517032 0.00012552 bond 6.14085680 6.14085268 -0.00000412 6.14085262 -0.00000418 6.13987519 -0.00098161 6.14085680 0.00000000 6.14085680 0.00000000 bonded 10.59598000 10.59585483 -0.00012517 10.59585345 -0.00012655 10.59478744 -0.00119256 10.59598000 0.00000000 10.59593816 -0.00004184 dihedral 0.22007840 0.21991562 -0.00016278 0.21991419 -0.00016421 0.21991690 -0.00016150 0.22007840 0.00000000 0.21991104 -0.00016736 nonbonded -53.09705200 -53.09125299 0.00579901 -53.09125298 0.00579902 -53.09141904 0.00563296 -53.09705200 0.00000000 -53.09437424 0.00267776 potential -42.50107200 -42.49539816 0.00567384 -42.49539850 0.00567350 -42.49668257 0.00438943 -42.50107200 0.00000000 -42.49843608 0.00263592 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -42.50107200 Difference in potential energy from amber=>gromacs conversion: 0.00567384 Difference in potential energy from amber=>lammps conversion: 0.00567350 Difference in potential energy from amber=>desmond conversion: 0.00438943 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00263592 ======================================================================= INFO 2017-03-18 22:57:57 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3169935.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3169935.inpcrd') INFO 2017-03-18 22:57:58 Beginning InterMol conversion INFO 2017-03-18 22:57:58 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:57:58 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:57:58 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3183805.inpcrd INFO 2017-03-18 22:57:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3183805/mobley_3183805_converted.input INFO 2017-03-18 22:57:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3183805/mobley_3183805_converted.cms WARNING 2017-03-18 22:58:13 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:58:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3183805/mobley_3183805_converted.inp INFO 2017-03-18 22:58:13 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3183805/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3183805/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3183805/mobley_3183805_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3183805/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 7.79285820 7.79285820 0.00000000 0.00000000 0.00000000 0.00000000 -29.47632184 -29.47632184 coulomb total -29.49259760 -29.47347812 0.01911948 -29.47347798 0.01911962 -29.47356588 0.01903172 -29.47632184 0.01627576 coulomb-14 -37.25057040 -37.26633633 -0.01576593 0.00000000 37.25057040 -37.26633525 -0.01576485 0.00000000 37.25057040 improper 0.00000000 0.00011900 0.00011900 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00167360 0.00158099 -0.00009261 0.00169997 0.00002637 0.00170081 0.00002721 0.00158992 -0.00008368 vdw (SR) 0.00000000 22.81201045 22.81201045 0.00000000 0.00000000 0.00000000 0.00000000 47.04648592 47.04648592 vdw total 47.04656960 47.04615084 -0.00041876 47.04615120 -0.00041840 47.04576937 -0.00080023 47.04648592 -0.00008368 vdw-14 24.23414640 24.23414039 -0.00000601 0.00000000 -24.23414640 24.23413096 -0.00001544 0.00000000 -24.23414640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.17988800 1.17979923 -0.00008877 1.17979922 -0.00008878 1.17967843 -0.00020957 1.17980432 -0.00008368 bond 2.55475040 2.55464991 -0.00010049 2.55464990 -0.00010050 2.55410848 -0.00064192 2.55466672 -0.00008368 bonded 3.73631200 3.73614913 -0.00016287 3.73614909 -0.00016291 3.73548772 -0.00082428 3.73618648 -0.00012552 dihedral 0.00167360 0.00169999 0.00002639 0.00169997 0.00002637 0.00170081 0.00002721 0.00171544 0.00004184 nonbonded 17.55397200 17.57267271 0.01870071 17.57267322 0.01870122 17.57220349 0.01823149 17.57016408 0.01619208 potential 21.29028400 21.30882184 0.01853784 21.30882247 0.01853847 21.30761823 0.01733423 21.30630872 0.01602472 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 21.29028400 Difference in potential energy from amber=>gromacs conversion: 0.01853784 Difference in potential energy from amber=>lammps conversion: 0.01853847 Difference in potential energy from amber=>desmond conversion: 0.01733423 Difference in potential energy from amber=>charmm conversion: 0.01602472 ======================================================================= INFO 2017-03-18 22:58:13 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3183805.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3183805.inpcrd') INFO 2017-03-18 22:58:14 Beginning InterMol conversion INFO 2017-03-18 22:58:14 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:58:14 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:58:14 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3187514.inpcrd INFO 2017-03-18 22:58:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3187514/mobley_3187514_converted.input INFO 2017-03-18 22:58:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3187514/mobley_3187514_converted.cms WARNING 2017-03-18 22:58:29 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:58:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3187514/mobley_3187514_converted.inp INFO 2017-03-18 22:58:30 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3187514/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3187514/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3187514/mobley_3187514_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3187514/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -25.68051858 -25.68051858 0.00000000 0.00000000 0.00000000 0.00000000 -100.20788784 -100.20788784 coulomb total -100.21809680 -100.22127740 -0.00318060 -100.22127664 -0.00317984 -100.22170897 -0.00361217 -100.20788784 0.01020896 coulomb-14 -74.53837840 -74.54075882 -0.00238042 0.00000000 74.53837840 -74.54080386 -0.00242546 0.00000000 74.53837840 improper 0.00000000 0.11596783 0.11596783 0.00000000 0.00000000 0.00000000 0.00000000 0.11598048 0.11598048 proper 0.22217040 0.10602363 -0.11614677 0.22199002 -0.00018038 0.22196785 -0.00020255 0.10602256 -0.11614784 vdw (SR) 0.00000000 0.53108681 0.53108681 0.00000000 0.00000000 0.00000000 0.00000000 21.24526416 21.24526416 vdw total 21.24509680 21.24527117 0.00017437 21.24527127 0.00017447 21.24523793 0.00014113 21.24526416 0.00016736 vdw-14 20.71414720 20.71418436 0.00003716 0.00000000 -20.71414720 20.71419502 0.00004782 0.00000000 -20.71414720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.00241440 4.00229618 -0.00011822 4.00229616 -0.00011824 4.00237635 -0.00003805 4.00237256 -0.00004184 bond 6.34294400 6.34285623 -0.00008777 6.34285614 -0.00008786 6.34353972 0.00059572 6.34286032 -0.00008368 bonded 10.56752880 10.56714386 -0.00038494 10.56714232 -0.00038648 10.56788393 0.00035513 10.56723592 -0.00029288 dihedral 0.22217040 0.22199145 -0.00017895 0.22199002 -0.00018038 0.22196785 -0.00020255 0.22200304 -0.00016736 nonbonded -78.97300000 -78.97600623 -0.00300623 -78.97600411 -0.00300411 -78.97647104 -0.00347104 -78.96262368 0.01037632 potential -68.40547120 -68.40886237 -0.00339117 -68.40886442 -0.00339322 -68.40863723 -0.00316603 -68.39538776 0.01008344 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -68.40547120 Difference in potential energy from amber=>gromacs conversion: -0.00339117 Difference in potential energy from amber=>lammps conversion: -0.00339322 Difference in potential energy from amber=>desmond conversion: -0.00316603 Difference in potential energy from amber=>charmm conversion: 0.01008344 ======================================================================= INFO 2017-03-18 22:58:30 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3187514.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3187514.inpcrd') INFO 2017-03-18 22:58:30 Beginning InterMol conversion INFO 2017-03-18 22:58:30 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:58:30 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:58:30 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3201701.inpcrd INFO 2017-03-18 22:58:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3201701/mobley_3201701_converted.input INFO 2017-03-18 22:58:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3201701/mobley_3201701_converted.cms WARNING 2017-03-18 22:58:46 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:58:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3201701/mobley_3201701_converted.inp INFO 2017-03-18 22:58:46 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3201701/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3201701/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3201701/mobley_3201701_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3201701/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 627.08415392 627.08415392 0.00000000 0.00000000 0.00000000 0.00000000 -1165.70926080 -1165.70926080 coulomb total -1165.65194000 -1165.69185701 -0.03991701 -1165.69185536 -0.03991536 -1165.69268379 -0.04074379 -1165.70926080 -0.05732080 coulomb-14 -1792.70341760 -1792.77601092 -0.07259332 0.00000000 1792.70341760 -1792.77661668 -0.07319908 0.00000000 1792.70341760 improper 0.00000000 0.00166131 0.00166131 0.00000000 0.00000000 0.00000000 0.00000000 0.00167360 0.00167360 proper 11.30726000 11.30579861 -0.00146139 11.30746878 0.00020878 11.30748527 0.00022527 11.30579560 -0.00146440 vdw (SR) 0.00000000 20.20258824 20.20258824 0.00000000 0.00000000 0.00000000 0.00000000 87.65534392 87.65534392 vdw total 87.65521840 87.65498345 -0.00023495 87.65498410 -0.00023430 87.65558329 0.00036489 87.65534392 0.00012552 vdw-14 67.45235600 67.45239521 0.00003921 0.00000000 -67.45235600 67.45274553 0.00038953 0.00000000 -67.45235600 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 12.76078160 12.76074724 -0.00003436 12.76074729 -0.00003431 12.76113527 0.00035367 12.76078160 0.00000000 bond 20.02085840 20.02067279 -0.00018561 20.02067263 -0.00018577 20.02161035 0.00075195 20.02069104 -0.00016736 bonded 44.08890000 44.08887995 -0.00002005 44.08888870 -0.00001130 44.09023089 0.00133089 44.08894184 0.00004184 dihedral 11.30726000 11.30745992 0.00019992 11.30746878 0.00020878 11.30748527 0.00022527 11.30746920 0.00020920 nonbonded -1077.99672160 -1078.03687356 -0.04015196 -1078.03684616 -0.04012456 -1078.03710051 -0.04037891 -1078.05391688 -0.05719528 potential -1033.90782160 -1033.94799361 -0.04017201 -1033.94798800 -0.04016640 -1033.94709262 -0.03927102 -1033.96497504 -0.05715344 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -1033.90782160 Difference in potential energy from amber=>gromacs conversion: -0.04017201 Difference in potential energy from amber=>lammps conversion: -0.04016640 Difference in potential energy from amber=>desmond conversion: -0.03927102 Difference in potential energy from amber=>charmm conversion: -0.05715344 ======================================================================= INFO 2017-03-18 22:58:46 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3201701.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3201701.inpcrd') INFO 2017-03-18 22:58:46 Beginning InterMol conversion INFO 2017-03-18 22:58:46 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:58:46 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:58:46 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3210206.inpcrd INFO 2017-03-18 22:58:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3210206/mobley_3210206_converted.input INFO 2017-03-18 22:58:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3210206/mobley_3210206_converted.cms WARNING 2017-03-18 22:59:02 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:59:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3210206/mobley_3210206_converted.inp INFO 2017-03-18 22:59:02 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3210206/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3210206/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3210206/mobley_3210206_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3210206/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -68.81469971 -68.81469971 0.00000000 0.00000000 0.00000000 0.00000000 -30.88904944 -30.88904944 coulomb total -30.89005360 -30.89141500 -0.00136140 -30.89141466 -0.00136106 -30.89118269 -0.00112909 -30.88904944 0.00100416 coulomb-14 37.92210240 37.92328471 0.00118231 0.00000000 -37.92210240 37.92354186 0.00143946 0.00000000 -37.92210240 proper 11.38842960 11.38842630 -0.00000330 11.38842625 -0.00000335 11.38839337 -0.00003623 11.38822040 -0.00020920 vdw (SR) 0.00000000 6.87871942 6.87871942 0.00000000 0.00000000 0.00000000 0.00000000 35.74910016 35.74910016 vdw total 35.74893280 35.74882086 -0.00011194 35.74882151 -0.00011129 35.74856231 -0.00037049 35.74910016 0.00016736 vdw-14 28.87001840 28.87010144 0.00008304 0.00000000 -28.87001840 28.86981334 -0.00020506 0.00000000 -28.87001840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 7.61320640 7.61338568 0.00017928 7.61338548 0.00017908 7.61327280 0.00006640 7.61354112 0.00033472 bond 3.26979600 3.26993228 0.00013628 3.26993227 0.00013627 3.26950221 -0.00029379 3.26992152 0.00012552 bonded 22.27143200 22.27174426 0.00031226 22.27174400 0.00031200 22.27116837 -0.00026363 22.27168304 0.00025104 dihedral 11.38842960 11.38842630 -0.00000330 11.38842625 -0.00000335 11.38839337 -0.00003623 11.38822040 -0.00020920 nonbonded 4.85887920 4.85740586 -0.00147334 4.85740685 -0.00147235 4.85737961 -0.00149959 4.86005072 0.00117152 potential 27.13031120 27.12915012 -0.00116108 27.12915098 -0.00116022 27.12846476 -0.00184644 27.13173376 0.00142256 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 27.13031120 Difference in potential energy from amber=>gromacs conversion: -0.00116108 Difference in potential energy from amber=>lammps conversion: -0.00116022 Difference in potential energy from amber=>desmond conversion: -0.00184644 Difference in potential energy from amber=>charmm conversion: 0.00142256 ======================================================================= INFO 2017-03-18 22:59:02 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3210206.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3210206.inpcrd') INFO 2017-03-18 22:59:02 Beginning InterMol conversion INFO 2017-03-18 22:59:02 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:59:02 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:59:02 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3211679.inpcrd INFO 2017-03-18 22:59:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3211679/mobley_3211679_converted.input INFO 2017-03-18 22:59:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3211679/mobley_3211679_converted.cms WARNING 2017-03-18 22:59:18 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:59:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3211679/mobley_3211679_converted.inp INFO 2017-03-18 22:59:18 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3211679/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3211679/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3211679/mobley_3211679_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3211679/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 7.83725900 7.83725900 0.00000000 0.00000000 0.00000000 0.00000000 6.51900672 6.51900672 coulomb total 6.53708160 6.52328556 -0.01379604 6.52328570 -0.01379590 6.52329081 -0.01379079 6.51900672 -0.01807488 coulomb-14 -1.31042880 -1.31397343 -0.00354463 0.00000000 1.31042880 -1.31397318 -0.00354438 0.00000000 1.31042880 improper 0.00000000 0.00025151 0.00025151 0.00000000 0.00000000 0.00000000 0.00000000 0.00025104 0.00025104 proper 17.10502880 17.10460945 -0.00041935 17.10484512 -0.00018368 17.10492002 -0.00010878 17.10502880 0.00000000 vdw (SR) 0.00000000 -1.63578619 -1.63578619 0.00000000 0.00000000 0.00000000 0.00000000 10.39410200 10.39410200 vdw total 10.39389280 10.39408027 0.00018747 10.39408066 0.00018786 10.39380692 -0.00008588 10.39410200 0.00020920 vdw-14 12.02983680 12.02986646 0.00002966 0.00000000 -12.02983680 12.02959413 -0.00024267 0.00000000 -12.02983680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.31751760 2.31738177 -0.00013583 2.31738175 -0.00013585 2.31748146 -0.00003614 2.31730840 -0.00020920 bond 1.28239600 1.28238694 -0.00000906 1.28238692 -0.00000908 1.28222590 -0.00017010 1.28239600 0.00000000 bonded 20.70494240 20.70462966 -0.00031274 20.70461379 -0.00032861 20.70462738 -0.00031502 20.70498424 0.00004184 dihedral 17.10502880 17.10486095 -0.00016785 17.10484512 -0.00018368 17.10492002 -0.00010878 17.10527984 0.00025104 nonbonded 16.93097440 16.91736583 -0.01360857 16.91736594 -0.01360846 16.91709772 -0.01387668 16.91310872 -0.01786568 potential 37.63591680 37.62199549 -0.01392131 37.62197990 -0.01393690 37.62168731 -0.01422949 37.61805112 -0.01786568 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 37.63591680 Difference in potential energy from amber=>gromacs conversion: -0.01392131 Difference in potential energy from amber=>lammps conversion: -0.01393690 Difference in potential energy from amber=>desmond conversion: -0.01422949 Difference in potential energy from amber=>charmm conversion: -0.01786568 ======================================================================= INFO 2017-03-18 22:59:18 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3211679.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3211679.inpcrd') INFO 2017-03-18 22:59:18 Beginning InterMol conversion INFO 2017-03-18 22:59:18 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:59:18 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:59:18 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3234716.inpcrd INFO 2017-03-18 22:59:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3234716/mobley_3234716_converted.input INFO 2017-03-18 22:59:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3234716/mobley_3234716_converted.cms WARNING 2017-03-18 22:59:34 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:59:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3234716/mobley_3234716_converted.inp INFO 2017-03-18 22:59:34 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3234716/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3234716/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3234716/mobley_3234716_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3234716/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 14.08346106 14.08346106 0.00000000 0.00000000 0.00000000 0.00000000 -19.86730560 -19.86730560 coulomb total -19.87609200 -19.87038527 0.00570673 -19.87038502 0.00570698 -19.87039017 0.00570183 -19.86730560 0.00878640 coulomb-14 -33.95023120 -33.95384633 -0.00361513 0.00000000 33.95023120 -33.95384174 -0.00361054 0.00000000 33.95023120 improper 0.00000000 0.00006772 0.00006772 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00083680 0.00060777 -0.00022903 0.00067554 -0.00016126 0.00067733 -0.00015947 0.00062760 -0.00020920 vdw (SR) 0.00000000 -2.15715782 -2.15715782 0.00000000 0.00000000 0.00000000 0.00000000 17.58167008 17.58167008 vdw total 17.58158640 17.58165855 0.00007215 17.58165836 0.00007196 17.58174424 0.00015784 17.58167008 0.00008368 vdw-14 19.73885680 19.73881636 -0.00004044 0.00000000 -19.73885680 19.73890140 0.00004460 0.00000000 -19.73885680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.71253520 0.71250769 -0.00002751 0.71250767 -0.00002753 0.71253255 -0.00000265 0.71249336 -0.00004184 bond 2.13425840 2.13445190 0.00019350 2.13445191 0.00019351 2.13432972 0.00007132 2.13446760 0.00020920 bonded 2.84763040 2.84763508 0.00000468 2.84763512 0.00000472 2.84753961 -0.00009079 2.84767224 0.00004184 dihedral 0.00083680 0.00067549 -0.00016131 0.00067554 -0.00016126 0.00067733 -0.00015947 0.00071128 -0.00012552 nonbonded -2.29450560 -2.28872672 0.00577888 -2.28872649 0.00577911 -2.28864593 0.00585967 -2.28563552 0.00887008 potential 0.55312480 0.55890836 0.00578356 0.55890864 0.00578384 0.55883890 0.00571410 0.56199488 0.00887008 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 0.55312480 Difference in potential energy from amber=>gromacs conversion: 0.00578356 Difference in potential energy from amber=>lammps conversion: 0.00578384 Difference in potential energy from amber=>desmond conversion: 0.00571410 Difference in potential energy from amber=>charmm conversion: 0.00887008 ======================================================================= INFO 2017-03-18 22:59:34 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3234716.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3234716.inpcrd') INFO 2017-03-18 22:59:34 Beginning InterMol conversion INFO 2017-03-18 22:59:34 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 22:59:34 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 22:59:34 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3259411.inpcrd INFO 2017-03-18 22:59:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3259411/mobley_3259411_converted.input INFO 2017-03-18 22:59:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3259411/mobley_3259411_converted.cms WARNING 2017-03-18 22:59:50 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 22:59:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3259411/mobley_3259411_converted.inp INFO 2017-03-18 22:59:50 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3259411/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3259411/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3259411/mobley_3259411_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3259411/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -214.75195899 -214.75195899 0.00000000 0.00000000 0.00000000 0.00000000 100.40474504 100.40474504 coulomb total 100.35742400 100.36818103 0.01075703 100.36818106 0.01075706 100.36936388 0.01193988 100.40474504 0.04732104 coulomb-14 315.11126560 315.12014002 0.00887442 0.00000000 -315.11126560 315.12030639 0.00904079 0.00000000 -315.11126560 proper 12.77793600 12.77798469 0.00004869 12.77798453 0.00004853 12.77794106 0.00000506 12.77801968 0.00008368 vdw (SR) 0.00000000 -0.75246311 -0.75246311 0.00000000 0.00000000 0.00000000 0.00000000 4.12178392 4.12178392 vdw total 4.12207680 4.12165328 -0.00042352 4.12165338 -0.00042342 4.12177202 -0.00030478 4.12178392 -0.00029288 vdw-14 4.87436000 4.87411639 -0.00024361 0.00000000 -4.87436000 4.87423523 -0.00012477 0.00000000 -4.87436000 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.06854560 3.06872232 0.00017672 3.06872233 0.00017673 3.06895031 0.00040471 3.06862928 0.00008368 bond 0.47572080 0.47557517 -0.00014563 0.47557515 -0.00014565 0.47559269 -0.00012811 0.47559528 -0.00012552 bonded 16.32220240 16.32228219 0.00007979 16.32228202 0.00007962 16.32248406 0.00028166 16.32224424 0.00004184 dihedral 12.77793600 12.77798469 0.00004869 12.77798453 0.00004853 12.77794106 0.00000506 12.77801968 0.00008368 nonbonded 104.47950080 104.48983431 0.01033351 104.48983528 0.01033448 104.49113590 0.01163510 104.52652896 0.04702816 potential 120.80170320 120.81211650 0.01041330 120.81211718 0.01041398 120.81360584 0.01190264 120.84873136 0.04702816 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 120.80170320 Difference in potential energy from amber=>gromacs conversion: 0.01041330 Difference in potential energy from amber=>lammps conversion: 0.01041398 Difference in potential energy from amber=>desmond conversion: 0.01190264 Difference in potential energy from amber=>charmm conversion: 0.04702816 ======================================================================= INFO 2017-03-18 22:59:50 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3259411.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3259411.inpcrd') INFO 2017-03-18 22:59:50 Beginning InterMol conversion INFO 2017-03-18 22:59:50 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 22:59:50 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3264884.inpcrd INFO 2017-03-18 22:59:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3264884/mobley_3264884_converted.input INFO 2017-03-18 22:59:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3264884/mobley_3264884_converted.cms INFO 2017-03-18 23:00:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3264884/mobley_3264884_converted.rst7 WARNING 2017-03-18 23:00:06 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:00:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3264884/mobley_3264884_converted.inp INFO 2017-03-18 23:00:06 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3264884/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3264884/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3264884/mobley_3264884_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_3264884/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3264884/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 71.42023500 71.42023500 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -123.15641656 -123.15641656 coulomb total -123.14139600 -123.13733434 0.00406166 -123.13733334 0.00406266 -123.13766973 0.00372627 -123.14139600 0.00000000 -123.15641656 -0.01502056 coulomb-14 -194.54679520 -194.55756934 -0.01077414 0.00000000 194.54679520 -194.55740875 -0.01061355 -194.54679520 0.00000000 0.00000000 194.54679520 improper 0.00000000 0.11713607 0.11713607 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.11715200 0.11715200 proper 0.22593600 0.10869055 -0.11724545 0.22582511 -0.00011089 0.22585828 -0.00007772 0.22593600 0.00000000 0.10870032 -0.11723568 vdw (SR) 0.00000000 -4.12726945 -4.12726945 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 26.71212040 26.71212040 vdw total 26.71232960 26.71216642 -0.00016318 26.71216642 -0.00016318 26.71229873 -0.00003087 26.71232960 0.00000000 26.71212040 -0.00020920 vdw-14 30.83942720 30.83943587 0.00000867 0.00000000 -30.83942720 30.83955749 0.00013029 30.83942720 0.00000000 0.00000000 -30.83942720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.41286480 4.41276011 -0.00010469 4.41276020 -0.00010460 4.41241761 -0.00044719 4.41286480 0.00000000 4.41282296 -0.00004184 bond 9.41232640 9.41215626 -0.00017014 9.41215611 -0.00017029 9.41267484 0.00034844 9.41232640 0.00000000 9.41215904 -0.00016736 bonded 14.05112720 14.05074299 -0.00038421 14.05074142 -0.00038578 14.05095073 -0.00017647 14.05112720 0.00000000 14.05083432 -0.00029288 dihedral 0.22593600 0.22582662 -0.00010938 0.22582511 -0.00011089 0.22585828 -0.00007772 0.22593600 0.00000000 0.22585232 -0.00008368 nonbonded -96.42906640 -96.42516792 0.00389848 -96.42516691 0.00389949 -96.42537100 0.00369540 -96.42906640 0.00000000 -96.44429616 -0.01522976 potential -82.37793920 -82.37442493 0.00351427 -82.37442464 0.00351456 -82.37451250 0.00342670 -82.37793920 0.00000000 -82.39346184 -0.01552264 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -82.37793920 Difference in potential energy from amber=>gromacs conversion: 0.00351427 Difference in potential energy from amber=>lammps conversion: 0.00351456 Difference in potential energy from amber=>desmond conversion: 0.00342670 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.01552264 ======================================================================= INFO 2017-03-18 23:00:06 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3264884.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3264884.inpcrd') INFO 2017-03-18 23:00:06 Beginning InterMol conversion INFO 2017-03-18 23:00:06 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:00:06 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:00:07 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3265457.inpcrd INFO 2017-03-18 23:00:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3265457/mobley_3265457_converted.input INFO 2017-03-18 23:00:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3265457/mobley_3265457_converted.cms WARNING 2017-03-18 23:00:22 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:00:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3265457/mobley_3265457_converted.inp INFO 2017-03-18 23:00:22 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3265457/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3265457/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3265457/mobley_3265457_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3265457/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -189.46433412 -189.46433412 0.00000000 0.00000000 0.00000000 0.00000000 24.73631008 24.73631008 coulomb total 24.71070400 24.70002654 -0.01067746 24.70002643 -0.01067757 24.70008794 -0.01061606 24.73631008 0.02560608 coulomb-14 214.15511120 214.16436066 0.00924946 0.00000000 -214.15511120 214.16423734 0.00912614 0.00000000 -214.15511120 improper 0.00000000 0.00033728 0.00033728 0.00000000 0.00000000 0.00000000 0.00000000 0.00033472 0.00033472 proper 55.18696000 55.18650815 -0.00045185 55.18686377 -0.00009623 55.18690268 -0.00005732 55.18654160 -0.00041840 vdw (SR) 0.00000000 -11.33342345 -11.33342345 0.00000000 0.00000000 0.00000000 0.00000000 15.89233824 15.89233824 vdw total 15.89208720 15.89224263 0.00015543 15.89224243 0.00015523 15.89225146 0.00016426 15.89233824 0.00025104 vdw-14 27.22570640 27.22566608 -0.00004032 0.00000000 -27.22570640 27.22567753 -0.00002887 0.00000000 -27.22570640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.98321600 1.98303741 -0.00017859 1.98303743 -0.00017857 1.98310654 -0.00010946 1.98309048 -0.00012552 bond 3.78693840 3.78689589 -0.00004251 3.78689589 -0.00004251 3.78701886 0.00008046 3.78689656 -0.00004184 bonded 60.95711440 60.95677873 -0.00033567 60.95679709 -0.00031731 60.95702808 -0.00008632 60.95686336 -0.00025104 dihedral 55.18696000 55.18684543 -0.00011457 55.18686377 -0.00009623 55.18690268 -0.00005732 55.18687632 -0.00008368 nonbonded 40.60279120 40.59226917 -0.01052203 40.59226886 -0.01052234 40.59233940 -0.01045180 40.62864832 0.02585712 potential 101.55990560 101.54904789 -0.01085771 101.54906904 -0.01083656 101.54922803 -0.01067757 101.58546984 0.02556424 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 101.55990560 Difference in potential energy from amber=>gromacs conversion: -0.01085771 Difference in potential energy from amber=>lammps conversion: -0.01083656 Difference in potential energy from amber=>desmond conversion: -0.01067757 Difference in potential energy from amber=>charmm conversion: 0.02556424 ======================================================================= INFO 2017-03-18 23:00:22 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3265457.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3265457.inpcrd') INFO 2017-03-18 23:00:22 Beginning InterMol conversion INFO 2017-03-18 23:00:22 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:00:23 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:00:23 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3266352.inpcrd INFO 2017-03-18 23:00:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3266352/mobley_3266352_converted.input INFO 2017-03-18 23:00:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3266352/mobley_3266352_converted.cms WARNING 2017-03-18 23:00:38 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:00:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3266352/mobley_3266352_converted.inp INFO 2017-03-18 23:00:38 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3266352/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3266352/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3266352/mobley_3266352_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3266352/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -91.13859186 -91.13859186 0.00000000 0.00000000 0.00000000 0.00000000 80.35915920 80.35915920 coulomb total 80.42024560 80.42881112 0.00856552 80.42881025 0.00856465 80.42905878 0.00881318 80.35915920 -0.06108640 coulomb-14 171.56324640 171.56740298 0.00415658 0.00000000 -171.56324640 171.56718731 0.00394091 0.00000000 -171.56324640 improper 0.00000000 0.00134718 0.00134718 0.00000000 0.00000000 0.00000000 0.00000000 0.00133888 0.00133888 proper 8.98974240 8.98842505 -0.00131735 8.98975621 0.00001381 8.98965278 -0.00008962 8.98840352 -0.00133888 vdw (SR) 0.00000000 66.20305548 66.20305548 0.00000000 0.00000000 0.00000000 0.00000000 96.21325568 96.21325568 vdw total 96.21317200 96.21333558 0.00016358 96.21333518 0.00016318 96.21263758 -0.00053442 96.21325568 0.00008368 vdw-14 30.01015840 30.01028010 0.00012170 0.00000000 -30.01015840 30.01053316 0.00037476 0.00000000 -30.01015840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.80278960 5.80290651 0.00011691 5.80290633 0.00011673 5.80285797 0.00006837 5.80299880 0.00020920 bond 6.68686880 6.68700200 0.00013320 6.68700185 0.00013305 6.68649375 -0.00037505 6.68699432 0.00012552 bonded 21.47940080 21.47968075 0.00027995 21.47966439 0.00026359 21.47900449 -0.00039631 21.47973552 0.00033472 dihedral 8.98974240 8.98977223 0.00002983 8.98975621 0.00001381 8.98965278 -0.00008962 8.98974240 0.00000000 nonbonded 176.63341760 176.64214670 0.00872910 176.64214542 0.00872782 176.64169636 0.00827876 176.57241488 -0.06100272 potential 198.11281840 198.12182745 0.00900905 198.12180982 0.00899142 198.12061738 0.00779898 198.05219224 -0.06062616 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 198.11281840 Difference in potential energy from amber=>gromacs conversion: 0.00900905 Difference in potential energy from amber=>lammps conversion: 0.00899142 Difference in potential energy from amber=>desmond conversion: 0.00779898 Difference in potential energy from amber=>charmm conversion: -0.06062616 ======================================================================= INFO 2017-03-18 23:00:38 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3266352.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3266352.inpcrd') INFO 2017-03-18 23:00:39 Beginning InterMol conversion INFO 2017-03-18 23:00:39 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:00:39 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:00:39 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3269565.inpcrd INFO 2017-03-18 23:00:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3269565/mobley_3269565_converted.input INFO 2017-03-18 23:00:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3269565/mobley_3269565_converted.cms WARNING 2017-03-18 23:00:54 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:00:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3269565/mobley_3269565_converted.inp INFO 2017-03-18 23:00:54 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3269565/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3269565/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3269565/mobley_3269565_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3269565/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 20.38393894 20.38393894 0.00000000 0.00000000 0.00000000 0.00000000 -32.35081352 -32.35081352 coulomb total -32.33478880 -32.34867327 -0.01388447 -32.34867299 -0.01388419 -32.34873867 -0.01394987 -32.35081352 -0.01602472 coulomb-14 -52.74643280 -52.73261222 0.01382058 0.00000000 52.74643280 -52.73263899 0.01379381 0.00000000 52.74643280 proper 9.91440640 9.91438347 -0.00002293 9.91438422 -0.00002218 9.91434808 -0.00005832 9.91432272 -0.00008368 vdw (SR) 0.00000000 3.58441835 3.58441835 0.00000000 0.00000000 0.00000000 0.00000000 11.50399168 11.50399168 vdw total 11.50390800 11.50385741 -0.00005059 11.50385779 -0.00005021 11.50386895 -0.00003905 11.50399168 0.00008368 vdw-14 7.91947520 7.91943905 -0.00003615 0.00000000 -7.91947520 7.91937976 -0.00009544 0.00000000 -7.91947520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.14641600 1.14660061 0.00018461 1.14660060 0.00018460 1.14662385 0.00020785 1.14662520 0.00020920 bond 1.33595120 1.33588739 -0.00006381 1.33588739 -0.00006381 1.33617766 0.00022646 1.33586752 -0.00008368 bonded 12.39677360 12.39687147 0.00009787 12.39687222 0.00009862 12.39714959 0.00037599 12.39681544 0.00004184 dihedral 9.91440640 9.91438347 -0.00002293 9.91438422 -0.00002218 9.91434808 -0.00005832 9.91432272 -0.00008368 nonbonded -20.83088080 -20.84481587 -0.01393507 -20.84481519 -0.01393439 -20.84486973 -0.01398893 -20.84682184 -0.01594104 potential -8.43410720 -8.44794439 -0.01383719 -8.44794327 -0.01383607 -8.44774838 -0.01364118 -8.44996456 -0.01585736 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -8.43410720 Difference in potential energy from amber=>gromacs conversion: -0.01383719 Difference in potential energy from amber=>lammps conversion: -0.01383607 Difference in potential energy from amber=>desmond conversion: -0.01364118 Difference in potential energy from amber=>charmm conversion: -0.01585736 ======================================================================= INFO 2017-03-18 23:00:54 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3269565.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3269565.inpcrd') INFO 2017-03-18 23:00:55 Beginning InterMol conversion INFO 2017-03-18 23:00:55 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:00:55 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3269819.inpcrd INFO 2017-03-18 23:00:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3269819/mobley_3269819_converted.input INFO 2017-03-18 23:00:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3269819/mobley_3269819_converted.cms INFO 2017-03-18 23:01:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3269819/mobley_3269819_converted.rst7 WARNING 2017-03-18 23:01:11 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:01:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3269819/mobley_3269819_converted.inp INFO 2017-03-18 23:01:11 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3269819/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3269819/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3269819/mobley_3269819_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_3269819/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3269819/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 3.50600457 3.50600457 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -9.89649888 -9.89649888 coulomb total -9.90813040 -9.89626339 0.01186701 -9.89626332 0.01186708 -9.89626273 0.01186767 -9.90813040 0.00000000 -9.89649888 0.01163152 coulomb-14 -13.39967840 -13.40226796 -0.00258956 0.00000000 13.39967840 -13.40227411 -0.00259571 -13.39967840 0.00000000 0.00000000 13.39967840 improper 0.00000000 0.00026609 0.00026609 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00025104 0.00025104 proper 33.47534720 33.47502849 -0.00031871 33.47529448 -0.00005272 33.47529812 -0.00004908 33.47534720 0.00000000 33.47501248 -0.00033472 vdw (SR) 0.00000000 -14.28979321 -14.28979321 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 32.85402320 32.85402320 vdw total 32.85402320 32.85395355 -0.00006965 32.85395375 -0.00006945 32.85416378 0.00014058 32.85402320 0.00000000 32.85402320 0.00000000 vdw-14 47.14363840 47.14374675 0.00010835 0.00000000 -47.14363840 47.14396977 0.00033137 47.14363840 0.00000000 0.00000000 -47.14363840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 6.00696880 6.00690815 -0.00006065 6.00690813 -0.00006067 6.00675479 -0.00021401 6.00696880 0.00000000 6.00696880 0.00000000 bond 4.43001920 4.43019845 0.00017925 4.43019828 0.00017908 4.43083111 0.00081191 4.43001920 0.00000000 4.43018656 0.00016736 bonded 43.91233520 43.91240118 0.00006598 43.91240089 0.00006569 43.91288402 0.00054882 43.91233520 0.00000000 43.91241888 0.00008368 dihedral 33.47534720 33.47529458 -0.00005262 33.47529448 -0.00005272 33.47529812 -0.00004908 33.47534720 0.00000000 33.47526352 -0.00008368 nonbonded 22.94589280 22.95769016 0.01179736 22.95769042 0.01179762 22.95790105 0.01200825 22.94589280 0.00000000 22.95752432 0.01163152 potential 66.85822800 66.87009134 0.01186334 66.87008964 0.01186164 66.87044905 0.01222105 66.85822800 0.00000000 66.86998504 0.01175704 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 66.85822800 Difference in potential energy from amber=>gromacs conversion: 0.01186334 Difference in potential energy from amber=>lammps conversion: 0.01186164 Difference in potential energy from amber=>desmond conversion: 0.01222105 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.01175704 ======================================================================= INFO 2017-03-18 23:01:11 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3269819.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3269819.inpcrd') INFO 2017-03-18 23:01:11 Beginning InterMol conversion INFO 2017-03-18 23:01:11 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:01:11 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:01:11 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3274817.inpcrd INFO 2017-03-18 23:01:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3274817/mobley_3274817_converted.input INFO 2017-03-18 23:01:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3274817/mobley_3274817_converted.cms WARNING 2017-03-18 23:01:27 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:01:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3274817/mobley_3274817_converted.inp INFO 2017-03-18 23:01:27 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3274817/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3274817/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3274817/mobley_3274817_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3274817/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 30.74201778 30.74201778 0.00000000 0.00000000 0.00000000 0.00000000 -94.28288360 -94.28288360 coulomb total -94.25045760 -94.24804350 0.00241410 -94.24804343 0.00241417 -94.24763470 0.00282290 -94.28288360 -0.03242600 coulomb-14 -124.98779520 -124.99006128 -0.00226608 0.00000000 124.98779520 -124.99001063 -0.00221543 0.00000000 124.98779520 improper 0.00000000 0.00016513 0.00016513 0.00000000 0.00000000 0.00000000 0.00000000 0.00016736 0.00016736 proper 22.03043360 22.03033504 -0.00009856 22.03050013 0.00006653 22.03048762 0.00005402 22.03034992 -0.00008368 vdw (SR) 0.00000000 -3.19139277 -3.19139277 0.00000000 0.00000000 0.00000000 0.00000000 34.92836672 34.92836672 vdw total 34.92845040 34.92807722 -0.00037318 34.92807719 -0.00037321 34.92795491 -0.00049549 34.92836672 -0.00008368 vdw-14 38.11958720 38.11946999 -0.00011721 0.00000000 -38.11958720 38.11923750 -0.00034970 0.00000000 -38.11958720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.70279200 5.70298379 0.00019179 5.70298363 0.00019163 5.70212963 -0.00066237 5.70291752 0.00012552 bond 22.87978560 22.87973071 -0.00005489 22.87973079 -0.00005481 22.87751871 -0.00226689 22.87974376 -0.00004184 bonded 50.61301120 50.61321466 0.00020346 50.61321454 0.00020334 50.61013596 -0.00287524 50.61317856 0.00016736 dihedral 22.03043360 22.03050017 0.00006657 22.03050013 0.00006653 22.03048762 0.00005402 22.03051728 0.00008368 nonbonded -59.32200720 -59.31996627 0.00204093 -59.31996541 0.00204179 -59.31967978 0.00232742 -59.35451688 -0.03250968 potential -8.70899600 -8.70675161 0.00224439 -8.70675045 0.00224555 -8.70974142 -0.00074542 -8.74133832 -0.03234232 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -8.70899600 Difference in potential energy from amber=>gromacs conversion: 0.00224439 Difference in potential energy from amber=>lammps conversion: 0.00224555 Difference in potential energy from amber=>desmond conversion: -0.00074542 Difference in potential energy from amber=>charmm conversion: -0.03234232 ======================================================================= INFO 2017-03-18 23:01:27 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3274817.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3274817.inpcrd') INFO 2017-03-18 23:01:27 Beginning InterMol conversion INFO 2017-03-18 23:01:27 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:01:27 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:01:27 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3318135.inpcrd INFO 2017-03-18 23:01:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3318135/mobley_3318135_converted.input INFO 2017-03-18 23:01:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3318135/mobley_3318135_converted.cms WARNING 2017-03-18 23:01:43 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:01:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3318135/mobley_3318135_converted.inp INFO 2017-03-18 23:01:43 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3318135/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3318135/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3318135/mobley_3318135_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3318135/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -22.29407921 -22.29407921 0.00000000 0.00000000 0.00000000 0.00000000 -24.70949064 -24.70949064 coulomb total -24.70024400 -24.70695465 -0.00671065 -24.70695430 -0.00671030 -24.70692410 -0.00668010 -24.70949064 -0.00924664 coulomb-14 -2.40914720 -2.41287545 -0.00372825 0.00000000 2.40914720 -2.41288762 -0.00374042 0.00000000 2.40914720 improper 0.00000000 0.00692456 0.00692456 0.00000000 0.00000000 0.00000000 0.00000000 0.00690360 0.00690360 proper 9.90018080 9.89341365 -0.00676715 9.90033770 0.00015690 9.90032925 0.00014845 9.89340272 -0.00677808 vdw (SR) 0.00000000 -3.94172328 -3.94172328 0.00000000 0.00000000 0.00000000 0.00000000 10.57618968 10.57618968 vdw total 10.57631520 10.57600988 -0.00030532 10.57601019 -0.00030501 10.57612014 -0.00019506 10.57618968 -0.00012552 vdw-14 14.51806160 14.51773316 -0.00032844 0.00000000 -14.51806160 14.51780671 -0.00025489 0.00000000 -14.51806160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.97940240 3.97942093 0.00001853 3.97942094 0.00001854 3.97977984 0.00037744 3.97936056 -0.00004184 bond 2.30705760 2.30723007 0.00017247 2.30723006 0.00017246 2.30722031 0.00016271 2.30722496 0.00016736 bonded 16.18664080 16.18698920 0.00034840 16.18698870 0.00034790 16.18732939 0.00068859 16.18689184 0.00025104 dihedral 9.90018080 9.90033821 0.00015741 9.90033770 0.00015690 9.90032925 0.00014845 9.90030632 0.00012552 nonbonded -14.12392880 -14.13094477 -0.00701597 -14.13094411 -0.00701531 -14.13080396 -0.00687516 -14.13330096 -0.00937216 potential 2.06271200 2.05604443 -0.00666757 2.05604438 -0.00666762 2.05641336 -0.00629864 2.05363272 -0.00907928 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 2.06271200 Difference in potential energy from amber=>gromacs conversion: -0.00666757 Difference in potential energy from amber=>lammps conversion: -0.00666762 Difference in potential energy from amber=>desmond conversion: -0.00629864 Difference in potential energy from amber=>charmm conversion: -0.00907928 ======================================================================= INFO 2017-03-18 23:01:43 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3318135.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3318135.inpcrd') INFO 2017-03-18 23:01:43 Beginning InterMol conversion INFO 2017-03-18 23:01:43 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:01:43 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:01:43 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3323117.inpcrd INFO 2017-03-18 23:01:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3323117/mobley_3323117_converted.input INFO 2017-03-18 23:01:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3323117/mobley_3323117_converted.cms WARNING 2017-03-18 23:01:59 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:01:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3323117/mobley_3323117_converted.inp INFO 2017-03-18 23:01:59 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3323117/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3323117/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3323117/mobley_3323117_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3323117/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -58.76330812 -58.76330812 0.00000000 0.00000000 0.00000000 0.00000000 -193.58104432 -193.58104432 coulomb total -193.62631520 -193.63819643 -0.01188123 -193.63819358 -0.01187838 -193.63793249 -0.01161729 -193.58104432 0.04527088 coulomb-14 -134.86872960 -134.87488832 -0.00615872 0.00000000 134.86872960 -134.87464870 -0.00591910 0.00000000 134.86872960 proper 26.46045280 26.46035269 -0.00010011 26.46035029 -0.00010251 26.46036247 -0.00009033 26.45635248 -0.00410032 vdw (SR) 0.00000000 -1.07015535 -1.07015535 0.00000000 0.00000000 0.00000000 0.00000000 -1.41850152 -1.41850152 vdw total -1.41879440 -1.41853421 0.00026019 -1.41853424 0.00026016 -1.41856244 0.00023196 -1.41850152 0.00029288 vdw-14 -0.34852720 -0.34837886 0.00014834 0.00000000 0.34852720 -0.34840910 0.00011810 0.00000000 0.34852720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 12.73191200 12.73196827 0.00005627 12.73196807 0.00005607 12.73203614 0.00012414 12.73191200 0.00000000 bond 1.44264320 1.44259669 -0.00004651 1.44259667 -0.00004653 1.44283991 0.00019671 1.44260136 -0.00004184 bonded 40.63500800 40.63491765 -0.00009035 40.63491503 -0.00009297 40.63523852 0.00023052 40.63086584 -0.00414216 dihedral 26.46045280 26.46035269 -0.00010011 26.46035029 -0.00010251 26.46036247 -0.00009033 26.45635248 -0.00410032 nonbonded -195.04510960 -195.05673065 -0.01162105 -195.05672857 -0.01161897 -195.05649494 -0.01138534 -194.99954584 0.04556376 potential -154.41010160 -154.42181300 -0.01171140 -154.42181262 -0.01171102 -154.42131012 -0.01120852 -154.36863816 0.04146344 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -154.41010160 Difference in potential energy from amber=>gromacs conversion: -0.01171140 Difference in potential energy from amber=>lammps conversion: -0.01171102 Difference in potential energy from amber=>desmond conversion: -0.01120852 Difference in potential energy from amber=>charmm conversion: 0.04146344 ======================================================================= INFO 2017-03-18 23:01:59 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3323117.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3323117.inpcrd') INFO 2017-03-18 23:01:59 Beginning InterMol conversion INFO 2017-03-18 23:01:59 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:01:59 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:01:59 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3325209.inpcrd INFO 2017-03-18 23:01:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3325209/mobley_3325209_converted.input INFO 2017-03-18 23:02:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3325209/mobley_3325209_converted.cms WARNING 2017-03-18 23:02:15 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:02:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3325209/mobley_3325209_converted.inp INFO 2017-03-18 23:02:15 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3325209/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3325209/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3325209/mobley_3325209_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3325209/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -175.38758509 -175.38758509 0.00000000 0.00000000 0.00000000 0.00000000 -114.98774232 -114.98774232 coulomb total -114.96000240 -114.99809024 -0.03808784 -114.99808935 -0.03808695 -114.99748351 -0.03748111 -114.98774232 -0.02773992 coulomb-14 60.43202240 60.38949485 -0.04252755 0.00000000 -60.43202240 60.38964601 -0.04237639 0.00000000 -60.43202240 improper 0.00000000 0.00006121 0.00006121 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 55.21206400 55.21204170 -0.00002230 55.21210166 0.00003766 55.21214475 0.00008075 55.21202216 -0.00004184 vdw (SR) 0.00000000 -1.69099764 -1.69099764 0.00000000 0.00000000 0.00000000 0.00000000 34.26206472 34.26206472 vdw total 34.26235760 34.26186163 -0.00049597 34.26186180 -0.00049580 34.26182574 -0.00053186 34.26206472 -0.00029288 vdw-14 35.95311200 35.95285928 -0.00025272 0.00000000 -35.95311200 35.95277038 -0.00034162 0.00000000 -35.95311200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.94509360 3.94508464 -0.00000896 3.94508465 -0.00000895 3.94539687 0.00030327 3.94517728 0.00008368 bond 2.54721920 2.54741184 0.00019264 2.54741183 0.00019263 2.54788915 0.00066995 2.54742840 0.00020920 bonded 61.70437680 61.70459940 0.00022260 61.70459813 0.00022133 61.70543077 0.00105397 61.70466968 0.00029288 dihedral 55.21206400 55.21210292 0.00003892 55.21210166 0.00003766 55.21214475 0.00008075 55.21206400 0.00000000 nonbonded -80.69764480 -80.73622860 -0.03858380 -80.73622546 -0.03858066 -80.73565777 -0.03801297 -80.72567760 -0.02803280 potential -18.99326800 -19.03162921 -0.03836121 -19.03162775 -0.03835975 -19.03036439 -0.03709639 -19.02100792 -0.02773992 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -18.99326800 Difference in potential energy from amber=>gromacs conversion: -0.03836121 Difference in potential energy from amber=>lammps conversion: -0.03835975 Difference in potential energy from amber=>desmond conversion: -0.03709639 Difference in potential energy from amber=>charmm conversion: -0.02773992 ======================================================================= INFO 2017-03-18 23:02:15 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3325209.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3325209.inpcrd') INFO 2017-03-18 23:02:15 Beginning InterMol conversion INFO 2017-03-18 23:02:15 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:02:16 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:02:16 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3359593.inpcrd INFO 2017-03-18 23:02:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3359593/mobley_3359593_converted.input INFO 2017-03-18 23:02:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3359593/mobley_3359593_converted.cms WARNING 2017-03-18 23:02:31 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:02:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3359593/mobley_3359593_converted.inp INFO 2017-03-18 23:02:31 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3359593/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3359593/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3359593/mobley_3359593_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3359593/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -101.67876766 -101.67876766 0.00000000 0.00000000 0.00000000 0.00000000 -32.37248664 -32.37248664 coulomb total -32.34901440 -32.33666453 0.01234987 -32.33666407 0.01235033 -32.33671386 0.01230054 -32.37248664 -0.02347224 coulomb-14 69.34310560 69.34210313 -0.00100247 0.00000000 -69.34310560 69.34227884 -0.00082676 0.00000000 -69.34310560 improper 0.00000000 0.00006504 0.00006504 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.04853440 0.04857648 0.00004208 0.04864149 0.00010709 0.04865094 0.00011654 0.04857624 0.00004184 vdw (SR) 0.00000000 10.81273255 10.81273255 0.00000000 0.00000000 0.00000000 0.00000000 43.75530968 43.75530968 vdw total 43.75501680 43.75512263 0.00010583 43.75512140 0.00010460 43.75457359 -0.00044321 43.75530968 0.00029288 vdw-14 32.94230560 32.94239008 0.00008448 0.00000000 -32.94230560 32.94203502 -0.00027058 0.00000000 -32.94230560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.24306640 1.24286529 -0.00020111 1.24286528 -0.00020112 1.24305432 -0.00001208 1.24285720 -0.00020920 bond 2.36479680 2.36486500 0.00006820 2.36486500 0.00006820 2.36528747 0.00049067 2.36488048 0.00008368 bonded 3.65639760 3.65637182 -0.00002578 3.65637176 -0.00002584 3.65699274 0.00059514 3.65639760 0.00000000 dihedral 0.04853440 0.04864152 0.00010712 0.04864149 0.00010709 0.04865094 0.00011654 0.04865992 0.00012552 nonbonded 11.40600240 11.41845810 0.01245570 11.41845900 0.01245660 11.41785973 0.01185733 11.38282304 -0.02317936 potential 15.06240000 15.07482992 0.01242992 15.07483066 0.01243066 15.07474732 0.01234732 15.03917880 -0.02322120 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 15.06240000 Difference in potential energy from amber=>gromacs conversion: 0.01242992 Difference in potential energy from amber=>lammps conversion: 0.01243066 Difference in potential energy from amber=>desmond conversion: 0.01234732 Difference in potential energy from amber=>charmm conversion: -0.02322120 ======================================================================= INFO 2017-03-18 23:02:31 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3359593.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3359593.inpcrd') INFO 2017-03-18 23:02:31 Beginning InterMol conversion INFO 2017-03-18 23:02:31 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:02:32 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:02:32 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3370989.inpcrd INFO 2017-03-18 23:02:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3370989/mobley_3370989_converted.input INFO 2017-03-18 23:02:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3370989/mobley_3370989_converted.cms WARNING 2017-03-18 23:02:47 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:02:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3370989/mobley_3370989_converted.inp INFO 2017-03-18 23:02:47 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3370989/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3370989/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3370989/mobley_3370989_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3370989/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -34.16947280 -34.16947280 coulomb total -34.12386720 -34.11762397 0.00624323 -34.11762342 0.00624378 -34.11762388 0.00624332 -34.16947280 -0.04560560 coulomb-14 -34.12386720 -34.11762397 0.00624323 0.00000000 34.12386720 -34.11762388 0.00624332 0.00000000 34.12386720 proper 4.76683120 4.76698662 0.00015542 4.76698643 0.00015523 4.76699187 0.00016067 4.76699856 0.00016736 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.21105880 1.21105880 vdw total 1.21126800 1.21107892 -0.00018908 1.21107893 -0.00018907 1.21106880 -0.00019920 1.21105880 -0.00020920 vdw-14 1.21126800 1.21107892 -0.00018908 0.00000000 -1.21126800 1.21106880 -0.00019920 0.00000000 -1.21126800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.27279680 0.27260966 -0.00018714 0.27260966 -0.00018714 0.27256134 -0.00023546 0.27262944 -0.00016736 bond 1.43009120 1.43002133 -0.00006987 1.43002133 -0.00006987 1.42974148 -0.00034972 1.43000752 -0.00008368 bonded 6.46971920 6.46961760 -0.00010160 6.46961741 -0.00010179 6.46929469 -0.00042451 6.46963552 -0.00008368 dihedral 4.76683120 4.76698662 0.00015542 4.76698643 0.00015523 4.76699187 0.00016067 4.76699856 0.00016736 nonbonded -32.91259920 -32.90654505 0.00605415 -32.90654453 0.00605467 -32.90655508 0.00604412 -32.95841400 -0.04581480 potential -26.44288000 -26.43692745 0.00595255 -26.43692700 0.00595300 -26.43726834 0.00561166 -26.48877848 -0.04589848 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -26.44288000 Difference in potential energy from amber=>gromacs conversion: 0.00595255 Difference in potential energy from amber=>lammps conversion: 0.00595300 Difference in potential energy from amber=>desmond conversion: 0.00561166 Difference in potential energy from amber=>charmm conversion: -0.04589848 ======================================================================= INFO 2017-03-18 23:02:47 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3370989.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3370989.inpcrd') INFO 2017-03-18 23:02:48 Beginning InterMol conversion INFO 2017-03-18 23:02:48 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:02:48 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:02:48 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_337666.inpcrd INFO 2017-03-18 23:02:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_337666/mobley_337666_converted.input INFO 2017-03-18 23:02:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_337666/mobley_337666_converted.cms WARNING 2017-03-18 23:03:03 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:03:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_337666/mobley_337666_converted.inp INFO 2017-03-18 23:03:03 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_337666/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_337666/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_337666/mobley_337666_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_337666/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 155.19634414 155.19634414 0.00000000 0.00000000 0.00000000 0.00000000 -528.24430928 -528.24430928 coulomb total -528.02456560 -528.03502713 -0.01046153 -528.03502560 -0.01046000 -528.03527078 -0.01070518 -528.24430928 -0.21974368 coulomb-14 -683.21038080 -683.23137127 -0.02099047 0.00000000 683.21038080 -683.23180288 -0.02142208 0.00000000 683.21038080 improper 0.00000000 0.00035746 0.00035746 0.00000000 0.00000000 0.00000000 0.00000000 0.00037656 0.00037656 proper 50.20883680 50.20844253 -0.00039427 50.20879914 -0.00003766 50.20879496 -0.00004184 50.20846024 -0.00037656 vdw (SR) 0.00000000 -1.71552919 -1.71552919 0.00000000 0.00000000 0.00000000 0.00000000 15.38490272 15.38490272 vdw total 15.38498640 15.38500199 0.00001559 15.38500188 0.00001548 15.38493537 -0.00005103 15.38490272 -0.00008368 vdw-14 17.10042640 17.10053118 0.00010478 0.00000000 -17.10042640 17.10046117 0.00003477 0.00000000 -17.10042640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 9.54412240 9.54403428 -0.00008812 9.54403412 -0.00008828 9.54468168 0.00055928 9.54403872 -0.00008368 bond 19.69366960 19.69352502 -0.00014458 19.69352483 -0.00014477 19.69404465 0.00037505 19.69354408 -0.00012552 bonded 79.44662880 79.44635928 -0.00026952 79.44635810 -0.00027070 79.44752129 0.00089249 79.44641960 -0.00020920 dihedral 50.20883680 50.20879998 -0.00003682 50.20879914 -0.00003766 50.20879496 -0.00004184 50.20883680 0.00000000 nonbonded -512.63957920 -512.65002514 -0.01044594 -512.65003920 -0.01046000 -512.65033541 -0.01075621 -512.85940656 -0.21982736 potential -433.19295040 -433.20366586 -0.01071546 -433.20366144 -0.01071104 -433.20288322 -0.00993282 -433.41302880 -0.22007840 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -433.19295040 Difference in potential energy from amber=>gromacs conversion: -0.01071546 Difference in potential energy from amber=>lammps conversion: -0.01071104 Difference in potential energy from amber=>desmond conversion: -0.00993282 Difference in potential energy from amber=>charmm conversion: -0.22007840 ======================================================================= INFO 2017-03-18 23:03:03 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_337666.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_337666.inpcrd') INFO 2017-03-18 23:03:04 Beginning InterMol conversion INFO 2017-03-18 23:03:04 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:03:04 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:03:04 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3378420.inpcrd INFO 2017-03-18 23:03:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3378420/mobley_3378420_converted.input INFO 2017-03-18 23:03:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3378420/mobley_3378420_converted.cms WARNING 2017-03-18 23:03:19 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:03:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3378420/mobley_3378420_converted.inp INFO 2017-03-18 23:03:19 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3378420/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3378420/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3378420/mobley_3378420_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3378420/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 14.74109606 14.74109606 0.00000000 0.00000000 0.00000000 0.00000000 -5.70182968 -5.70182968 coulomb total -5.70739440 -5.70070510 0.00668930 -5.70070502 0.00668938 -5.70078439 0.00661001 -5.70182968 0.00556472 coulomb-14 -20.44260560 -20.44180116 0.00080444 0.00000000 20.44260560 -20.44183382 0.00077178 0.00000000 20.44260560 proper 13.49088960 13.49093007 0.00004047 13.49093018 0.00004058 13.49092521 0.00003561 13.49093144 0.00004184 vdw (SR) 0.00000000 -4.42242697 -4.42242697 0.00000000 0.00000000 0.00000000 0.00000000 6.10976968 6.10976968 vdw total 6.10947680 6.10959704 0.00012024 6.10959730 0.00012050 6.10956638 0.00008958 6.10976968 0.00029288 vdw-14 10.53196480 10.53202401 0.00005921 0.00000000 -10.53196480 10.53199873 0.00003393 0.00000000 -10.53196480 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 6.91447840 6.91434697 -0.00013143 6.91434702 -0.00013138 6.91432928 -0.00014912 6.91426920 -0.00020920 bond 1.04139760 1.04124893 -0.00014867 1.04124894 -0.00014866 1.04142683 0.00002923 1.04123024 -0.00016736 bonded 21.44676560 21.44652597 -0.00023963 21.44652615 -0.00023945 21.44668131 -0.00008429 21.44643088 -0.00033472 dihedral 13.49088960 13.49093007 0.00004047 13.49093018 0.00004058 13.49092521 0.00003561 13.49093144 0.00004184 nonbonded 0.40208240 0.40889194 0.00680954 0.40889208 0.00680968 0.40878199 0.00669959 0.40794000 0.00585760 potential 21.84884800 21.85541791 0.00656991 21.85541814 0.00657014 21.85534333 0.00649533 21.85437088 0.00552288 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 21.84884800 Difference in potential energy from amber=>gromacs conversion: 0.00656991 Difference in potential energy from amber=>lammps conversion: 0.00657014 Difference in potential energy from amber=>desmond conversion: 0.00649533 Difference in potential energy from amber=>charmm conversion: 0.00552288 ======================================================================= INFO 2017-03-18 23:03:19 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3378420.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3378420.inpcrd') INFO 2017-03-18 23:03:20 Beginning InterMol conversion INFO 2017-03-18 23:03:20 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:03:20 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:03:20 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3395921.inpcrd INFO 2017-03-18 23:03:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3395921/mobley_3395921_converted.input INFO 2017-03-18 23:03:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3395921/mobley_3395921_converted.cms WARNING 2017-03-18 23:03:36 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:03:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3395921/mobley_3395921_converted.inp INFO 2017-03-18 23:03:36 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3395921/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3395921/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3395921/mobley_3395921_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3395921/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 7.49170115 7.49170115 0.00000000 0.00000000 0.00000000 0.00000000 -4.05228768 -4.05228768 coulomb total -4.03504960 -4.05433231 -0.01928271 -4.05433228 -0.01928268 -4.05435621 -0.01930661 -4.05228768 -0.01723808 coulomb-14 -11.53989040 -11.54603346 -0.00614306 0.00000000 11.53989040 -11.54605000 -0.00615960 0.00000000 11.53989040 proper 8.77384800 8.77379454 -0.00005346 8.77379444 -0.00005356 8.77376482 -0.00008318 8.77388984 0.00004184 vdw (SR) 0.00000000 -1.87220491 -1.87220491 0.00000000 0.00000000 0.00000000 0.00000000 11.55486912 11.55486912 vdw total 11.55453440 11.55481754 0.00028314 11.55481808 0.00028368 11.55473545 0.00020105 11.55486912 0.00033472 vdw-14 13.42687440 13.42702245 0.00014805 0.00000000 -13.42687440 13.42693984 0.00006544 0.00000000 -13.42687440 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.29408720 2.29406422 -0.00002298 2.29406423 -0.00002297 2.29364286 -0.00044434 2.29404536 -0.00004184 bond 1.09955520 1.09938915 -0.00016605 1.09938914 -0.00016606 1.09910679 -0.00044841 1.09938784 -0.00016736 bonded 12.16749040 12.16724791 -0.00024249 12.16724781 -0.00024259 12.16651447 -0.00097593 12.16732304 -0.00016736 dihedral 8.77384800 8.77379454 -0.00005346 8.77379444 -0.00005356 8.77376482 -0.00008318 8.77388984 0.00004184 nonbonded 7.51948480 7.50048522 -0.01899958 7.50048567 -0.01899913 7.50037924 -0.01910556 7.50258144 -0.01690336 potential 19.68697520 19.66773313 -0.01924207 19.66773340 -0.01924180 19.66685727 -0.02011793 19.66990448 -0.01707072 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 19.68697520 Difference in potential energy from amber=>gromacs conversion: -0.01924207 Difference in potential energy from amber=>lammps conversion: -0.01924180 Difference in potential energy from amber=>desmond conversion: -0.02011793 Difference in potential energy from amber=>charmm conversion: -0.01707072 ======================================================================= INFO 2017-03-18 23:03:36 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3395921.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3395921.inpcrd') INFO 2017-03-18 23:03:36 Beginning InterMol conversion INFO 2017-03-18 23:03:36 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:03:36 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3398536.inpcrd INFO 2017-03-18 23:03:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3398536/mobley_3398536_converted.input INFO 2017-03-18 23:03:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3398536/mobley_3398536_converted.cms INFO 2017-03-18 23:03:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3398536/mobley_3398536_converted.rst7 WARNING 2017-03-18 23:03:52 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:03:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3398536/mobley_3398536_converted.inp INFO 2017-03-18 23:03:52 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3398536/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3398536/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3398536/mobley_3398536_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_3398536/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3398536/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 3.48899748 3.48899748 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 4.14433568 4.14433568 coulomb total 4.13128160 4.13879042 0.00750882 4.13879037 0.00750877 4.13876989 0.00748829 4.13128160 0.00000000 4.14433568 0.01305408 coulomb-14 0.64684640 0.64979294 0.00294654 0.00000000 -0.64684640 0.64976394 0.00291754 0.64684640 0.00000000 0.00000000 -0.64684640 improper 0.00000000 0.00002517 0.00002517 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00025559 -0.00016281 0.00028074 -0.00013766 0.00028031 -0.00013809 0.00041840 0.00000000 0.00025104 -0.00016736 vdw (SR) 0.00000000 -1.24041200 -1.24041200 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 13.93288736 13.93288736 vdw total 13.93272000 13.93291306 0.00019306 13.93291288 0.00019288 13.93298726 0.00026726 13.93272000 0.00000000 13.93288736 0.00016736 vdw-14 15.17327600 15.17332506 0.00004906 0.00000000 -15.17327600 15.17339688 0.00012088 15.17327600 0.00000000 0.00000000 -15.17327600 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.69454400 0.69433756 -0.00020644 0.69433756 -0.00020644 0.69420410 -0.00033990 0.69454400 0.00000000 0.69437664 -0.00016736 bond 1.05980720 1.05992568 0.00011848 1.05992569 0.00011849 1.05957697 -0.00023023 1.05980720 0.00000000 1.05993272 0.00012552 bonded 1.75476960 1.75454400 -0.00022560 1.75454399 -0.00022561 1.75406138 -0.00070822 1.75476960 0.00000000 1.75460224 -0.00016736 dihedral 0.00041840 0.00028076 -0.00013764 0.00028074 -0.00013766 0.00028031 -0.00013809 0.00041840 0.00000000 0.00029288 -0.00012552 nonbonded 18.06400160 18.07170348 0.00770188 18.07170351 0.00770191 18.07175715 0.00775555 18.06400160 0.00000000 18.07722304 0.01322144 potential 19.81877120 19.82624748 0.00747628 19.82624759 0.00747639 19.82576342 0.00699222 19.81877120 0.00000000 19.83178344 0.01301224 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 19.81877120 Difference in potential energy from amber=>gromacs conversion: 0.00747628 Difference in potential energy from amber=>lammps conversion: 0.00747639 Difference in potential energy from amber=>desmond conversion: 0.00699222 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.01301224 ======================================================================= INFO 2017-03-18 23:03:52 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3398536.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3398536.inpcrd') INFO 2017-03-18 23:03:52 Beginning InterMol conversion INFO 2017-03-18 23:03:52 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:03:52 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:03:52 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3414356.inpcrd INFO 2017-03-18 23:03:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3414356/mobley_3414356_converted.input INFO 2017-03-18 23:03:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3414356/mobley_3414356_converted.cms WARNING 2017-03-18 23:04:08 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:04:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3414356/mobley_3414356_converted.inp INFO 2017-03-18 23:04:08 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3414356/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3414356/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3414356/mobley_3414356_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3414356/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 56.12503354 56.12503354 0.00000000 0.00000000 0.00000000 0.00000000 -79.30336864 -79.30336864 coulomb total -79.29516800 -79.28589679 0.00927121 -79.28589626 0.00927174 -79.28610378 0.00906422 -79.30336864 -0.00820064 coulomb-14 -135.38210640 -135.41093033 -0.02882393 0.00000000 135.38210640 -135.41092663 -0.02882023 0.00000000 135.38210640 proper 16.46069280 16.46065507 -0.00003773 16.46065724 -0.00003556 16.46064598 -0.00004682 16.46065096 -0.00004184 vdw (SR) 0.00000000 2.31388951 2.31388951 0.00000000 0.00000000 0.00000000 0.00000000 12.81450416 12.81450416 vdw total 12.81475520 12.81428972 -0.00046548 12.81428994 -0.00046526 12.81400469 -0.00075051 12.81450416 -0.00025104 vdw-14 10.50058480 10.50040022 -0.00018458 0.00000000 -10.50058480 10.50031439 -0.00027041 0.00000000 -10.50058480 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.32207200 4.32206091 -0.00001109 4.32206070 -0.00001130 4.32200209 -0.00006991 4.32203016 -0.00004184 bond 0.68617600 0.68620727 0.00003127 0.68620725 0.00003125 0.68580880 -0.00036720 0.68621784 0.00004184 bonded 21.46894080 21.46892324 -0.00001756 21.46892519 -0.00001561 21.46845686 -0.00048394 21.46889896 -0.00004184 dihedral 16.46069280 16.46065507 -0.00003773 16.46065724 -0.00003556 16.46064598 -0.00004682 16.46065096 -0.00004184 nonbonded -66.48041280 -66.47160707 0.00880573 -66.47160548 0.00880732 -66.47209910 0.00831370 -66.48886448 -0.00845168 potential -45.01147200 -45.00268382 0.00878818 -45.00268142 0.00879058 -45.00369855 0.00777345 -45.01996552 -0.00849352 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -45.01147200 Difference in potential energy from amber=>gromacs conversion: 0.00878818 Difference in potential energy from amber=>lammps conversion: 0.00879058 Difference in potential energy from amber=>desmond conversion: 0.00777345 Difference in potential energy from amber=>charmm conversion: -0.00849352 ======================================================================= INFO 2017-03-18 23:04:08 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3414356.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3414356.inpcrd') INFO 2017-03-18 23:04:08 Beginning InterMol conversion INFO 2017-03-18 23:04:08 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:04:08 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:04:08 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3452749.inpcrd INFO 2017-03-18 23:04:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3452749/mobley_3452749_converted.input INFO 2017-03-18 23:04:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3452749/mobley_3452749_converted.cms WARNING 2017-03-18 23:04:24 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:04:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3452749/mobley_3452749_converted.inp INFO 2017-03-18 23:04:24 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3452749/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3452749/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3452749/mobley_3452749_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3452749/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -5.84086252 -5.84086252 0.00000000 0.00000000 0.00000000 0.00000000 -23.18115912 -23.18115912 coulomb total -23.18521760 -23.18122570 0.00399190 -23.18122523 0.00399237 -23.18151823 0.00369937 -23.18115912 0.00405848 coulomb-14 -17.33682240 -17.34036318 -0.00354078 0.00000000 17.33682240 -17.34037922 -0.00355682 0.00000000 17.33682240 improper 0.00000000 0.00012753 0.00012753 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00125520 0.00123107 -0.00002413 0.00135850 0.00010330 0.00135965 0.00010445 0.00121336 -0.00004184 vdw (SR) 0.00000000 60.97236547 60.97236547 0.00000000 0.00000000 0.00000000 0.00000000 88.05177792 88.05177792 vdw total 88.05186160 88.05104702 -0.00081458 88.05104572 -0.00081588 88.05012901 -0.00173259 88.05177792 -0.00008368 vdw-14 27.07884800 27.07868155 -0.00016645 0.00000000 -27.07884800 27.07865010 -0.00019790 0.00000000 -27.07884800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.22382000 1.22393381 0.00011381 1.22393380 0.00011380 1.22415076 0.00033076 1.22394552 0.00012552 bond 2.26396240 2.26377192 -0.00019048 2.26377190 -0.00019050 2.26330059 -0.00066181 2.26375320 -0.00020920 bonded 3.48903760 3.48906432 0.00002672 3.48906420 0.00002660 3.48881100 -0.00022660 3.48903760 0.00000000 dihedral 0.00125520 0.00135860 0.00010340 0.00135850 0.00010330 0.00135965 0.00010445 0.00133888 0.00008368 nonbonded 64.86664400 64.86982132 0.00317732 64.86982384 0.00317984 64.86861077 0.00196677 64.87061880 0.00397480 potential 68.35568160 68.35888565 0.00320405 68.35888654 0.00320494 68.35735102 0.00166942 68.35969824 0.00401664 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 68.35568160 Difference in potential energy from amber=>gromacs conversion: 0.00320405 Difference in potential energy from amber=>lammps conversion: 0.00320494 Difference in potential energy from amber=>desmond conversion: 0.00166942 Difference in potential energy from amber=>charmm conversion: 0.00401664 ======================================================================= INFO 2017-03-18 23:04:24 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3452749.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3452749.inpcrd') INFO 2017-03-18 23:04:24 Beginning InterMol conversion INFO 2017-03-18 23:04:24 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:04:24 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:04:24 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_349850.inpcrd INFO 2017-03-18 23:04:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_349850/mobley_349850_converted.input INFO 2017-03-18 23:04:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_349850/mobley_349850_converted.cms WARNING 2017-03-18 23:04:40 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:04:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_349850/mobley_349850_converted.inp INFO 2017-03-18 23:04:40 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_349850/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_349850/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_349850/mobley_349850_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_349850/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -11.16207389 -11.16207389 0.00000000 0.00000000 0.00000000 0.00000000 -34.41532464 -34.41532464 coulomb total -34.36612080 -34.36872236 -0.00260156 -34.36872199 -0.00260119 -34.36862250 -0.00250170 -34.41532464 -0.04920384 coulomb-14 -23.20906640 -23.20664848 0.00241792 0.00000000 23.20906640 -23.20673332 0.00233308 0.00000000 23.20906640 improper 0.00000000 0.00326492 0.00326492 0.00000000 0.00000000 0.00000000 0.00000000 0.00326352 0.00326352 proper 19.52630960 19.52290594 -0.00340366 19.52615270 -0.00015690 19.52611793 -0.00019167 19.52287872 -0.00343088 vdw (SR) 0.00000000 -0.79574009 -0.79574009 0.00000000 0.00000000 0.00000000 0.00000000 22.20101528 22.20101528 vdw total 22.20114080 22.20099007 -0.00015073 22.20099018 -0.00015062 22.20096038 -0.00018042 22.20101528 -0.00012552 vdw-14 22.99693760 22.99673016 -0.00020744 0.00000000 -22.99693760 22.99676852 -0.00016908 0.00000000 -22.99693760 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 7.78098480 7.78111252 0.00012772 7.78111241 0.00012761 7.78128145 0.00029665 7.78106848 0.00008368 bond 4.49194240 4.49202010 0.00007770 4.49202022 0.00007782 4.49174190 -0.00020050 4.49202608 0.00008368 bonded 31.79923680 31.79930348 0.00006668 31.79928533 0.00004853 31.79914128 -0.00009552 31.79923680 0.00000000 dihedral 19.52630960 19.52617086 -0.00013874 19.52615270 -0.00015690 19.52611793 -0.00019167 19.52614224 -0.00016736 nonbonded -12.16498000 -12.16773229 -0.00275229 -12.16773182 -0.00275182 -12.16766212 -0.00268212 -12.21430936 -0.04932936 potential 19.63425680 19.63157119 -0.00268561 19.63155352 -0.00270328 19.63140599 -0.00285081 19.58496928 -0.04928752 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 19.63425680 Difference in potential energy from amber=>gromacs conversion: -0.00268561 Difference in potential energy from amber=>lammps conversion: -0.00270328 Difference in potential energy from amber=>desmond conversion: -0.00285081 Difference in potential energy from amber=>charmm conversion: -0.04928752 ======================================================================= INFO 2017-03-18 23:04:40 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_349850.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_349850.inpcrd') INFO 2017-03-18 23:04:40 Beginning InterMol conversion INFO 2017-03-18 23:04:40 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:04:40 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:04:40 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3515580.inpcrd INFO 2017-03-18 23:04:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3515580/mobley_3515580_converted.input INFO 2017-03-18 23:04:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3515580/mobley_3515580_converted.cms WARNING 2017-03-18 23:04:56 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:04:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3515580/mobley_3515580_converted.inp INFO 2017-03-18 23:04:56 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3515580/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3515580/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3515580/mobley_3515580_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3515580/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -120.07535972 -120.07535972 0.00000000 0.00000000 0.00000000 0.00000000 -29.75485072 -29.75485072 coulomb total -29.72104400 -29.73749489 -0.01645089 -29.73749465 -0.01645065 -29.73729424 -0.01625024 -29.75485072 -0.03380672 coulomb-14 90.33130480 90.33786484 0.00656004 0.00000000 -90.33130480 90.33785443 0.00654963 0.00000000 -90.33130480 improper 0.00000000 0.00009340 0.00009340 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00292880 0.00301352 0.00008472 0.00310687 0.00017807 0.00308839 0.00015959 0.00301248 0.00008368 vdw (SR) 0.00000000 14.75171139 14.75171139 0.00000000 0.00000000 0.00000000 0.00000000 42.82198480 42.82198480 vdw total 42.82198480 42.82184638 -0.00013842 42.82184673 -0.00013807 42.82243634 0.00045154 42.82198480 0.00000000 vdw-14 28.07003760 28.07013499 0.00009739 0.00000000 -28.07003760 28.07022283 0.00018523 0.00000000 -28.07003760 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.49496720 0.49485744 -0.00010976 0.49485745 -0.00010975 0.49480281 -0.00016439 0.49488352 -0.00008368 bond 1.26147600 1.26146041 -0.00001559 1.26146039 -0.00001561 1.26158851 0.00011251 1.26147600 0.00000000 bonded 1.75937200 1.75942477 0.00005277 1.75942472 0.00005272 1.75947972 0.00010772 1.75945568 0.00008368 dihedral 0.00292880 0.00310692 0.00017812 0.00310687 0.00017807 0.00308839 0.00015959 0.00309616 0.00016736 nonbonded 13.10094080 13.08435149 -0.01658931 13.08435208 -0.01658872 13.08514210 -0.01579870 13.06713408 -0.03380672 potential 14.86031280 14.84377626 -0.01653654 14.84377680 -0.01653600 14.84455845 -0.01575435 14.82654792 -0.03376488 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 14.86031280 Difference in potential energy from amber=>gromacs conversion: -0.01653654 Difference in potential energy from amber=>lammps conversion: -0.01653600 Difference in potential energy from amber=>desmond conversion: -0.01575435 Difference in potential energy from amber=>charmm conversion: -0.03376488 ======================================================================= INFO 2017-03-18 23:04:56 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3515580.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3515580.inpcrd') INFO 2017-03-18 23:04:56 Beginning InterMol conversion INFO 2017-03-18 23:04:56 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:04:56 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:04:56 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_352111.inpcrd INFO 2017-03-18 23:04:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_352111/mobley_352111_converted.input INFO 2017-03-18 23:04:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_352111/mobley_352111_converted.cms WARNING 2017-03-18 23:05:12 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:05:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_352111/mobley_352111_converted.inp INFO 2017-03-18 23:05:12 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_352111/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_352111/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_352111/mobley_352111_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_352111/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -127.35922939 -127.35922939 0.00000000 0.00000000 0.00000000 0.00000000 -215.86921232 -215.86921232 coulomb total -215.91071760 -215.94046033 -0.02974273 -215.94045747 -0.02973987 -215.94048718 -0.02976958 -215.86921232 0.04150528 coulomb-14 -88.55728880 -88.58123094 -0.02394214 0.00000000 88.55728880 -88.58128948 -0.02400068 0.00000000 88.55728880 improper 0.00000000 0.00000520 0.00000520 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 41.13499600 41.13480854 -0.00018746 41.13481358 -0.00018242 41.13473291 -0.00026309 41.13482864 -0.00016736 vdw (SR) 0.00000000 -4.60723574 -4.60723574 0.00000000 0.00000000 0.00000000 0.00000000 11.79959128 11.79959128 vdw total 11.79929840 11.79942900 0.00013060 11.79942894 0.00013054 11.79958153 0.00028313 11.79959128 0.00029288 vdw-14 16.40671920 16.40666475 -0.00005445 0.00000000 -16.40671920 16.40680137 0.00008217 0.00000000 -16.40671920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.82626800 3.82642001 0.00015201 3.82642000 0.00015200 3.82617166 -0.00009634 3.82651904 0.00025104 bond 3.56686000 3.56677557 -0.00008443 3.56677557 -0.00008443 3.56701325 0.00015325 3.56677632 -0.00008368 bonded 48.52812400 48.52800933 -0.00011467 48.52800915 -0.00011485 48.52791783 -0.00020617 48.52812400 0.00000000 dihedral 41.13499600 41.13481375 -0.00018225 41.13481358 -0.00018242 41.13473291 -0.00026309 41.13482864 -0.00016736 nonbonded -204.11141920 -204.14103132 -0.02961212 -204.14102937 -0.02961017 -204.14090565 -0.02948645 -204.06962104 0.04179816 potential -155.58329520 -155.61302199 -0.02972679 -155.61301834 -0.02972314 -155.61305474 -0.02975954 -155.54153888 0.04175632 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -155.58329520 Difference in potential energy from amber=>gromacs conversion: -0.02972679 Difference in potential energy from amber=>lammps conversion: -0.02972314 Difference in potential energy from amber=>desmond conversion: -0.02975954 Difference in potential energy from amber=>charmm conversion: 0.04175632 ======================================================================= INFO 2017-03-18 23:05:12 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_352111.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_352111.inpcrd') INFO 2017-03-18 23:05:12 Beginning InterMol conversion INFO 2017-03-18 23:05:12 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:05:13 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:05:13 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3525176.inpcrd INFO 2017-03-18 23:05:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3525176/mobley_3525176_converted.input INFO 2017-03-18 23:05:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3525176/mobley_3525176_converted.cms WARNING 2017-03-18 23:05:28 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:05:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3525176/mobley_3525176_converted.inp INFO 2017-03-18 23:05:28 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3525176/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3525176/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3525176/mobley_3525176_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3525176/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 7.92170622 7.92170622 0.00000000 0.00000000 0.00000000 0.00000000 -0.54312504 -0.54312504 coulomb total -0.54852240 -0.54862504 -0.00010264 -0.54862503 -0.00010263 -0.54865202 -0.00012962 -0.54312504 0.00539736 coulomb-14 -8.47008960 -8.47033126 -0.00024166 0.00000000 8.47008960 -8.47030407 -0.00021447 0.00000000 8.47008960 improper 0.00000000 0.00008888 0.00008888 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 3.49907920 3.49889521 -0.00018399 3.49898410 -0.00009510 3.49898169 -0.00009751 3.49891184 -0.00016736 vdw (SR) 0.00000000 -5.47162442 -5.47162442 0.00000000 0.00000000 0.00000000 0.00000000 18.03521568 18.03521568 vdw total 18.03555040 18.03515764 -0.00039276 18.03515752 -0.00039288 18.03497694 -0.00057346 18.03521568 -0.00033472 vdw-14 23.50696720 23.50678206 -0.00018514 0.00000000 -23.50696720 23.50661662 -0.00035058 0.00000000 -23.50696720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.44136400 2.44126508 -0.00009892 2.44126509 -0.00009891 2.44133598 -0.00002802 2.44119664 -0.00016736 bond 1.62715760 1.62696934 -0.00018826 1.62696932 -0.00018828 1.62746407 0.00030647 1.62699024 -0.00016736 bonded 7.56760080 7.56721850 -0.00038230 7.56721851 -0.00038229 7.56778174 0.00018094 7.56718240 -0.00041840 dihedral 3.49907920 3.49898408 -0.00009512 3.49898410 -0.00009510 3.49898169 -0.00009751 3.49899552 -0.00008368 nonbonded 17.48702800 17.48653260 -0.00049540 17.48653261 -0.00049539 17.48632492 -0.00070308 17.49209064 0.00506264 potential 25.05462880 25.05375110 -0.00087770 25.05375100 -0.00087780 25.05399451 -0.00063429 25.05927304 0.00464424 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 25.05462880 Difference in potential energy from amber=>gromacs conversion: -0.00087770 Difference in potential energy from amber=>lammps conversion: -0.00087780 Difference in potential energy from amber=>desmond conversion: -0.00063429 Difference in potential energy from amber=>charmm conversion: 0.00464424 ======================================================================= INFO 2017-03-18 23:05:28 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3525176.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3525176.inpcrd') INFO 2017-03-18 23:05:29 Beginning InterMol conversion INFO 2017-03-18 23:05:29 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:05:29 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:05:29 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3546460.inpcrd INFO 2017-03-18 23:05:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3546460/mobley_3546460_converted.input INFO 2017-03-18 23:05:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3546460/mobley_3546460_converted.cms WARNING 2017-03-18 23:05:44 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:05:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3546460/mobley_3546460_converted.inp INFO 2017-03-18 23:05:44 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3546460/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3546460/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3546460/mobley_3546460_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3546460/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 11.96557643 11.96557643 0.00000000 0.00000000 0.00000000 0.00000000 -6.69368872 -6.69368872 coulomb total -6.69858400 -6.69869574 -0.00011174 -6.69869571 -0.00011171 -6.69864643 -0.00006243 -6.69368872 0.00489528 coulomb-14 -18.66356880 -18.66427217 -0.00070337 0.00000000 18.66356880 -18.66420983 -0.00064103 0.00000000 18.66356880 proper 8.39017520 8.39030162 0.00012642 8.39030156 0.00012636 8.39027541 0.00010021 8.39030072 0.00012552 vdw (SR) 0.00000000 -2.42462783 -2.42462783 0.00000000 0.00000000 0.00000000 0.00000000 3.97613888 3.97613888 vdw total 3.97605520 3.97604413 -0.00001107 3.97604420 -0.00001100 3.97606786 0.00001266 3.97613888 0.00008368 vdw-14 6.40068320 6.40067196 -0.00001124 0.00000000 -6.40068320 6.40069362 0.00001042 0.00000000 -6.40068320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.51999920 3.51987713 -0.00012207 3.51987715 -0.00012205 3.51980764 -0.00019156 3.51983184 -0.00016736 bond 0.88407920 0.88405215 -0.00002705 0.88405213 -0.00002707 0.88382013 -0.00025907 0.88403736 -0.00004184 bonded 12.79425360 12.79423090 -0.00002270 12.79423084 -0.00002276 12.79390317 -0.00035043 12.79416992 -0.00008368 dihedral 8.39017520 8.39030162 0.00012642 8.39030156 0.00012636 8.39027541 0.00010021 8.39030072 0.00012552 nonbonded -2.72252880 -2.72265161 -0.00012281 -2.72265147 -0.00012267 -2.72257856 -0.00004976 -2.71754984 0.00497896 potential 10.07172480 10.07157929 -0.00014551 10.07157962 -0.00014518 10.07126632 -0.00045848 10.07662008 0.00489528 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 10.07172480 Difference in potential energy from amber=>gromacs conversion: -0.00014551 Difference in potential energy from amber=>lammps conversion: -0.00014518 Difference in potential energy from amber=>desmond conversion: -0.00045848 Difference in potential energy from amber=>charmm conversion: 0.00489528 ======================================================================= INFO 2017-03-18 23:05:44 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3546460.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3546460.inpcrd') INFO 2017-03-18 23:05:45 Beginning InterMol conversion INFO 2017-03-18 23:05:45 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:05:45 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:05:45 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3572203.inpcrd INFO 2017-03-18 23:05:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3572203/mobley_3572203_converted.input INFO 2017-03-18 23:05:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3572203/mobley_3572203_converted.cms WARNING 2017-03-18 23:06:01 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:06:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3572203/mobley_3572203_converted.inp INFO 2017-03-18 23:06:01 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3572203/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3572203/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3572203/mobley_3572203_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3572203/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -54.13367176 -54.13367176 0.00000000 0.00000000 0.00000000 0.00000000 -65.04714176 -65.04714176 coulomb total -65.05910800 -65.06278203 -0.00367403 -65.06278155 -0.00367355 -65.06291184 -0.00380384 -65.04714176 0.01196624 coulomb-14 -10.92609760 -10.92911027 -0.00301267 0.00000000 10.92609760 -10.92925962 -0.00316202 0.00000000 10.92609760 improper 0.00000000 0.00001026 0.00001026 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 16.60253040 16.60232929 -0.00020111 16.60233961 -0.00019079 16.60233756 -0.00019284 16.60232120 -0.00020920 vdw (SR) 0.00000000 -4.30222150 -4.30222150 0.00000000 0.00000000 0.00000000 0.00000000 10.85856784 10.85856784 vdw total 10.85873520 10.85841579 -0.00031941 10.85841596 -0.00031924 10.85840061 -0.00033459 10.85856784 -0.00016736 vdw-14 15.16072400 15.16063729 -0.00008671 0.00000000 -15.16072400 15.16063572 -0.00008828 0.00000000 -15.16072400 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.30201280 3.30198810 -0.00002470 3.30198811 -0.00002469 3.30229686 0.00028406 3.30201280 0.00000000 bond 3.26686720 3.26680100 -0.00006620 3.26680101 -0.00006619 3.26676519 -0.00010201 3.26678352 -0.00008368 bonded 23.17141040 23.17112865 -0.00028175 23.17112873 -0.00028167 23.17139961 -0.00001079 23.17111752 -0.00029288 dihedral 16.60253040 16.60233955 -0.00019085 16.60233961 -0.00019079 16.60233756 -0.00019284 16.60232120 -0.00020920 nonbonded -54.20037280 -54.20436624 -0.00399344 -54.20436434 -0.00399154 -54.20451124 -0.00413844 -54.18857392 0.01179888 potential -31.02896240 -31.03323759 -0.00427519 -31.03323677 -0.00427437 -31.03321406 -0.00425166 -31.01737272 0.01158968 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -31.02896240 Difference in potential energy from amber=>gromacs conversion: -0.00427519 Difference in potential energy from amber=>lammps conversion: -0.00427437 Difference in potential energy from amber=>desmond conversion: -0.00425166 Difference in potential energy from amber=>charmm conversion: 0.01158968 ======================================================================= INFO 2017-03-18 23:06:01 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3572203.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3572203.inpcrd') INFO 2017-03-18 23:06:01 Beginning InterMol conversion INFO 2017-03-18 23:06:01 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:06:01 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:06:01 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3573480.inpcrd INFO 2017-03-18 23:06:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3573480/mobley_3573480_converted.input INFO 2017-03-18 23:06:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3573480/mobley_3573480_converted.cms WARNING 2017-03-18 23:06:17 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:06:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3573480/mobley_3573480_converted.inp INFO 2017-03-18 23:06:17 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3573480/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3573480/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3573480/mobley_3573480_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3573480/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -4.74793659 -4.74793659 0.00000000 0.00000000 0.00000000 0.00000000 -60.42838232 -60.42838232 coulomb total -60.35420000 -60.35675259 -0.00255259 -60.35675224 -0.00255224 -60.35667015 -0.00247015 -60.42838232 -0.07418232 coulomb-14 -55.60410480 -55.60881600 -0.00471120 0.00000000 55.60410480 -55.60878126 -0.00467646 0.00000000 55.60410480 improper 0.00000000 0.00204478 0.00204478 0.00000000 0.00000000 0.00000000 0.00000000 0.00205016 0.00205016 proper 17.54936960 17.54730528 -0.00206432 17.54935119 -0.00001841 17.54936291 -0.00000669 17.54731944 -0.00205016 vdw (SR) 0.00000000 -2.24434091 -2.24434091 0.00000000 0.00000000 0.00000000 0.00000000 8.29356664 8.29356664 vdw total 8.29352480 8.29342472 -0.00010008 8.29342480 -0.00010000 8.29358305 0.00005825 8.29356664 0.00004184 vdw-14 10.53782240 10.53776563 -0.00005677 0.00000000 -10.53782240 10.53790190 0.00007950 0.00000000 -10.53782240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.10159920 3.10171377 0.00011457 3.10171376 0.00011456 3.10141204 -0.00018716 3.10168288 0.00008368 bond 1.65895600 1.65903348 0.00007748 1.65903349 0.00007749 1.65860306 -0.00035294 1.65903968 0.00008368 bonded 22.30992480 22.31009730 0.00017250 22.31009844 0.00017364 22.30937800 -0.00054680 22.31009216 0.00016736 dihedral 17.54936960 17.54935006 -0.00001954 17.54935119 -0.00001841 17.54936291 -0.00000669 17.54936960 0.00000000 nonbonded -52.06067520 -52.06332787 -0.00265267 -52.06332786 -0.00265266 -52.06308710 -0.00241190 -52.13481568 -0.07414048 potential -29.75075040 -29.75323057 -0.00248017 -29.75322858 -0.00247818 -29.75377522 -0.00302482 -29.82472352 -0.07397312 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -29.75075040 Difference in potential energy from amber=>gromacs conversion: -0.00248017 Difference in potential energy from amber=>lammps conversion: -0.00247818 Difference in potential energy from amber=>desmond conversion: -0.00302482 Difference in potential energy from amber=>charmm conversion: -0.07397312 ======================================================================= INFO 2017-03-18 23:06:17 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3573480.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3573480.inpcrd') INFO 2017-03-18 23:06:17 Beginning InterMol conversion INFO 2017-03-18 23:06:17 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:06:17 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:06:17 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3589456.inpcrd INFO 2017-03-18 23:06:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3589456/mobley_3589456_converted.input INFO 2017-03-18 23:06:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3589456/mobley_3589456_converted.cms WARNING 2017-03-18 23:06:33 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:06:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3589456/mobley_3589456_converted.inp INFO 2017-03-18 23:06:33 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3589456/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3589456/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3589456/mobley_3589456_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3589456/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -58.00496198 -58.00496198 0.00000000 0.00000000 0.00000000 0.00000000 -125.34870704 -125.34870704 coulomb total -125.32126000 -125.32915663 -0.00789663 -125.32915521 -0.00789521 -125.32901044 -0.00775044 -125.34870704 -0.02744704 coulomb-14 -67.32139680 -67.32419465 -0.00279785 0.00000000 67.32139680 -67.32415782 -0.00276102 0.00000000 67.32139680 proper 61.72948080 61.72946227 -0.00001853 61.72944314 -0.00003766 61.72934942 -0.00013138 61.72969000 0.00020920 vdw (SR) 0.00000000 0.35175592 0.35175592 0.00000000 0.00000000 0.00000000 0.00000000 20.31691824 20.31691824 vdw total 20.31708560 20.31666835 -0.00041725 20.31666887 -0.00041673 20.31681391 -0.00027169 20.31691824 -0.00016736 vdw-14 19.96521120 19.96491243 -0.00029877 0.00000000 -19.96521120 19.96504610 -0.00016510 0.00000000 -19.96521120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.36767760 4.36759655 -0.00008105 4.36759643 -0.00008117 4.36767036 -0.00000724 4.36771944 0.00004184 bond 1.53176240 1.53162348 -0.00013892 1.53162349 -0.00013891 1.53150213 -0.00026027 1.53163688 -0.00012552 bonded 67.62892080 67.62868231 -0.00023849 67.62866307 -0.00025773 67.62852191 -0.00039889 67.62904632 0.00012552 dihedral 61.72948080 61.72946227 -0.00001853 61.72944314 -0.00003766 61.72934942 -0.00013138 61.72969000 0.00020920 nonbonded -105.00417440 -105.01248827 -0.00831387 -105.01248801 -0.00831361 -105.01219653 -0.00802213 -105.03178880 -0.02761440 potential -37.37525360 -37.38380597 -0.00855237 -37.38382452 -0.00857092 -37.38374210 -0.00848850 -37.40274248 -0.02748888 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -37.37525360 Difference in potential energy from amber=>gromacs conversion: -0.00855237 Difference in potential energy from amber=>lammps conversion: -0.00857092 Difference in potential energy from amber=>desmond conversion: -0.00848850 Difference in potential energy from amber=>charmm conversion: -0.02748888 ======================================================================= INFO 2017-03-18 23:06:33 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3589456.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3589456.inpcrd') INFO 2017-03-18 23:06:33 Beginning InterMol conversion INFO 2017-03-18 23:06:33 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:06:33 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:06:33 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_36119.inpcrd INFO 2017-03-18 23:06:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_36119/mobley_36119_converted.input INFO 2017-03-18 23:06:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_36119/mobley_36119_converted.cms WARNING 2017-03-18 23:06:49 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:06:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_36119/mobley_36119_converted.inp INFO 2017-03-18 23:06:49 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_36119/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_36119/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_36119/mobley_36119_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_36119/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 13.86172468 13.86172468 0.00000000 0.00000000 0.00000000 0.00000000 -6.10274056 -6.10274056 coulomb total -6.10069040 -6.10068746 0.00000294 -6.10068747 0.00000293 -6.10077429 -0.00008389 -6.10274056 -0.00205016 coulomb-14 -19.96186400 -19.96241215 -0.00054815 0.00000000 19.96186400 -19.96244980 -0.00058580 0.00000000 19.96186400 proper 11.77042880 11.77048871 0.00005991 11.77048863 0.00005983 11.77049001 0.00006121 11.77051248 0.00008368 vdw (SR) 0.00000000 -3.70678920 -3.70678920 0.00000000 0.00000000 0.00000000 0.00000000 6.10918392 6.10918392 vdw total 6.10947680 6.10904520 -0.00043160 6.10904543 -0.00043137 6.10913969 -0.00033711 6.10918392 -0.00029288 vdw-14 9.81608240 9.81583441 -0.00024799 0.00000000 -9.81608240 9.81593625 -0.00014615 0.00000000 -9.81608240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.72376000 3.72382701 0.00006701 3.72382703 0.00006703 3.72415649 0.00039649 3.72376000 0.00000000 bond 1.09871840 1.09866642 -0.00005198 1.09866643 -0.00005197 1.09857570 -0.00014270 1.09867656 -0.00004184 bonded 16.59290720 16.59298213 0.00007493 16.59298209 0.00007489 16.59322221 0.00031501 16.59294904 0.00004184 dihedral 11.77042880 11.77048871 0.00005991 11.77048863 0.00005983 11.77049001 0.00006121 11.77051248 0.00008368 nonbonded 0.00878640 0.00835774 -0.00042866 0.00835789 -0.00042851 0.00836540 -0.00042100 0.00644336 -0.00234304 potential 16.60169360 16.60133987 -0.00035373 16.60134005 -0.00035355 16.60149486 -0.00019874 16.59939240 -0.00230120 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 16.60169360 Difference in potential energy from amber=>gromacs conversion: -0.00035373 Difference in potential energy from amber=>lammps conversion: -0.00035355 Difference in potential energy from amber=>desmond conversion: -0.00019874 Difference in potential energy from amber=>charmm conversion: -0.00230120 ======================================================================= INFO 2017-03-18 23:06:49 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_36119.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_36119.inpcrd') INFO 2017-03-18 23:06:49 Beginning InterMol conversion INFO 2017-03-18 23:06:49 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:06:49 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:06:49 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3639400.inpcrd INFO 2017-03-18 23:06:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3639400/mobley_3639400_converted.input INFO 2017-03-18 23:06:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3639400/mobley_3639400_converted.cms WARNING 2017-03-18 23:07:05 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:07:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3639400/mobley_3639400_converted.inp INFO 2017-03-18 23:07:05 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3639400/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3639400/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3639400/mobley_3639400_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3639400/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 6.54765812 6.54765812 0.00000000 0.00000000 0.00000000 0.00000000 3.37138352 3.37138352 coulomb total 3.35724160 3.36698457 0.00974297 3.36698455 0.00974295 3.36695463 0.00971303 3.37138352 0.01414192 coulomb-14 -3.18486080 -3.18067355 0.00418725 0.00000000 3.18486080 -3.18067559 0.00418521 0.00000000 3.18486080 proper 4.88816720 4.88798799 -0.00017921 4.88798812 -0.00017908 4.88800549 -0.00016171 4.88799984 -0.00016736 vdw (SR) 0.00000000 -1.03997570 -1.03997570 0.00000000 0.00000000 0.00000000 0.00000000 2.29981928 2.29981928 vdw total 2.29952640 2.29977776 0.00025136 2.29977782 0.00025142 2.29975906 0.00023266 2.29981928 0.00029288 vdw-14 3.33966880 3.33975346 0.00008466 0.00000000 -3.33966880 3.33972853 0.00005973 0.00000000 -3.33966880 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.99746560 0.99760190 0.00013630 0.99760191 0.00013631 0.99777337 0.00030777 0.99763296 0.00016736 bond 0.78784720 0.78790395 0.00005675 0.78790394 0.00005674 0.78827845 0.00043125 0.78788904 0.00004184 bonded 6.67348000 6.67349384 0.00001384 6.67349397 0.00001397 6.67405731 0.00057731 6.67352184 0.00004184 dihedral 4.88816720 4.88798799 -0.00017921 4.88798812 -0.00017908 4.88800549 -0.00016171 4.88799984 -0.00016736 nonbonded 5.65676800 5.66676233 0.00999433 5.66676232 0.00999432 5.66671369 0.00994569 5.67120280 0.01443480 potential 12.33024800 12.34025617 0.01000817 12.34025613 0.01000813 12.34073587 0.01048787 12.34472464 0.01447664 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 12.33024800 Difference in potential energy from amber=>gromacs conversion: 0.01000817 Difference in potential energy from amber=>lammps conversion: 0.01000813 Difference in potential energy from amber=>desmond conversion: 0.01048787 Difference in potential energy from amber=>charmm conversion: 0.01447664 ======================================================================= INFO 2017-03-18 23:07:05 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3639400.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3639400.inpcrd') INFO 2017-03-18 23:07:05 Beginning InterMol conversion INFO 2017-03-18 23:07:05 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:07:05 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3663158.inpcrd INFO 2017-03-18 23:07:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3663158/mobley_3663158_converted.input INFO 2017-03-18 23:07:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3663158/mobley_3663158_converted.cms INFO 2017-03-18 23:07:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3663158/mobley_3663158_converted.rst7 WARNING 2017-03-18 23:07:21 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:07:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3663158/mobley_3663158_converted.inp INFO 2017-03-18 23:07:21 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3663158/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3663158/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3663158/mobley_3663158_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_3663158/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3663158/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 47.79177269 47.79177269 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -75.64969064 -75.64969064 coulomb total -75.67475280 -75.67718870 -0.00243590 -75.67718789 -0.00243509 -75.67775859 -0.00300579 -75.67475280 0.00000000 -75.64969064 0.02506216 coulomb-14 -123.46481920 -123.46896139 -0.00414219 0.00000000 123.46481920 -123.46898102 -0.00416182 -123.46481920 0.00000000 0.00000000 123.46481920 improper 0.00000000 0.00011617 0.00011617 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00125520 0.00098266 -0.00027254 0.00109881 -0.00015639 0.00108982 -0.00016538 0.00125520 0.00000000 0.00096232 -0.00029288 vdw (SR) 0.00000000 -3.97414408 -3.97414408 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 26.68793688 26.68793688 vdw total 26.68806240 26.68796842 -0.00009398 26.68796826 -0.00009414 26.68813037 0.00006797 26.68806240 0.00000000 26.68793688 -0.00012552 vdw-14 30.66202560 30.66211250 0.00008690 0.00000000 -30.66202560 30.66227848 0.00025288 30.66202560 0.00000000 0.00000000 -30.66202560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.14850800 1.14833575 -0.00017225 1.14833574 -0.00017226 1.14803763 -0.00047037 1.14850800 0.00000000 1.14834064 -0.00016736 bond 4.70951040 4.70941887 -0.00009153 4.70941877 -0.00009163 4.70909175 -0.00041865 4.70951040 0.00000000 4.70942672 -0.00008368 bonded 5.85927360 5.85885345 -0.00042015 5.85885332 -0.00042028 5.85821919 -0.00105441 5.85927360 0.00000000 5.85885520 -0.00041840 dihedral 0.00125520 0.00109883 -0.00015637 0.00109881 -0.00015639 0.00108982 -0.00016538 0.00125520 0.00000000 0.00108784 -0.00016736 nonbonded -48.98669040 -48.98922029 -0.00252989 -48.98921754 -0.00252714 -48.98962822 -0.00293782 -48.98669040 0.00000000 -48.96175376 0.02493664 potential -43.12741680 -43.13036684 -0.00295004 -43.13036652 -0.00294972 -43.13148783 -0.00407103 -43.12741680 0.00000000 -43.10289856 0.02451824 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -43.12741680 Difference in potential energy from amber=>gromacs conversion: -0.00295004 Difference in potential energy from amber=>lammps conversion: -0.00294972 Difference in potential energy from amber=>desmond conversion: -0.00407103 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.02451824 ======================================================================= INFO 2017-03-18 23:07:21 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3663158.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3663158.inpcrd') INFO 2017-03-18 23:07:21 Beginning InterMol conversion INFO 2017-03-18 23:07:21 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:07:21 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:07:21 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3682850.inpcrd INFO 2017-03-18 23:07:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3682850/mobley_3682850_converted.input INFO 2017-03-18 23:07:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3682850/mobley_3682850_converted.cms WARNING 2017-03-18 23:07:37 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:07:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3682850/mobley_3682850_converted.inp INFO 2017-03-18 23:07:37 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3682850/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3682850/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3682850/mobley_3682850_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3682850/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -5.98337066 -5.98337066 0.00000000 0.00000000 0.00000000 0.00000000 -35.60676048 -35.60676048 coulomb total -35.58324640 -35.58166790 0.00157850 -35.58166736 0.00157904 -35.58161267 0.00163373 -35.60676048 -0.02351408 coulomb-14 -29.59803440 -29.59829725 -0.00026285 0.00000000 29.59803440 -29.59822431 -0.00018991 0.00000000 29.59803440 improper 0.00000000 0.08788701 0.08788701 0.00000000 0.00000000 0.00000000 0.00000000 0.08790584 0.08790584 proper 23.72076960 23.63305925 -0.08771035 23.72094491 0.00017531 23.72089575 0.00012615 23.63315664 -0.08761296 vdw (SR) 0.00000000 -2.76904034 -2.76904034 0.00000000 0.00000000 0.00000000 0.00000000 9.41416736 9.41416736 vdw total 9.41441840 9.41411185 -0.00030655 9.41411213 -0.00030627 9.41414616 -0.00027224 9.41416736 -0.00025104 vdw-14 12.18338960 12.18315219 -0.00023741 0.00000000 -12.18338960 12.18318224 -0.00020736 0.00000000 -12.18338960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.54138560 1.54130630 -0.00007930 1.54130631 -0.00007929 1.54120947 -0.00017613 1.54121824 -0.00016736 bond 1.61711600 1.61731223 0.00019623 1.61731223 0.00019623 1.61757382 0.00045782 1.61732520 0.00020920 bonded 26.87927120 26.87956479 0.00029359 26.87956345 0.00029225 26.87967904 0.00040784 26.87960592 0.00033472 dihedral 23.72076960 23.72094626 0.00017666 23.72094491 0.00017531 23.72089575 0.00012615 23.72106248 0.00029288 nonbonded -26.16882800 -26.16755605 0.00127195 -26.16755523 0.00127277 -26.16746651 0.00136149 -26.19259312 -0.02376512 potential 0.71044320 0.71200873 0.00156553 0.71200814 0.00156494 0.71216255 0.00171935 0.68697096 -0.02347224 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 0.71044320 Difference in potential energy from amber=>gromacs conversion: 0.00156553 Difference in potential energy from amber=>lammps conversion: 0.00156494 Difference in potential energy from amber=>desmond conversion: 0.00171935 Difference in potential energy from amber=>charmm conversion: -0.02347224 ======================================================================= INFO 2017-03-18 23:07:37 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3682850.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3682850.inpcrd') INFO 2017-03-18 23:07:37 Beginning InterMol conversion INFO 2017-03-18 23:07:37 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:07:38 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:07:38 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3686115.inpcrd INFO 2017-03-18 23:07:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3686115/mobley_3686115_converted.input INFO 2017-03-18 23:07:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3686115/mobley_3686115_converted.cms WARNING 2017-03-18 23:07:53 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:07:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3686115/mobley_3686115_converted.inp INFO 2017-03-18 23:07:53 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3686115/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3686115/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3686115/mobley_3686115_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3686115/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 39.91393535 39.91393535 0.00000000 0.00000000 0.00000000 0.00000000 -105.51173544 -105.51173544 coulomb total -105.48533440 -105.48862967 -0.00329527 -105.48862721 -0.00329281 -105.48863340 -0.00329900 -105.51173544 -0.02640104 coulomb-14 -145.39776560 -145.40256502 -0.00479942 0.00000000 145.39776560 -145.40261109 -0.00484549 0.00000000 145.39776560 proper 40.01493920 40.01504778 0.00010858 40.01505844 0.00011924 40.01501819 0.00007899 40.01493920 0.00000000 vdw (SR) 0.00000000 -1.91101078 -1.91101078 0.00000000 0.00000000 0.00000000 0.00000000 5.79170200 5.79170200 vdw total 5.79191120 5.79156691 -0.00034429 5.79156686 -0.00034434 5.79167982 -0.00023138 5.79170200 -0.00020920 vdw-14 7.70274400 7.70257768 -0.00016632 0.00000000 -7.70274400 7.70259405 -0.00014995 0.00000000 -7.70274400 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.94472320 1.94467046 -0.00005274 1.94467048 -0.00005272 1.94451574 -0.00020746 1.94472320 0.00000000 bond 2.27651440 2.27634387 -0.00017053 2.27634386 -0.00017054 2.27598919 -0.00052521 2.27634704 -0.00016736 bonded 44.23617680 44.23606212 -0.00011468 44.23607279 -0.00010401 44.23552312 -0.00065368 44.23600944 -0.00016736 dihedral 40.01493920 40.01504778 0.00010858 40.01505844 0.00011924 40.01501819 0.00007899 40.01493920 0.00000000 nonbonded -99.69342320 -99.69706276 -0.00363956 -99.69706328 -0.00364008 -99.69695358 -0.00353038 -99.72003344 -0.02661024 potential -55.45724640 -55.46100065 -0.00375425 -55.46098690 -0.00374050 -55.46150320 -0.00425680 -55.48398216 -0.02673576 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -55.45724640 Difference in potential energy from amber=>gromacs conversion: -0.00375425 Difference in potential energy from amber=>lammps conversion: -0.00374050 Difference in potential energy from amber=>desmond conversion: -0.00425680 Difference in potential energy from amber=>charmm conversion: -0.02673576 ======================================================================= INFO 2017-03-18 23:07:53 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3686115.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3686115.inpcrd') INFO 2017-03-18 23:07:54 Beginning InterMol conversion INFO 2017-03-18 23:07:54 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:07:54 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:07:54 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3690931.inpcrd INFO 2017-03-18 23:07:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3690931/mobley_3690931_converted.input INFO 2017-03-18 23:07:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3690931/mobley_3690931_converted.cms WARNING 2017-03-18 23:08:09 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:08:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3690931/mobley_3690931_converted.inp INFO 2017-03-18 23:08:09 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3690931/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3690931/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3690931/mobley_3690931_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3690931/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -27.87124914 -27.87124914 0.00000000 0.00000000 0.00000000 0.00000000 -66.39526840 -66.39526840 coulomb total -66.35740320 -66.35940793 -0.00200473 -66.35940734 -0.00200414 -66.35928993 -0.00188673 -66.39526840 -0.03786520 coulomb-14 -38.48694240 -38.48815879 -0.00121639 0.00000000 38.48694240 -38.48812195 -0.00117955 0.00000000 38.48694240 improper 0.00000000 0.00003780 0.00003780 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 13.21014320 13.21024266 0.00009946 13.21028044 0.00013724 13.21028663 0.00014343 13.21026872 0.00012552 vdw (SR) 0.00000000 -3.68736563 -3.68736563 0.00000000 0.00000000 0.00000000 0.00000000 9.90804672 9.90804672 vdw total 9.90813040 9.90791057 -0.00021983 9.90791074 -0.00021966 9.90782949 -0.00030091 9.90804672 -0.00008368 vdw-14 13.59548960 13.59527621 -0.00021339 0.00000000 -13.59548960 13.59521153 -0.00027807 0.00000000 -13.59548960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.50075280 3.50069803 -0.00005477 3.50069803 -0.00005477 3.50090726 0.00015446 3.50071096 -0.00004184 bond 2.60579520 2.60562239 -0.00017281 2.60562240 -0.00017280 2.60480055 -0.00099465 2.60562784 -0.00016736 bonded 19.31669120 19.31660088 -0.00009032 19.31660087 -0.00009033 19.31599443 -0.00069677 19.31664936 -0.00004184 dihedral 13.21014320 13.21028046 0.00013726 13.21028044 0.00013724 13.21028663 0.00014343 13.21031056 0.00016736 nonbonded -56.44927280 -56.45149736 -0.00222456 -56.45149450 -0.00222170 -56.45146044 -0.00218764 -56.48722168 -0.03794888 potential -37.13258160 -37.13489648 -0.00231488 -37.13489535 -0.00231375 -37.13554073 -0.00295913 -37.17057232 -0.03799072 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -37.13258160 Difference in potential energy from amber=>gromacs conversion: -0.00231488 Difference in potential energy from amber=>lammps conversion: -0.00231375 Difference in potential energy from amber=>desmond conversion: -0.00295913 Difference in potential energy from amber=>charmm conversion: -0.03799072 ======================================================================= INFO 2017-03-18 23:08:09 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3690931.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3690931.inpcrd') INFO 2017-03-18 23:08:10 Beginning InterMol conversion INFO 2017-03-18 23:08:10 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:08:10 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:08:10 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3709920.inpcrd INFO 2017-03-18 23:08:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3709920/mobley_3709920_converted.input INFO 2017-03-18 23:08:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3709920/mobley_3709920_converted.cms WARNING 2017-03-18 23:08:26 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:08:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3709920/mobley_3709920_converted.inp INFO 2017-03-18 23:08:26 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3709920/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3709920/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3709920/mobley_3709920_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3709920/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 8.62784004 8.62784004 0.00000000 0.00000000 0.00000000 0.00000000 10.96362808 10.96362808 coulomb total 10.97421360 10.96818119 -0.00603241 10.96818111 -0.00603249 10.96810962 -0.00610398 10.96362808 -0.01058552 coulomb-14 2.34136640 2.34034115 -0.00102525 0.00000000 -2.34136640 2.34031104 -0.00105536 0.00000000 -2.34136640 improper 0.00000000 0.00133480 0.00133480 0.00000000 0.00000000 0.00000000 0.00000000 0.00133888 0.00133888 proper 18.99577840 18.99455741 -0.00122099 18.99589304 0.00011464 18.99591405 0.00013565 18.99456504 -0.00121336 vdw (SR) 0.00000000 -4.00570608 -4.00570608 0.00000000 0.00000000 0.00000000 0.00000000 5.81228728 5.81228728 vdw total 5.81199440 5.81214443 0.00015003 5.81214461 0.00015021 5.81211646 0.00012206 5.81228728 0.00029288 vdw-14 9.81775600 9.81785050 0.00009450 0.00000000 -9.81775600 9.81779449 0.00003849 0.00000000 -9.81775600 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.98646720 5.98633798 -0.00012922 5.98633791 -0.00012929 5.98616014 -0.00030706 5.98625800 -0.00020920 bond 1.40289520 1.40300564 0.00011044 1.40300562 0.00011042 1.40265231 -0.00024289 1.40302072 0.00012552 bonded 26.38514080 26.38523583 0.00009503 26.38523657 0.00009577 26.38472649 -0.00041431 26.38518264 0.00004184 dihedral 18.99577840 18.99589221 0.00011381 18.99589304 0.00011464 18.99591405 0.00013565 18.99590392 0.00012552 nonbonded 16.78620800 16.78032562 -0.00588238 16.78032571 -0.00588229 16.78022608 -0.00598192 16.77591536 -0.01029264 potential 43.17134880 43.16556145 -0.00578735 43.16556233 -0.00578647 43.16485774 -0.00649106 43.16109800 -0.01025080 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 43.17134880 Difference in potential energy from amber=>gromacs conversion: -0.00578735 Difference in potential energy from amber=>lammps conversion: -0.00578647 Difference in potential energy from amber=>desmond conversion: -0.00649106 Difference in potential energy from amber=>charmm conversion: -0.01025080 ======================================================================= INFO 2017-03-18 23:08:26 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3709920.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3709920.inpcrd') INFO 2017-03-18 23:08:26 Beginning InterMol conversion INFO 2017-03-18 23:08:26 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:08:26 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:08:26 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3715043.inpcrd INFO 2017-03-18 23:08:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3715043/mobley_3715043_converted.input INFO 2017-03-18 23:08:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3715043/mobley_3715043_converted.cms WARNING 2017-03-18 23:08:42 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:08:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3715043/mobley_3715043_converted.inp INFO 2017-03-18 23:08:42 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3715043/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3715043/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3715043/mobley_3715043_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3715043/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -17.65230736 -17.65230736 0.00000000 0.00000000 0.00000000 0.00000000 -6.86786864 -6.86786864 coulomb total -6.86385200 -6.86992066 -0.00606866 -6.86992047 -0.00606847 -6.87026570 -0.00641370 -6.86786864 -0.00401664 coulomb-14 10.78049440 10.78238670 0.00189230 0.00000000 -10.78049440 10.78241632 0.00192192 0.00000000 -10.78049440 improper 0.00000000 0.00004581 0.00004581 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00039472 -0.00002368 0.00044050 0.00002210 0.00042844 0.00001004 0.00037656 -0.00004184 vdw (SR) 0.00000000 15.42335660 15.42335660 0.00000000 0.00000000 0.00000000 0.00000000 54.15757048 54.15757048 vdw total 54.15727760 54.15738096 0.00010336 54.15738220 0.00010460 54.15733844 0.00006084 54.15757048 0.00029288 vdw-14 38.73379840 38.73402436 0.00022596 0.00000000 -38.73379840 38.73413617 0.00033777 0.00000000 -38.73379840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.09362560 4.09363558 0.00000998 4.09363556 0.00000996 4.09373318 0.00010758 4.09362560 0.00000000 bond 5.38941040 5.38953357 0.00012317 5.38953341 0.00012301 5.38914790 -0.00026250 5.38953592 0.00012552 bonded 9.48345440 9.48360968 0.00015528 9.48360946 0.00015506 9.48330952 -0.00014488 9.48357992 0.00012552 dihedral 0.00041840 0.00044053 0.00002213 0.00044050 0.00002210 0.00042844 0.00001004 0.00041840 0.00000000 nonbonded 47.29342560 47.28746030 -0.00596530 47.28745922 -0.00596638 47.28707274 -0.00635286 47.28970184 -0.00372376 potential 56.77688000 56.77106998 -0.00581002 56.77106842 -0.00581158 56.77027388 -0.00660612 56.77332360 -0.00355640 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 56.77688000 Difference in potential energy from amber=>gromacs conversion: -0.00581002 Difference in potential energy from amber=>lammps conversion: -0.00581158 Difference in potential energy from amber=>desmond conversion: -0.00660612 Difference in potential energy from amber=>charmm conversion: -0.00355640 ======================================================================= INFO 2017-03-18 23:08:42 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3715043.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3715043.inpcrd') INFO 2017-03-18 23:08:42 Beginning InterMol conversion INFO 2017-03-18 23:08:42 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:08:42 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3727287.inpcrd INFO 2017-03-18 23:08:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3727287/mobley_3727287_converted.input INFO 2017-03-18 23:08:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3727287/mobley_3727287_converted.cms INFO 2017-03-18 23:08:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3727287/mobley_3727287_converted.rst7 WARNING 2017-03-18 23:08:58 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:08:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3727287/mobley_3727287_converted.inp INFO 2017-03-31 06:51:09 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/fixcharmm/amber.out gromacs output energy file: $RUNPATH/FreeSolv/fixcharmm/mobley_3727287/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/fixcharmm/mobley_3727287/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/fixcharmm/mobley_3727287/mobley_3727287_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/fixcharmm/mobley_3727287/amber.out charmm output energy file: $RUNPATH/FreeSolv/fixcharmm/mobley_3727287/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -223.33368931 -223.33368931 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -4.92013296 -4.92013296 coulomb total -5.17309760 -5.17344607 -0.00034847 -5.17344613 -0.00034853 -5.17319802 -0.00010042 -5.17351600 -0.00041840 -4.92013296 0.25296464 coulomb-14 218.15292320 218.16024324 0.00732004 0.00000000 -218.15292320 218.16041591 0.00749271 218.15250480 -0.00041840 0.00000000 -218.15292320 improper 0.00000000 0.00009530 0.00009530 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00041840 0.00047641 0.00005801 0.00057159 0.00015319 0.00055713 0.00013873 0.00041840 0.00000000 0.00046024 0.00004184 vdw (SR) 0.00000000 -1.48483776 -1.48483776 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 9.16082616 9.16082616 vdw total 9.16086800 9.16083040 -0.00003760 9.16083034 -0.00003766 9.16077064 -0.00009736 9.16086800 0.00000000 9.16082616 -0.00004184 vdw-14 10.64576960 10.64566816 -0.00010144 0.00000000 -10.64576960 10.64560496 -0.00016464 10.64576960 0.00000000 0.00000000 -10.64576960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 11.50976560 11.50957578 -0.00018982 11.50957565 -0.00018995 11.51048085 0.00071525 11.50976560 0.00000000 11.50947272 -0.00029288 bond 7.86173600 7.86162067 -0.00011533 7.86162052 -0.00011548 7.86142822 -0.00030778 7.86173600 0.00000000 7.86161048 -0.00012552 bonded 19.37192000 19.37176815 -0.00015185 19.37176776 -0.00015224 19.37246621 0.00054621 19.37192000 0.00000000 19.37162712 -0.00029288 dihedral 0.00041840 0.00057171 0.00015331 0.00057159 0.00015319 0.00055713 0.00013873 0.00041840 0.00000000 0.00054392 0.00012552 nonbonded 3.98777040 3.98738433 -0.00038607 3.98738438 -0.00038602 3.98757262 -0.00019778 3.98735200 -0.00041840 4.24069320 0.25292280 potential 23.35969040 23.35915249 -0.00053791 23.35915234 -0.00053806 23.35999144 0.00030104 23.35927200 -0.00041840 23.61232032 0.25262992 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 23.35969040 Difference in potential energy from amber=>gromacs conversion: -0.00053791 Difference in potential energy from amber=>lammps conversion: -0.00053806 Difference in potential energy from amber=>desmond conversion: 0.00030104 Difference in potential energy from amber=>amber conversion: -0.00041840 Difference in potential energy from amber=>charmm conversion: 0.25262992 ======================================================================= INFO 2017-03-31 06:51:09 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3727287.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3727287.inpcrd') INFO 2017-03-18 23:08:58 Beginning InterMol conversion INFO 2017-03-18 23:08:58 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:08:58 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:08:58 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3738859.inpcrd INFO 2017-03-18 23:08:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3738859/mobley_3738859_converted.input INFO 2017-03-18 23:08:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3738859/mobley_3738859_converted.cms WARNING 2017-03-18 23:09:14 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:09:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3738859/mobley_3738859_converted.inp INFO 2017-03-18 23:09:14 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3738859/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3738859/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3738859/mobley_3738859_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3738859/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 6.47811749 6.47811749 0.00000000 0.00000000 0.00000000 0.00000000 4.21119600 4.21119600 coulomb total 4.22584000 4.21993523 -0.00590477 4.21993512 -0.00590488 4.21990264 -0.00593736 4.21119600 -0.01464400 coulomb-14 -2.25601280 -2.25818226 -0.00216946 0.00000000 2.25601280 -2.25818263 -0.00216983 0.00000000 2.25601280 proper 10.51104480 10.51087702 -0.00016778 10.51087702 -0.00016778 10.51087321 -0.00017159 10.51087744 -0.00016736 vdw (SR) 0.00000000 -1.89523307 -1.89523307 0.00000000 0.00000000 0.00000000 0.00000000 2.37165856 2.37165856 vdw total 2.37149120 2.37159109 0.00009989 2.37159111 0.00009991 2.37158278 0.00009158 2.37165856 0.00016736 vdw-14 4.26684320 4.26682416 -0.00001904 0.00000000 -4.26684320 4.26681872 -0.00002448 0.00000000 -4.26684320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.10073840 4.10059677 -0.00014163 4.10059677 -0.00014163 4.10032089 -0.00041751 4.10065472 -0.00008368 bond 1.12173040 1.12177769 0.00004729 1.12177768 0.00004728 1.12132939 -0.00040101 1.12177224 0.00004184 bonded 15.73351360 15.73325148 -0.00026212 15.73325147 -0.00026213 15.73252349 -0.00099011 15.73330440 -0.00020920 dihedral 10.51104480 10.51087702 -0.00016778 10.51087702 -0.00016778 10.51087321 -0.00017159 10.51087744 -0.00016736 nonbonded 6.59733120 6.59152631 -0.00580489 6.59152632 -0.00580488 6.59148543 -0.00584577 6.58285456 -0.01447664 potential 22.33084480 22.32477780 -0.00606700 22.32477758 -0.00606722 22.32395417 -0.00689063 22.31620080 -0.01464400 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 22.33084480 Difference in potential energy from amber=>gromacs conversion: -0.00606700 Difference in potential energy from amber=>lammps conversion: -0.00606722 Difference in potential energy from amber=>desmond conversion: -0.00689063 Difference in potential energy from amber=>charmm conversion: -0.01464400 ======================================================================= INFO 2017-03-18 23:09:14 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3738859.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3738859.inpcrd') INFO 2017-03-18 23:09:14 Beginning InterMol conversion INFO 2017-03-18 23:09:14 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:09:14 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:09:14 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3746675.inpcrd INFO 2017-03-18 23:09:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3746675/mobley_3746675_converted.input INFO 2017-03-18 23:09:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3746675/mobley_3746675_converted.cms WARNING 2017-03-18 23:09:30 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:09:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3746675/mobley_3746675_converted.inp INFO 2017-03-18 23:09:30 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3746675/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3746675/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3746675/mobley_3746675_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3746675/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -12.80525379 -12.80525379 0.00000000 0.00000000 0.00000000 0.00000000 -16.98302336 -16.98302336 coulomb total -16.99582640 -16.98332142 0.01250498 -16.98332126 0.01250514 -16.98329721 0.01252919 -16.98302336 0.01280304 coulomb-14 -4.17521360 -4.17806763 -0.00285403 0.00000000 4.17521360 -4.17803170 -0.00281810 0.00000000 4.17521360 improper 0.00000000 0.00174110 0.00174110 0.00000000 0.00000000 0.00000000 0.00000000 0.00175728 0.00175728 proper 55.78610880 55.78433195 -0.00177685 55.78608370 -0.00002510 55.78618453 0.00007573 55.78435152 -0.00175728 vdw (SR) 0.00000000 -3.68811896 -3.68811896 0.00000000 0.00000000 0.00000000 0.00000000 16.55299184 16.55299184 vdw total 16.55274080 16.55300651 0.00026571 16.55300648 0.00026568 16.55304399 0.00030319 16.55299184 0.00025104 vdw-14 20.24093680 20.24112547 0.00018867 0.00000000 -20.24093680 20.24116742 0.00023062 0.00000000 -20.24093680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.51785920 5.51800225 0.00014305 5.51800229 0.00014309 5.51811112 0.00025192 5.51794288 0.00008368 bond 1.39954800 1.39959781 0.00004981 1.39959779 0.00004979 1.39977099 0.00022299 1.39958984 0.00004184 bonded 62.70351600 62.70367311 0.00015711 62.70368378 0.00016778 62.70406664 0.00055064 62.70364152 0.00012552 dihedral 55.78610880 55.78607305 -0.00003575 55.78608370 -0.00002510 55.78618453 0.00007573 55.78610880 0.00000000 nonbonded -0.44308560 -0.43031491 0.01277069 -0.43031469 0.01277091 -0.43025322 0.01283238 -0.43003152 0.01305408 potential 62.26043040 62.27335820 0.01292780 62.27337151 0.01294111 62.27375267 0.01332227 62.27361000 0.01317960 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 62.26043040 Difference in potential energy from amber=>gromacs conversion: 0.01292780 Difference in potential energy from amber=>lammps conversion: 0.01294111 Difference in potential energy from amber=>desmond conversion: 0.01332227 Difference in potential energy from amber=>charmm conversion: 0.01317960 ======================================================================= INFO 2017-03-18 23:09:30 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3746675.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3746675.inpcrd') INFO 2017-03-18 23:09:30 Beginning InterMol conversion INFO 2017-03-18 23:09:30 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:09:30 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:09:30 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3761215.inpcrd INFO 2017-03-18 23:09:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3761215/mobley_3761215_converted.input INFO 2017-03-18 23:09:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3761215/mobley_3761215_converted.cms WARNING 2017-03-18 23:09:46 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:09:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3761215/mobley_3761215_converted.inp INFO 2017-03-18 23:09:46 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3761215/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3761215/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3761215/mobley_3761215_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3761215/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -29.98266952 -29.98266952 coulomb total -29.92229440 -29.92528225 -0.00298785 -29.92528178 -0.00298738 -29.92529726 -0.00300286 -29.98266952 -0.06037512 coulomb-14 -29.92229440 -29.92528225 -0.00298785 0.00000000 29.92229440 -29.92529726 -0.00300286 0.00000000 29.92229440 proper 9.41400000 9.41399959 -0.00000041 9.41399958 -0.00000042 9.41399992 -0.00000008 9.41400000 0.00000000 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.01675384 1.01675384 vdw total 1.01671200 1.01673044 0.00001844 1.01673045 0.00001845 1.01674509 0.00003309 1.01675384 0.00004184 vdw-14 1.01671200 1.01673044 0.00001844 0.00000000 -1.01671200 1.01674509 0.00003309 0.00000000 -1.01671200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.25980240 1.25978888 -0.00001352 1.25978889 -0.00001351 1.25971229 -0.00009011 1.25976056 -0.00004184 bond 0.28953280 0.28933443 -0.00019837 0.28933443 -0.00019837 0.28916544 -0.00036736 0.28932360 -0.00020920 bonded 10.96333520 10.96312290 -0.00021230 10.96312290 -0.00021230 10.96287764 -0.00045756 10.96308416 -0.00025104 dihedral 9.41400000 9.41399959 -0.00000041 9.41399958 -0.00000042 9.41399992 -0.00000008 9.41400000 0.00000000 nonbonded -28.90558240 -28.90855181 -0.00296941 -28.90855137 -0.00296897 -28.90855217 -0.00296977 -28.96591568 -0.06033328 potential -17.94224720 -17.94542891 -0.00318171 -17.94542871 -0.00318151 -17.94571072 -0.00346352 -18.00283152 -0.06058432 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -17.94224720 Difference in potential energy from amber=>gromacs conversion: -0.00318171 Difference in potential energy from amber=>lammps conversion: -0.00318151 Difference in potential energy from amber=>desmond conversion: -0.00346352 Difference in potential energy from amber=>charmm conversion: -0.06058432 ======================================================================= INFO 2017-03-18 23:09:46 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3761215.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3761215.inpcrd') INFO 2017-03-18 23:09:46 Beginning InterMol conversion INFO 2017-03-18 23:09:46 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:09:46 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:09:46 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3775790.inpcrd INFO 2017-03-18 23:09:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3775790/mobley_3775790_converted.input INFO 2017-03-18 23:09:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3775790/mobley_3775790_converted.cms WARNING 2017-03-18 23:10:02 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:10:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3775790/mobley_3775790_converted.inp INFO 2017-03-18 23:10:02 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3775790/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3775790/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3775790/mobley_3775790_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3775790/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 40.10953106 40.10953106 0.00000000 0.00000000 0.00000000 0.00000000 -13.85406080 -13.85406080 coulomb total -13.86242880 -13.86292712 -0.00049832 -13.86292711 -0.00049831 -13.86301657 -0.00058777 -13.85406080 0.00836800 coulomb-14 -53.97067120 -53.97245818 -0.00178698 0.00000000 53.97067120 -53.97248873 -0.00181753 0.00000000 53.97067120 improper 0.00000000 0.00005178 0.00005178 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00046658 0.00004818 0.00051848 0.00010008 0.00051373 0.00009533 0.00046024 0.00004184 vdw (SR) 0.00000000 -0.76621961 -0.76621961 0.00000000 0.00000000 0.00000000 0.00000000 -0.71182392 -0.71182392 vdw total -0.71169840 -0.71181921 -0.00012081 -0.71181919 -0.00012079 -0.71182263 -0.00012423 -0.71182392 -0.00012552 vdw-14 0.05439200 0.05440041 0.00000841 0.00000000 -0.05439200 0.05440156 0.00000956 0.00000000 -0.05439200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 14.96323920 14.96328888 0.00004968 14.96328899 0.00004979 14.96344873 0.00020953 14.96328104 0.00004184 bond 0.65981680 0.65983234 0.00001554 0.65983232 0.00001552 0.65960385 -0.00021295 0.65981680 0.00000000 bonded 15.62347440 15.62363958 0.00016518 15.62363979 0.00016539 15.62356632 0.00009192 15.62359992 0.00012552 dihedral 0.00041840 0.00051836 0.00009996 0.00051848 0.00010008 0.00051373 0.00009533 0.00050208 0.00008368 nonbonded -14.57412720 -14.57474633 -0.00061913 -14.57474601 -0.00061881 -14.57483920 -0.00071200 -14.56588472 0.00824248 potential 1.04934720 1.04889325 -0.00045395 1.04889353 -0.00045367 1.04869781 -0.00064939 1.05775704 0.00840984 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 1.04934720 Difference in potential energy from amber=>gromacs conversion: -0.00045395 Difference in potential energy from amber=>lammps conversion: -0.00045367 Difference in potential energy from amber=>desmond conversion: -0.00064939 Difference in potential energy from amber=>charmm conversion: 0.00840984 ======================================================================= INFO 2017-03-18 23:10:02 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3775790.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3775790.inpcrd') INFO 2017-03-18 23:10:02 Beginning InterMol conversion INFO 2017-03-18 23:10:02 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:10:02 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3777264.inpcrd INFO 2017-03-18 23:10:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3777264/mobley_3777264_converted.input INFO 2017-03-18 23:10:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3777264/mobley_3777264_converted.cms INFO 2017-03-18 23:10:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3777264/mobley_3777264_converted.rst7 WARNING 2017-03-18 23:10:18 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:10:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3777264/mobley_3777264_converted.inp INFO 2017-03-18 23:10:18 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3777264/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3777264/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3777264/mobley_3777264_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_3777264/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3777264/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.35829136 0.35829136 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -71.11959016 -71.11959016 coulomb total -71.09787520 -71.08495235 0.01292285 -71.08495082 0.01292438 -71.08520074 0.01267446 -71.09787520 0.00000000 -71.11959016 -0.02171496 coulomb-14 -71.43552400 -71.44324371 -0.00771971 0.00000000 71.43552400 -71.44319411 -0.00767011 -71.43552400 0.00000000 0.00000000 71.43552400 improper 0.00000000 0.11500862 0.11500862 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.11501816 0.11501816 proper 0.22091520 0.10578069 -0.11513451 0.22078788 -0.00012732 0.22076781 -0.00014739 0.22091520 0.00000000 0.10577152 -0.11514368 vdw (SR) 0.00000000 1.55834257 1.55834257 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 26.10230240 26.10230240 vdw total 26.10230240 26.10224887 -0.00005353 26.10224884 -0.00005356 26.10219201 -0.00011039 26.10230240 0.00000000 26.10230240 -0.00000000 vdw-14 24.54376240 24.54390630 0.00014390 0.00000000 -24.54376240 24.54387323 0.00011083 24.54376240 0.00000000 0.00000000 -24.54376240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.51746480 4.51762099 0.00015619 4.51762086 0.00015606 4.51758183 0.00011703 4.51746480 0.00000000 4.51767400 0.00020920 bond 16.61257200 16.61245388 -0.00011812 16.61245401 -0.00011799 16.61068853 -0.00188347 16.61257200 0.00000000 16.61244648 -0.00012552 bonded 21.35095200 21.35086419 -0.00008781 21.35086275 -0.00008925 21.34903817 -0.00191383 21.35095200 0.00000000 21.35091016 -0.00004184 dihedral 0.22091520 0.22078932 -0.00012588 0.22078788 -0.00012732 0.22076781 -0.00014739 0.22091520 0.00000000 0.22078968 -0.00012552 nonbonded -44.99557280 -44.98270348 0.01286932 -44.98270282 0.01286998 -44.98300874 0.01256406 -44.99557280 0.00000000 -45.01728776 -0.02171496 potential -23.64462080 -23.63183929 0.01278151 -23.63183994 0.01278086 -23.63403733 0.01058347 -23.64462080 0.00000000 -23.66633576 -0.02171496 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -23.64462080 Difference in potential energy from amber=>gromacs conversion: 0.01278151 Difference in potential energy from amber=>lammps conversion: 0.01278086 Difference in potential energy from amber=>desmond conversion: 0.01058347 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.02171496 ======================================================================= INFO 2017-03-18 23:10:18 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3777264.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3777264.inpcrd') INFO 2017-03-18 23:10:19 Beginning InterMol conversion INFO 2017-03-18 23:10:19 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:10:19 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:10:19 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3802803.inpcrd INFO 2017-03-18 23:10:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3802803/mobley_3802803_converted.input INFO 2017-03-18 23:10:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3802803/mobley_3802803_converted.cms WARNING 2017-03-18 23:10:34 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:10:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3802803/mobley_3802803_converted.inp INFO 2017-03-18 23:10:34 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3802803/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3802803/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3802803/mobley_3802803_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3802803/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -4.11674326 -4.11674326 0.00000000 0.00000000 0.00000000 0.00000000 -16.92469840 -16.92469840 coulomb total -16.90252320 -16.91571341 -0.01319021 -16.91571326 -0.01319006 -16.91563350 -0.01311030 -16.92469840 -0.02217520 coulomb-14 -12.79132480 -12.79897015 -0.00764535 0.00000000 12.79132480 -12.79887341 -0.00754861 0.00000000 12.79132480 proper 8.39184880 8.39203470 0.00018590 8.39203457 0.00018577 8.39201043 0.00016163 8.39205800 0.00020920 vdw (SR) 0.00000000 -2.42038262 -2.42038262 0.00000000 0.00000000 0.00000000 0.00000000 15.89982760 15.89982760 vdw total 15.89961840 15.89963889 0.00002049 15.89963932 0.00002092 15.89954029 -0.00007811 15.89982760 0.00020920 vdw-14 18.32006240 18.32002151 -0.00004089 0.00000000 -18.32006240 18.31990374 -0.00015866 0.00000000 -18.32006240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 6.40988800 6.41003109 0.00014309 6.41003109 0.00014309 6.40960872 -0.00027928 6.41005536 0.00016736 bond 2.38236960 2.38250688 0.00013728 2.38250688 0.00013728 2.38312455 0.00075495 2.38249512 0.00012552 bonded 17.18410640 17.18457267 0.00046627 17.18457254 0.00046614 17.18474370 0.00063730 17.18460848 0.00050208 dihedral 8.39184880 8.39203470 0.00018590 8.39203457 0.00018577 8.39201043 0.00016163 8.39205800 0.00020920 nonbonded -1.00290480 -1.01607452 -0.01316972 -1.01607407 -0.01316927 -1.01609320 -0.01318840 -1.02487080 -0.02196600 potential 16.18120160 16.16849814 -0.01270346 16.16849856 -0.01270304 16.16855107 -0.01265053 16.15973768 -0.02146392 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 16.18120160 Difference in potential energy from amber=>gromacs conversion: -0.01270346 Difference in potential energy from amber=>lammps conversion: -0.01270304 Difference in potential energy from amber=>desmond conversion: -0.01265053 Difference in potential energy from amber=>charmm conversion: -0.02146392 ======================================================================= INFO 2017-03-18 23:10:34 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3802803.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3802803.inpcrd') INFO 2017-03-18 23:10:35 Beginning InterMol conversion INFO 2017-03-18 23:10:35 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:10:35 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3843583.inpcrd INFO 2017-03-18 23:10:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3843583/mobley_3843583_converted.input INFO 2017-03-18 23:10:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3843583/mobley_3843583_converted.cms INFO 2017-03-18 23:10:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3843583/mobley_3843583_converted.rst7 WARNING 2017-03-18 23:10:50 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:10:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3843583/mobley_3843583_converted.inp INFO 2017-03-18 23:10:51 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3843583/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3843583/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3843583/mobley_3843583_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_3843583/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3843583/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -2.94606068 -2.94606068 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -77.60684032 -77.60684032 coulomb total -77.70399280 -77.68973510 0.01425770 -77.68973373 0.01425907 -77.68966842 0.01432438 -77.70399280 0.00000000 -77.60684032 0.09715248 coulomb-14 -74.73586320 -74.74367443 -0.00781123 0.00000000 74.73586320 -74.74358226 -0.00771906 -74.73586320 0.00000000 0.00000000 74.73586320 improper 0.00000000 0.11625516 0.11625516 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.11627336 0.11627336 proper 0.22175200 0.10556769 -0.11618431 0.22182133 0.00006933 0.22181873 0.00006673 0.22175200 0.00000000 0.10556232 -0.11618968 vdw (SR) 0.00000000 -2.57958019 -2.57958019 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 30.58319904 30.58319904 vdw total 30.58336640 30.58326619 -0.00010021 30.58326640 -0.00010000 30.58348135 0.00011495 30.58336640 0.00000000 30.58319904 -0.00016736 vdw-14 33.16280240 33.16284639 0.00004399 0.00000000 -33.16280240 33.16305620 0.00025380 33.16280240 0.00000000 0.00000000 -33.16280240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.62204080 5.62185143 -0.00018937 5.62185126 -0.00018954 5.62130262 -0.00073818 5.62204080 0.00000000 5.62191528 -0.00012552 bond 10.65581120 10.65587303 0.00006183 10.65587312 0.00006192 10.65411342 -0.00169778 10.65581120 0.00000000 10.65585304 0.00004184 bonded 16.49960400 16.49954732 -0.00005668 16.49954572 -0.00005828 16.49723476 -0.00236924 16.49960400 0.00000000 16.49960400 0.00000000 dihedral 0.22175200 0.22182285 0.00007085 0.22182133 0.00006933 0.22181873 0.00006673 0.22175200 0.00000000 0.22183568 0.00008368 nonbonded -47.12062640 -47.10646891 0.01415749 -47.10646774 0.01415866 -47.10618707 0.01443933 -47.12062640 0.00000000 -47.02364128 0.09698512 potential -30.62102240 -30.60692159 0.01410081 -30.60692232 0.01410008 -30.60903972 0.01198268 -30.62102240 0.00000000 -30.52399544 0.09702696 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -30.62102240 Difference in potential energy from amber=>gromacs conversion: 0.01410081 Difference in potential energy from amber=>lammps conversion: 0.01410008 Difference in potential energy from amber=>desmond conversion: 0.01198268 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.09702696 ======================================================================= INFO 2017-03-18 23:10:51 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3843583.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3843583.inpcrd') INFO 2017-03-18 23:10:51 Beginning InterMol conversion INFO 2017-03-18 23:10:51 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:10:51 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:10:51 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3867265.inpcrd INFO 2017-03-18 23:10:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3867265/mobley_3867265_converted.input INFO 2017-03-18 23:10:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3867265/mobley_3867265_converted.cms WARNING 2017-03-18 23:11:07 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:11:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3867265/mobley_3867265_converted.inp INFO 2017-03-18 23:11:07 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3867265/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3867265/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3867265/mobley_3867265_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3867265/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 14.78697166 14.78697166 0.00000000 0.00000000 0.00000000 0.00000000 -96.20551528 -96.20551528 coulomb total -96.19559920 -96.21859279 -0.02299359 -96.21859028 -0.02299108 -96.21854823 -0.02294903 -96.20551528 -0.00991608 coulomb-14 -110.97265040 -111.00556446 -0.03291406 0.00000000 110.97265040 -111.00548894 -0.03283854 0.00000000 110.97265040 improper 0.00000000 0.00002594 0.00002594 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 22.11034800 22.11050858 0.00016058 22.11053461 0.00018661 22.11052369 0.00017569 22.11051536 0.00016736 vdw (SR) 0.00000000 0.82989440 0.82989440 0.00000000 0.00000000 0.00000000 0.00000000 3.29745224 3.29745224 vdw total 3.29782880 3.29738636 -0.00044244 3.29738638 -0.00044242 3.29729352 -0.00053528 3.29745224 -0.00037656 vdw-14 2.46772320 2.46749196 -0.00023124 0.00000000 -2.46772320 2.46744134 -0.00028186 0.00000000 -2.46772320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.82090080 0.82077143 -0.00012937 0.82077143 -0.00012937 0.82088324 -0.00001756 0.82077528 -0.00012552 bond 0.72257680 0.72253136 -0.00004544 0.72253136 -0.00004544 0.72321341 0.00063661 0.72253496 -0.00004184 bonded 23.65382560 23.65383731 0.00001171 23.65383740 0.00001180 23.65462034 0.00079474 23.65386744 0.00004184 dihedral 22.11034800 22.11053452 0.00018652 22.11053461 0.00018661 22.11052369 0.00017569 22.11055720 0.00020920 nonbonded -92.89777040 -92.92120643 -0.02343603 -92.92120498 -0.02343458 -92.92125471 -0.02348431 -92.90806304 -0.01029264 potential -69.24394480 -69.26736912 -0.02342432 -69.26736683 -0.02342203 -69.26664802 -0.02270322 -69.25423744 -0.01029264 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -69.24394480 Difference in potential energy from amber=>gromacs conversion: -0.02342432 Difference in potential energy from amber=>lammps conversion: -0.02342203 Difference in potential energy from amber=>desmond conversion: -0.02270322 Difference in potential energy from amber=>charmm conversion: -0.01029264 ======================================================================= INFO 2017-03-18 23:11:07 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3867265.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3867265.inpcrd') INFO 2017-03-18 23:11:07 Beginning InterMol conversion INFO 2017-03-18 23:11:07 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:11:07 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:11:07 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3968043.inpcrd INFO 2017-03-18 23:11:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3968043/mobley_3968043_converted.input INFO 2017-03-18 23:11:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3968043/mobley_3968043_converted.cms WARNING 2017-03-18 23:11:23 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:11:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3968043/mobley_3968043_converted.inp INFO 2017-03-18 23:11:23 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3968043/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3968043/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3968043/mobley_3968043_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3968043/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -15.28829580 -15.28829580 0.00000000 0.00000000 0.00000000 0.00000000 -36.95162360 -36.95162360 coulomb total -36.95476160 -36.95621591 -0.00145431 -36.95621554 -0.00145394 -36.95619194 -0.00143034 -36.95162360 0.00313800 coulomb-14 -21.66768080 -21.66792011 -0.00023931 0.00000000 21.66768080 -21.66789715 -0.00021635 0.00000000 21.66768080 improper 0.00000000 0.00000337 0.00000337 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 34.70460640 34.70444846 -0.00015794 34.70445285 -0.00015355 34.70446440 -0.00014200 34.70544320 0.00083680 vdw (SR) 0.00000000 -0.68477681 -0.68477681 0.00000000 0.00000000 0.00000000 0.00000000 0.62237000 0.62237000 vdw total 0.62216080 0.62230957 0.00014877 0.62230958 0.00014878 0.62229825 0.00013745 0.62237000 0.00020920 vdw-14 1.30708160 1.30708639 0.00000479 0.00000000 -1.30708160 1.30707478 -0.00000682 0.00000000 -1.30708160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 22.82581200 22.82599745 0.00018545 22.82599735 0.00018535 22.82585656 0.00004456 22.82585384 0.00004184 bond 0.92801120 0.92793231 -0.00007889 0.92793229 -0.00007891 0.92805507 0.00004387 0.92792752 -0.00008368 bonded 58.45842960 58.45838159 -0.00004801 58.45838249 -0.00004711 58.45837602 -0.00005358 58.45922456 0.00079496 dihedral 34.70460640 34.70445183 -0.00015457 34.70445285 -0.00015355 34.70446440 -0.00014200 34.70544320 0.00083680 nonbonded -36.33260080 -36.33390634 -0.00130554 -36.33390579 -0.00130499 -36.33389369 -0.00129289 -36.32925360 0.00334720 potential 22.12582880 22.12447525 -0.00135355 22.12447653 -0.00135227 22.12444929 -0.00137951 22.12992912 0.00410032 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 22.12582880 Difference in potential energy from amber=>gromacs conversion: -0.00135355 Difference in potential energy from amber=>lammps conversion: -0.00135227 Difference in potential energy from amber=>desmond conversion: -0.00137951 Difference in potential energy from amber=>charmm conversion: 0.00410032 ======================================================================= INFO 2017-03-18 23:11:23 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3968043.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3968043.inpcrd') INFO 2017-03-18 23:11:23 Beginning InterMol conversion INFO 2017-03-18 23:11:23 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:11:23 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:11:23 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3968739.inpcrd INFO 2017-03-18 23:11:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3968739/mobley_3968739_converted.input INFO 2017-03-18 23:11:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3968739/mobley_3968739_converted.cms WARNING 2017-03-18 23:11:39 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:11:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3968739/mobley_3968739_converted.inp INFO 2017-03-18 23:11:39 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3968739/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3968739/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3968739/mobley_3968739_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3968739/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -88.14727940 -88.14727940 0.00000000 0.00000000 0.00000000 0.00000000 -0.90537576 -0.90537576 coulomb total -0.90750960 -0.90155855 0.00595105 -0.90155853 0.00595107 -0.90118716 0.00632244 -0.90537576 0.00213384 coulomb-14 87.22886880 87.24572085 0.01685205 0.00000000 -87.22886880 87.24581484 0.01694604 0.00000000 -87.22886880 improper 0.00000000 0.00004997 0.00004997 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 8.38306240 8.38306523 0.00000283 8.38309504 0.00003264 8.38322127 0.00015887 8.38306240 0.00000000 vdw (SR) 0.00000000 -0.97900797 -0.97900797 0.00000000 0.00000000 0.00000000 0.00000000 27.08868040 27.08868040 vdw total 27.08847120 27.08857700 0.00010580 27.08857706 0.00010586 27.08855383 0.00008263 27.08868040 0.00020920 vdw-14 28.06752720 28.06758497 0.00005777 0.00000000 -28.06752720 28.06753753 0.00001033 0.00000000 -28.06752720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.45180000 3.45176211 -0.00003789 3.45176209 -0.00003791 3.45165382 -0.00014618 3.45175816 -0.00004184 bond 2.79114640 2.79132628 0.00017988 2.79132627 0.00017987 2.79154240 0.00039600 2.79131376 0.00016736 bonded 14.62600880 14.62620359 0.00019479 14.62618340 0.00017460 14.62641749 0.00040869 14.62617616 0.00016736 dihedral 8.38306240 8.38311520 0.00005280 8.38309504 0.00003264 8.38322127 0.00015887 8.38310424 0.00004184 nonbonded 26.18096160 26.18701846 0.00605686 26.18701836 0.00605676 26.18736667 0.00640507 26.18330464 0.00234304 potential 40.80697040 40.81322204 0.00625164 40.81320205 0.00623165 40.81371856 0.00674816 40.80948080 0.00251040 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 40.80697040 Difference in potential energy from amber=>gromacs conversion: 0.00625164 Difference in potential energy from amber=>lammps conversion: 0.00623165 Difference in potential energy from amber=>desmond conversion: 0.00674816 Difference in potential energy from amber=>charmm conversion: 0.00251040 ======================================================================= INFO 2017-03-18 23:11:39 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3968739.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3968739.inpcrd') INFO 2017-03-18 23:11:39 Beginning InterMol conversion INFO 2017-03-18 23:11:39 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:11:39 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3969312.inpcrd INFO 2017-03-18 23:11:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3969312/mobley_3969312_converted.input INFO 2017-03-18 23:11:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3969312/mobley_3969312_converted.cms INFO 2017-03-18 23:11:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3969312/mobley_3969312_converted.rst7 WARNING 2017-03-18 23:11:55 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:11:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3969312/mobley_3969312_converted.inp INFO 2017-03-18 23:11:55 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3969312/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3969312/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3969312/mobley_3969312_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_3969312/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3969312/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -7.85170063 -7.85170063 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 38.96061304 38.96061304 coulomb total 38.95680560 38.95782264 0.00101704 38.95782231 0.00101671 38.95808503 0.00127943 38.95680560 0.00000000 38.96061304 0.00380744 coulomb-14 46.80808160 46.80952327 0.00144167 0.00000000 -46.80808160 46.80950458 0.00142298 46.80808160 0.00000000 0.00000000 -46.80808160 improper 0.00000000 0.00002039 0.00002039 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00000000 0.00012330 0.00012330 0.00014362 0.00014362 0.00014564 0.00014564 0.00000000 0.00000000 0.00012552 0.00012552 vdw (SR) 0.00000000 -0.75586329 -0.75586329 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 17.87957088 17.87957088 vdw total 17.87948720 17.87956908 0.00008188 17.87956921 0.00008201 17.87959028 0.00010308 17.87948720 0.00000000 17.87957088 0.00008368 vdw-14 18.63553600 18.63543236 -0.00010364 0.00000000 -18.63553600 18.63548366 -0.00005234 18.63553600 0.00000000 0.00000000 -18.63553600 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.54852240 0.54850360 -0.00001880 0.54850361 -0.00001879 0.54860007 0.00007767 0.54852240 0.00000000 0.54852240 0.00000000 bond 3.43506400 3.43517971 0.00011571 3.43517969 0.00011569 3.43457863 -0.00048537 3.43506400 0.00000000 3.43518952 0.00012552 bonded 3.98358640 3.98382700 0.00024060 3.98382692 0.00024052 3.98332434 -0.00026206 3.98358640 0.00000000 3.98383744 0.00025104 dihedral 0.00000000 0.00014369 0.00014369 0.00014362 0.00014362 0.00014564 0.00014564 0.00000000 0.00000000 0.00012552 0.00012552 nonbonded 56.83629280 56.83739172 0.00109892 56.83739319 0.00110039 56.83767531 0.00138251 56.83629280 0.00000000 56.84018392 0.00389112 potential 60.81987920 60.82121871 0.00133951 60.82121808 0.00133888 60.82096495 0.00108575 60.81987920 0.00000000 60.82402136 0.00414216 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 60.81987920 Difference in potential energy from amber=>gromacs conversion: 0.00133951 Difference in potential energy from amber=>lammps conversion: 0.00133888 Difference in potential energy from amber=>desmond conversion: 0.00108575 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00414216 ======================================================================= INFO 2017-03-18 23:11:55 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3969312.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3969312.inpcrd') INFO 2017-03-18 23:11:55 Beginning InterMol conversion INFO 2017-03-18 23:11:55 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:11:55 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:11:55 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_397645.inpcrd INFO 2017-03-18 23:11:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_397645/mobley_397645_converted.input INFO 2017-03-18 23:11:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_397645/mobley_397645_converted.cms WARNING 2017-03-18 23:12:11 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:12:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_397645/mobley_397645_converted.inp INFO 2017-03-18 23:12:11 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_397645/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_397645/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_397645/mobley_397645_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_397645/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -50.86395480 -50.86395480 0.00000000 0.00000000 0.00000000 0.00000000 -17.59351080 -17.59351080 coulomb total -17.58702560 -17.58314711 0.00387849 -17.58314703 0.00387857 -17.58276282 0.00426278 -17.59351080 -0.00648520 coulomb-14 33.27074960 33.28080769 0.01005809 0.00000000 -33.27074960 33.28089509 0.01014549 0.00000000 -33.27074960 improper 0.00000000 0.00004997 0.00004997 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 18.24684240 18.24697933 0.00013693 18.24700892 0.00016652 18.24714319 0.00030079 18.24696792 0.00012552 vdw (SR) 0.00000000 -2.34875319 -2.34875319 0.00000000 0.00000000 0.00000000 0.00000000 26.15790776 26.15790776 vdw total 26.15753120 26.15779435 0.00026315 26.15779437 0.00026317 26.15772962 0.00019842 26.15790776 0.00037656 vdw-14 28.50642880 28.50654754 0.00011874 0.00000000 -28.50642880 28.50646579 0.00003699 0.00000000 -28.50642880 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.65556080 3.65557278 0.00001198 3.65557277 0.00001197 3.65560912 0.00004832 3.65556080 0.00000000 bond 3.37941680 3.37927965 -0.00013715 3.37927965 -0.00013715 3.37970936 0.00029256 3.37929128 -0.00012552 bonded 25.28182000 25.28188174 0.00006174 25.28186134 0.00004134 25.28246167 0.00064167 25.28186184 0.00004184 dihedral 18.24684240 18.24702930 0.00018690 18.24700892 0.00016652 18.24714319 0.00030079 18.24700976 0.00016736 nonbonded 8.57050560 8.57464724 0.00414164 8.57464734 0.00414174 8.57496681 0.00446121 8.56439696 -0.00610864 potential 33.85232560 33.85652898 0.00420338 33.85650918 0.00418358 33.85734075 0.00501515 33.84625880 -0.00606680 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 33.85232560 Difference in potential energy from amber=>gromacs conversion: 0.00420338 Difference in potential energy from amber=>lammps conversion: 0.00418358 Difference in potential energy from amber=>desmond conversion: 0.00501515 Difference in potential energy from amber=>charmm conversion: -0.00606680 ======================================================================= INFO 2017-03-18 23:12:11 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_397645.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_397645.inpcrd') INFO 2017-03-18 23:12:11 Beginning InterMol conversion INFO 2017-03-18 23:12:11 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:12:11 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3976574.inpcrd INFO 2017-03-18 23:12:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3976574/mobley_3976574_converted.input INFO 2017-03-18 23:12:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3976574/mobley_3976574_converted.cms INFO 2017-03-18 23:12:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3976574/mobley_3976574_converted.rst7 WARNING 2017-03-18 23:12:27 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:12:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3976574/mobley_3976574_converted.inp INFO 2017-03-18 23:12:27 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3976574/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3976574/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3976574/mobley_3976574_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_3976574/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3976574/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -6.77212352 -6.77212352 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.93834568 -0.93834568 coulomb total -0.93972640 -0.94056034 -0.00083394 -0.94056031 -0.00083391 -0.94054805 -0.00082165 -0.93972640 0.00000000 -0.93834568 0.00138072 coulomb-14 5.83040400 5.83156317 0.00115917 0.00000000 -5.83040400 5.83155845 0.00115445 5.83040400 0.00000000 0.00000000 -5.83040400 improper 0.00000000 0.00009978 0.00009978 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00083680 0.00092710 0.00009030 0.00102685 0.00019005 0.00102348 0.00018668 0.00083680 0.00000000 0.00092048 0.00008368 vdw (SR) 0.00000000 -12.54287877 -12.54287877 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 47.85433264 47.85433264 vdw total 47.85450000 47.85427071 -0.00022929 47.85426988 -0.00023012 47.85430264 -0.00019736 47.85450000 0.00000000 47.85433264 -0.00016736 vdw-14 60.39729520 60.39714948 -0.00014572 0.00000000 -60.39729520 60.39718516 -0.00011004 60.39729520 0.00000000 0.00000000 -60.39729520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 7.73914480 7.73912801 -0.00001679 7.73912806 -0.00001674 7.73990583 0.00076103 7.73914480 0.00000000 7.73914480 0.00000000 bond 2.27316720 2.27300143 -0.00016577 2.27300143 -0.00016577 2.27331303 0.00014583 2.27316720 0.00000000 2.27299984 -0.00016736 bonded 10.01314880 10.01315632 0.00000752 10.01315635 0.00000755 10.01424234 0.00109354 10.01314880 0.00000000 10.01314880 0.00000000 dihedral 0.00083680 0.00102687 0.00019007 0.00102685 0.00019005 0.00102348 0.00018668 0.00083680 0.00000000 0.00100416 0.00016736 nonbonded 46.91477360 46.91371037 -0.00106323 46.91371086 -0.00106274 46.91375459 -0.00101901 46.91477360 0.00000000 46.91598696 0.00121336 potential 56.92792240 56.92686668 -0.00105572 56.92686803 -0.00105437 56.92770651 -0.00021589 56.92792240 0.00000000 56.92917760 0.00125520 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 56.92792240 Difference in potential energy from amber=>gromacs conversion: -0.00105572 Difference in potential energy from amber=>lammps conversion: -0.00105437 Difference in potential energy from amber=>desmond conversion: -0.00021589 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00125520 ======================================================================= INFO 2017-03-18 23:12:27 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3976574.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3976574.inpcrd') INFO 2017-03-18 23:12:27 Beginning InterMol conversion INFO 2017-03-18 23:12:27 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:12:28 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3980099.inpcrd INFO 2017-03-18 23:12:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3980099/mobley_3980099_converted.input INFO 2017-03-18 23:12:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3980099/mobley_3980099_converted.cms INFO 2017-03-18 23:12:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3980099/mobley_3980099_converted.rst7 WARNING 2017-03-18 23:12:43 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:12:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3980099/mobley_3980099_converted.inp INFO 2017-03-18 23:12:43 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3980099/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3980099/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3980099/mobley_3980099_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_3980099/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3980099/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 2.70892625 2.70892625 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 12.95947976 12.95947976 coulomb total 12.95784800 12.95853522 0.00068722 12.95853501 0.00068701 12.95853823 0.00069023 12.95784800 0.00000000 12.95947976 0.00163176 coulomb-14 10.24912640 10.24960896 0.00048256 0.00000000 -10.24912640 10.24960999 0.00048359 10.24912640 0.00000000 0.00000000 -10.24912640 improper 0.00000000 0.00001078 0.00001078 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00000000 0.00010537 0.00010537 0.00011614 0.00011614 0.00011172 0.00011172 0.00000000 0.00000000 0.00012552 0.00012552 vdw (SR) 0.00000000 -2.07197258 -2.07197258 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 17.44594112 17.44594112 vdw total 17.44602480 17.44590840 -0.00011640 17.44590848 -0.00011632 17.44594851 -0.00007629 17.44602480 0.00000000 17.44594112 -0.00008368 vdw-14 19.51794160 19.51788099 -0.00006061 0.00000000 -19.51794160 19.51792114 -0.00002046 19.51794160 0.00000000 0.00000000 -19.51794160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.48027520 2.48028716 0.00001196 2.48028717 0.00001197 2.48049445 0.00021925 2.48027520 0.00000000 2.48031704 0.00004184 bond 0.84474960 0.84460111 -0.00014849 0.84460111 -0.00014849 0.84465833 -0.00009127 0.84474960 0.00000000 0.84458224 -0.00016736 bonded 3.32502480 3.32500442 -0.00002038 3.32500441 -0.00002039 3.32526451 0.00023971 3.32502480 0.00000000 3.32502480 0.00000000 dihedral 0.00000000 0.00011615 0.00011615 0.00011614 0.00011614 0.00011172 0.00011172 0.00000000 0.00000000 0.00012552 0.00012552 nonbonded 30.40387280 30.40444362 0.00057082 30.40444350 0.00057070 30.40448674 0.00061394 30.40387280 0.00000000 30.40542088 0.00154808 potential 33.72889760 33.72944804 0.00055044 33.72944780 0.00055020 33.72967645 0.00077885 33.72889760 0.00000000 33.73044568 0.00154808 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 33.72889760 Difference in potential energy from amber=>gromacs conversion: 0.00055044 Difference in potential energy from amber=>lammps conversion: 0.00055020 Difference in potential energy from amber=>desmond conversion: 0.00077885 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00154808 ======================================================================= INFO 2017-03-18 23:12:43 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3980099.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3980099.inpcrd') INFO 2017-03-18 23:12:44 Beginning InterMol conversion INFO 2017-03-18 23:12:44 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:12:44 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:12:44 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3982371.inpcrd INFO 2017-03-18 23:12:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3982371/mobley_3982371_converted.input INFO 2017-03-18 23:12:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3982371/mobley_3982371_converted.cms WARNING 2017-03-18 23:12:59 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:12:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3982371/mobley_3982371_converted.inp INFO 2017-03-18 23:12:59 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3982371/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3982371/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3982371/mobley_3982371_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3982371/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -25.12350862 -25.12350862 0.00000000 0.00000000 0.00000000 0.00000000 -112.23814304 -112.23814304 coulomb total -112.22157440 -112.23627228 -0.01469788 -112.23627279 -0.01469839 -112.23625832 -0.01468392 -112.23814304 -0.01656864 coulomb-14 -87.10334880 -87.11276366 -0.00941486 0.00000000 87.10334880 -87.11279544 -0.00944664 0.00000000 87.10334880 improper 0.00000000 0.00000919 0.00000919 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 11.01270640 11.01267496 -0.00003144 11.01268255 -0.00002385 11.01263356 -0.00007284 11.01266456 -0.00004184 vdw (SR) 0.00000000 -0.54629430 -0.54629430 0.00000000 0.00000000 0.00000000 0.00000000 7.24447048 7.24447048 vdw total 7.24417760 7.24439268 0.00021508 7.24439266 0.00021506 7.24447329 0.00029569 7.24447048 0.00029288 vdw-14 7.79060800 7.79068698 0.00007898 0.00000000 -7.79060800 7.79077992 0.00017192 0.00000000 -7.79060800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.93217120 1.93212853 -0.00004267 1.93212852 -0.00004268 1.93210370 -0.00006750 1.93217120 0.00000000 bond 1.23511680 1.23501124 -0.00010556 1.23501124 -0.00010556 1.23502815 -0.00008865 1.23499128 -0.00012552 bonded 14.17999440 14.17982392 -0.00017048 14.17982231 -0.00017209 14.17976541 -0.00022899 14.17982704 -0.00016736 dihedral 11.01270640 11.01268416 -0.00002224 11.01268255 -0.00002385 11.01263356 -0.00007284 11.01266456 -0.00004184 nonbonded -104.97739680 -104.99187960 -0.01448280 -104.99187762 -0.01448082 -104.99178503 -0.01438823 -104.99367256 -0.01627576 potential -90.79740240 -90.81205568 -0.01465328 -90.81205477 -0.01465237 -90.81203929 -0.01463689 -90.81384552 -0.01644312 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -90.79740240 Difference in potential energy from amber=>gromacs conversion: -0.01465328 Difference in potential energy from amber=>lammps conversion: -0.01465237 Difference in potential energy from amber=>desmond conversion: -0.01463689 Difference in potential energy from amber=>charmm conversion: -0.01644312 ======================================================================= INFO 2017-03-18 23:12:59 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3982371.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3982371.inpcrd') INFO 2017-03-18 23:13:00 Beginning InterMol conversion INFO 2017-03-18 23:13:00 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:13:00 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:13:00 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3999471.inpcrd INFO 2017-03-18 23:13:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3999471/mobley_3999471_converted.input INFO 2017-03-18 23:13:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3999471/mobley_3999471_converted.cms WARNING 2017-03-18 23:13:15 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:13:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3999471/mobley_3999471_converted.inp INFO 2017-03-18 23:13:15 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3999471/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3999471/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3999471/mobley_3999471_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3999471/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -14.91344960 -14.91344960 coulomb total -14.88834560 -14.88929995 -0.00095435 -14.88929997 -0.00095437 -14.88929415 -0.00094855 -14.91344960 -0.02510400 coulomb-14 -14.88834560 -14.88929995 -0.00095435 0.00000000 14.88834560 -14.88929415 -0.00094855 0.00000000 14.88834560 proper 6.28269440 6.28290257 0.00020817 6.28290276 0.00020836 6.28290251 0.00020811 6.28290360 0.00020920 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.66015152 0.66015152 vdw total 0.66023520 0.66014617 -0.00008903 0.66014616 -0.00008904 0.66013759 -0.00009761 0.66015152 -0.00008368 vdw-14 0.66023520 0.66014617 -0.00008903 0.00000000 -0.66023520 0.66013759 -0.00009761 0.00000000 -0.66023520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.51839760 0.51858035 0.00018275 0.51858036 0.00018276 0.51872258 0.00032498 0.51856496 0.00016736 bond 0.62676320 0.62676401 0.00000081 0.62676399 0.00000079 0.62692145 0.00015825 0.62676320 0.00000000 bonded 7.42785520 7.42824694 0.00039174 7.42824712 0.00039192 7.42854655 0.00069135 7.42823176 0.00037656 dihedral 6.28269440 6.28290257 0.00020817 6.28290276 0.00020836 6.28290251 0.00020811 6.28290360 0.00020920 nonbonded -14.22811040 -14.22915379 -0.00104339 -14.22915347 -0.00104307 -14.22915657 -0.00104617 -14.25329808 -0.02518768 potential -6.80025520 -6.80090685 -0.00065165 -6.80090665 -0.00065145 -6.80063398 -0.00037878 -6.82502448 -0.02476928 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -6.80025520 Difference in potential energy from amber=>gromacs conversion: -0.00065165 Difference in potential energy from amber=>lammps conversion: -0.00065145 Difference in potential energy from amber=>desmond conversion: -0.00037878 Difference in potential energy from amber=>charmm conversion: -0.02476928 ======================================================================= INFO 2017-03-18 23:13:15 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3999471.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3999471.inpcrd') INFO 2017-03-18 23:13:16 Beginning InterMol conversion INFO 2017-03-18 23:13:16 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:13:16 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:13:16 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4013838.inpcrd INFO 2017-03-18 23:13:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4013838/mobley_4013838_converted.input INFO 2017-03-18 23:13:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4013838/mobley_4013838_converted.cms WARNING 2017-03-18 23:13:31 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:13:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4013838/mobley_4013838_converted.inp INFO 2017-03-18 23:13:31 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4013838/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4013838/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4013838/mobley_4013838_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4013838/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -121.76054697 -121.76054697 0.00000000 0.00000000 0.00000000 0.00000000 44.54545808 44.54545808 coulomb total 44.49391120 44.49570788 0.00179668 44.49570614 0.00179494 44.49569024 0.00177904 44.54545808 0.05154688 coulomb-14 166.29140640 166.25625485 -0.03515155 0.00000000 -166.29140640 166.25631477 -0.03509163 0.00000000 -166.29140640 improper 0.00000000 0.00000369 0.00000369 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 1.69242800 1.69241980 -0.00000820 1.69242440 -0.00000360 1.69241580 -0.00001220 1.69242800 0.00000000 vdw (SR) 0.00000000 -3.87523538 -3.87523538 0.00000000 0.00000000 0.00000000 0.00000000 9.06413392 9.06413392 vdw total 9.06421760 9.06398250 -0.00023510 9.06398246 -0.00023514 9.06395756 -0.00026004 9.06413392 -0.00008368 vdw-14 12.93943840 12.93921788 -0.00022052 0.00000000 -12.93943840 12.93919698 -0.00024142 0.00000000 -12.93943840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.57734400 2.57737284 0.00002884 2.57737283 0.00002883 2.57739312 0.00004912 2.57734400 0.00000000 bond 2.57776240 2.57762529 -0.00013711 2.57762529 -0.00013711 2.57721529 -0.00054711 2.57763688 -0.00012552 bonded 6.84753440 6.84742162 -0.00011278 6.84742252 -0.00011188 6.84702420 -0.00051020 6.84740888 -0.00012552 dihedral 1.69242800 1.69242348 -0.00000452 1.69242440 -0.00000360 1.69241580 -0.00001220 1.69242800 0.00000000 nonbonded 53.55812880 53.55969038 0.00156158 53.55968943 0.00156063 53.55964780 0.00151900 53.60959200 0.05146320 potential 60.40566320 60.40711200 0.00144880 60.40711086 0.00144766 60.40660000 0.00093680 60.45695904 0.05129584 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 60.40566320 Difference in potential energy from amber=>gromacs conversion: 0.00144880 Difference in potential energy from amber=>lammps conversion: 0.00144766 Difference in potential energy from amber=>desmond conversion: 0.00093680 Difference in potential energy from amber=>charmm conversion: 0.05129584 ======================================================================= INFO 2017-03-18 23:13:31 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4013838.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4013838.inpcrd') INFO 2017-03-18 23:13:32 Beginning InterMol conversion INFO 2017-03-18 23:13:32 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:13:32 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:13:32 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4035953.inpcrd INFO 2017-03-18 23:13:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4035953/mobley_4035953_converted.input INFO 2017-03-18 23:13:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4035953/mobley_4035953_converted.cms WARNING 2017-03-18 23:13:47 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:13:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4035953/mobley_4035953_converted.inp INFO 2017-03-18 23:13:47 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4035953/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4035953/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4035953/mobley_4035953_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4035953/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -17.17296642 -17.17296642 0.00000000 0.00000000 0.00000000 0.00000000 -53.73352208 -53.73352208 coulomb total -53.73678560 -53.74548380 -0.00869820 -53.74548414 -0.00869854 -53.74608174 -0.00929614 -53.73352208 0.00326352 coulomb-14 -36.57234400 -36.57251738 -0.00017338 0.00000000 36.57234400 -36.57259077 -0.00024677 0.00000000 36.57234400 improper 0.00000000 0.00008581 0.00008581 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00083680 0.00082302 -0.00001378 0.00090875 0.00007195 0.00090577 0.00006897 0.00083680 0.00000000 vdw (SR) 0.00000000 0.12177184 0.12177184 0.00000000 0.00000000 0.00000000 0.00000000 20.25081104 20.25081104 vdw total 20.25056000 20.25076920 0.00020920 20.25076920 0.00020920 20.25090213 0.00034213 20.25081104 0.00025104 vdw-14 20.12880560 20.12899736 0.00019176 0.00000000 -20.12880560 20.12908133 0.00027573 0.00000000 -20.12880560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.51672400 0.51659968 -0.00012432 0.51659969 -0.00012431 0.51655783 -0.00016617 0.51659848 -0.00012552 bond 1.31754160 1.31747034 -0.00007126 1.31747035 -0.00007125 1.31745207 -0.00008953 1.31745792 -0.00008368 bonded 1.83510240 1.83497885 -0.00012355 1.83497879 -0.00012361 1.83491567 -0.00018673 1.83497688 -0.00012552 dihedral 0.00083680 0.00090883 0.00007203 0.00090875 0.00007195 0.00090577 0.00006897 0.00092048 0.00008368 nonbonded -33.48622560 -33.49471460 -0.00848900 -33.49471368 -0.00848808 -33.49517961 -0.00895401 -33.48271104 0.00351456 potential -31.65112320 -31.65973575 -0.00861255 -31.65973513 -0.00861193 -31.66031474 -0.00919154 -31.64769232 0.00343088 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -31.65112320 Difference in potential energy from amber=>gromacs conversion: -0.00861255 Difference in potential energy from amber=>lammps conversion: -0.00861193 Difference in potential energy from amber=>desmond conversion: -0.00919154 Difference in potential energy from amber=>charmm conversion: 0.00343088 ======================================================================= INFO 2017-03-18 23:13:47 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4035953.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4035953.inpcrd') INFO 2017-03-18 23:13:48 Beginning InterMol conversion INFO 2017-03-18 23:13:48 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:13:48 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:13:48 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4039055.inpcrd INFO 2017-03-18 23:13:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4039055/mobley_4039055_converted.input INFO 2017-03-18 23:13:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4039055/mobley_4039055_converted.cms WARNING 2017-03-18 23:14:04 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:14:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4039055/mobley_4039055_converted.inp INFO 2017-03-18 23:14:04 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4039055/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4039055/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4039055/mobley_4039055_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4039055/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 262.18835535 262.18835535 0.00000000 0.00000000 0.00000000 0.00000000 -680.81010368 -680.81010368 coulomb total -680.40375360 -680.42695704 -0.02320344 -680.42693296 -0.02317936 -680.42701371 -0.02326011 -680.81010368 -0.40635008 coulomb-14 -942.58323520 -942.61531239 -0.03207719 0.00000000 942.58323520 -942.61521770 -0.03198250 0.00000000 942.58323520 improper 0.00000000 0.00024782 0.00024782 0.00000000 0.00000000 0.00000000 0.00000000 0.00025104 0.00025104 proper 50.20883680 50.20840406 -0.00043274 50.20865270 -0.00018410 50.20864643 -0.00019037 50.20841840 -0.00041840 vdw (SR) 0.00000000 -2.04092504 -2.04092504 0.00000000 0.00000000 0.00000000 0.00000000 13.97857664 13.97857664 vdw total 13.97832560 13.97861124 0.00028564 13.97861137 0.00028577 13.97862791 0.00030231 13.97857664 0.00025104 vdw-14 16.01928080 16.01953628 0.00025548 0.00000000 -16.01928080 16.01955481 0.00027401 0.00000000 -16.01928080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 12.13443680 12.13429104 -0.00014576 12.13429120 -0.00014560 12.13470131 0.00026451 12.13426944 -0.00016736 bond 18.90624080 18.90626706 0.00002626 18.90626716 0.00002636 18.90734638 0.00110558 18.90628264 0.00004184 bonded 81.24951440 81.24920998 -0.00030442 81.24921106 -0.00030334 81.25069412 0.00117972 81.24922152 -0.00029288 dihedral 50.20883680 50.20865188 -0.00018492 50.20865270 -0.00018410 50.20864643 -0.00019037 50.20866944 -0.00016736 nonbonded -666.42542800 -666.44834580 -0.02291780 -666.44835632 -0.02292832 -666.44838580 -0.02295780 -666.83152704 -0.40609904 potential -585.17591360 -585.19913582 -0.02322222 -585.19913480 -0.02322120 -585.19774990 -0.02183630 -585.58234736 -0.40643376 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -585.17591360 Difference in potential energy from amber=>gromacs conversion: -0.02322222 Difference in potential energy from amber=>lammps conversion: -0.02322120 Difference in potential energy from amber=>desmond conversion: -0.02183630 Difference in potential energy from amber=>charmm conversion: -0.40643376 ======================================================================= INFO 2017-03-18 23:14:04 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4039055.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4039055.inpcrd') INFO 2017-03-18 23:14:04 Beginning InterMol conversion INFO 2017-03-18 23:14:04 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:14:04 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:14:04 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4043951.inpcrd INFO 2017-03-18 23:14:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4043951/mobley_4043951_converted.input INFO 2017-03-18 23:14:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4043951/mobley_4043951_converted.cms WARNING 2017-03-18 23:14:20 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:14:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4043951/mobley_4043951_converted.inp INFO 2017-03-18 23:14:20 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4043951/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4043951/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4043951/mobley_4043951_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4043951/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 5.16923378 5.16923378 0.00000000 0.00000000 0.00000000 0.00000000 9.96063960 9.96063960 coulomb total 9.94913360 9.95577764 0.00664404 9.95577737 0.00664377 9.95574055 0.00660695 9.96063960 0.01150600 coulomb-14 4.78482240 4.78654386 0.00172146 0.00000000 -4.78482240 4.78653441 0.00171201 0.00000000 -4.78482240 improper 0.00000000 0.00077908 0.00077908 0.00000000 0.00000000 0.00000000 0.00000000 0.00079496 0.00079496 proper 12.15535680 12.15454361 -0.00081319 12.15532124 -0.00003556 12.15530755 -0.00004925 12.15456184 -0.00079496 vdw (SR) 0.00000000 -0.96062770 -0.96062770 0.00000000 0.00000000 0.00000000 0.00000000 2.94059888 2.94059888 vdw total 2.94051520 2.94056371 0.00004851 2.94056373 0.00004853 2.94055125 0.00003605 2.94059888 0.00008368 vdw-14 3.90116160 3.90119141 0.00002981 0.00000000 -3.90116160 3.90117066 0.00000906 0.00000000 -3.90116160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.19285840 1.19303035 0.00017195 1.19303036 0.00017196 1.19285144 -0.00000696 1.19298392 0.00012552 bond 1.01671200 1.01659768 -0.00011432 1.01659769 -0.00011431 1.01675920 0.00004720 1.01658648 -0.00012552 bonded 14.36492720 14.36495072 0.00002352 14.36494929 0.00002209 14.36491819 -0.00000901 14.36492720 0.00000000 dihedral 12.15535680 12.15532269 -0.00003411 12.15532124 -0.00003556 12.15530755 -0.00004925 12.15535680 0.00000000 nonbonded 12.88964880 12.89634135 0.00669255 12.89634111 0.00669231 12.89629180 0.00664300 12.90123848 0.01158968 potential 27.25457600 27.26129207 0.00671607 27.26129048 0.00671448 27.26118429 0.00660829 27.26616568 0.01158968 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 27.25457600 Difference in potential energy from amber=>gromacs conversion: 0.00671607 Difference in potential energy from amber=>lammps conversion: 0.00671448 Difference in potential energy from amber=>desmond conversion: 0.00660829 Difference in potential energy from amber=>charmm conversion: 0.01158968 ======================================================================= INFO 2017-03-18 23:14:20 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4043951.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4043951.inpcrd') INFO 2017-03-18 23:14:20 Beginning InterMol conversion INFO 2017-03-18 23:14:20 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:14:20 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:14:20 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4043987.inpcrd INFO 2017-03-18 23:14:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4043987/mobley_4043987_converted.input INFO 2017-03-18 23:14:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4043987/mobley_4043987_converted.cms WARNING 2017-03-18 23:14:36 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:14:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4043987/mobley_4043987_converted.inp INFO 2017-03-18 23:14:36 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4043987/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4043987/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4043987/mobley_4043987_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4043987/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 9.02651454 9.02651454 0.00000000 0.00000000 0.00000000 0.00000000 -1.85614792 -1.85614792 coulomb total -1.87024800 -1.85921983 0.01102817 -1.85921981 0.01102819 -1.85928705 0.01096095 -1.85614792 0.01410008 coulomb-14 -10.88551280 -10.88573437 -0.00022157 0.00000000 10.88551280 -10.88573899 -0.00022619 0.00000000 10.88551280 proper 7.21698160 7.21714305 0.00016145 7.21714519 0.00016359 7.21714967 0.00016807 7.21714896 0.00016736 vdw (SR) 0.00000000 5.56958535 5.56958535 0.00000000 0.00000000 0.00000000 0.00000000 16.15136968 16.15136968 vdw total 16.15149520 16.15113670 -0.00035850 16.15113705 -0.00035815 16.15099797 -0.00049723 16.15136968 -0.00012552 vdw-14 10.58175440 10.58155135 -0.00020305 0.00000000 -10.58175440 10.58154110 -0.00021330 0.00000000 -10.58175440 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.10452800 3.10438976 -0.00013824 3.10438976 -0.00013824 3.10450595 -0.00002205 3.10436064 -0.00016736 bond 0.78450000 0.78443110 -0.00006890 0.78443109 -0.00006891 0.78441635 -0.00008365 0.78441632 -0.00008368 bonded 11.10600960 11.10596391 -0.00004569 11.10596604 -0.00004356 11.10607197 0.00006237 11.10592592 -0.00008368 dihedral 7.21698160 7.21714305 0.00016145 7.21714519 0.00016359 7.21714967 0.00016807 7.21714896 0.00016736 nonbonded 14.28124720 14.29191687 0.01066967 14.29191724 0.01067004 14.29171092 0.01046372 14.29522176 0.01397456 potential 25.38725680 25.39788078 0.01062398 25.39788332 0.01062652 25.39772015 0.01046335 25.40110584 0.01384904 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 25.38725680 Difference in potential energy from amber=>gromacs conversion: 0.01062398 Difference in potential energy from amber=>lammps conversion: 0.01062652 Difference in potential energy from amber=>desmond conversion: 0.01046335 Difference in potential energy from amber=>charmm conversion: 0.01384904 ======================================================================= INFO 2017-03-18 23:14:36 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4043987.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4043987.inpcrd') INFO 2017-03-18 23:14:36 Beginning InterMol conversion INFO 2017-03-18 23:14:36 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:14:36 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:14:36 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4059279.inpcrd INFO 2017-03-18 23:14:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4059279/mobley_4059279_converted.input INFO 2017-03-18 23:14:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4059279/mobley_4059279_converted.cms WARNING 2017-03-18 23:14:52 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:14:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4059279/mobley_4059279_converted.inp INFO 2017-03-18 23:14:52 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4059279/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4059279/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4059279/mobley_4059279_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4059279/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -14.53089476 -14.53089476 0.00000000 0.00000000 0.00000000 0.00000000 234.28383312 234.28383312 coulomb total 234.21864640 234.28015593 0.06150953 234.28015120 0.06150480 234.28010020 0.06145380 234.28383312 0.06518672 coulomb-14 248.79361040 248.81105068 0.01744028 0.00000000 -248.79361040 248.81105308 0.01744268 0.00000000 -248.79361040 proper 12.10975120 12.10974092 -0.00001028 12.10974074 -0.00001046 12.10977538 0.00002418 12.10987672 0.00012552 vdw (SR) 0.00000000 -4.52112988 -4.52112988 0.00000000 0.00000000 0.00000000 0.00000000 15.88016280 15.88016280 vdw total 15.87995360 15.88011846 0.00016486 15.88011887 0.00016527 15.88004259 0.00008899 15.88016280 0.00020920 vdw-14 20.40118400 20.40124834 0.00006434 0.00000000 -20.40118400 20.40117910 -0.00000490 0.00000000 -20.40118400 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.47190720 2.47188940 -0.00001780 2.47188942 -0.00001778 2.47175302 -0.00015418 2.47178168 -0.00012552 bond 0.72759760 0.72780055 0.00020295 0.72780057 0.00020297 0.72780995 0.00021235 0.72780680 0.00020920 bonded 15.30925600 15.30943086 0.00017486 15.30943072 0.00017472 15.30933835 0.00008235 15.30946520 0.00020920 dihedral 12.10975120 12.10974092 -0.00001028 12.10974074 -0.00001046 12.10977538 0.00002418 12.10987672 0.00012552 nonbonded 250.09860000 250.16027439 0.06167439 250.16027216 0.06167216 250.16014279 0.06154279 250.16399592 0.06539592 potential 265.40785600 265.46970525 0.06184925 265.46970389 0.06184789 265.46941561 0.06155961 265.47346112 0.06560512 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 265.40785600 Difference in potential energy from amber=>gromacs conversion: 0.06184925 Difference in potential energy from amber=>lammps conversion: 0.06184789 Difference in potential energy from amber=>desmond conversion: 0.06155961 Difference in potential energy from amber=>charmm conversion: 0.06560512 ======================================================================= INFO 2017-03-18 23:14:52 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4059279.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4059279.inpcrd') INFO 2017-03-18 23:14:52 Beginning InterMol conversion INFO 2017-03-18 23:14:52 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:14:52 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4149784.inpcrd INFO 2017-03-18 23:14:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4149784/mobley_4149784_converted.input INFO 2017-03-18 23:14:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4149784/mobley_4149784_converted.cms INFO 2017-03-18 23:15:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4149784/mobley_4149784_converted.rst7 WARNING 2017-03-18 23:15:08 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:15:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4149784/mobley_4149784_converted.inp INFO 2017-03-18 23:15:08 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4149784/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4149784/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4149784/mobley_4149784_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_4149784/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4149784/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -28.51418412 -28.51418412 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -28.98348848 -28.98348848 coulomb total -29.05244080 -29.04983507 0.00260573 -29.04983459 0.00260621 -29.04989740 0.00254340 -29.05244080 0.00000000 -28.98348848 0.06895232 coulomb-14 -0.53513360 -0.53565095 -0.00051735 0.00000000 0.53513360 -0.53573598 -0.00060238 -0.53513360 0.00000000 0.00000000 0.53513360 improper 0.00000000 0.00012646 0.00012646 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00125520 0.00100852 -0.00024668 0.00113494 -0.00012026 0.00112872 -0.00012648 0.00125520 0.00000000 0.00100416 -0.00025104 vdw (SR) 0.00000000 -8.36201550 -8.36201550 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 39.08299504 39.08299504 vdw total 39.08274400 39.08305386 0.00030986 39.08305403 0.00031003 39.08310558 0.00036158 39.08274400 0.00000000 39.08299504 0.00025104 vdw-14 47.44488640 47.44506936 0.00018296 0.00000000 -47.44488640 47.44512865 0.00024225 47.44488640 0.00000000 0.00000000 -47.44488640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 7.14334320 7.14338104 0.00003784 7.14338086 0.00003766 7.14408343 0.00074023 7.14334320 0.00000000 7.14338504 0.00004184 bond 1.68071280 1.68084675 0.00013395 1.68084677 0.00013397 1.68109012 0.00037732 1.68071280 0.00000000 1.68083832 0.00012552 bonded 8.82531120 8.82536277 0.00005157 8.82536257 0.00005137 8.82630228 0.00099108 8.82531120 0.00000000 8.82535304 0.00004184 dihedral 0.00125520 0.00113498 -0.00012022 0.00113494 -0.00012026 0.00112872 -0.00012648 0.00125520 0.00000000 0.00112968 -0.00012552 nonbonded 10.03030320 10.03321879 0.00291559 10.03321903 0.00291583 10.03320818 0.00290498 10.03030320 0.00000000 10.09950656 0.06920336 potential 18.85561440 18.85858156 0.00296716 18.85858169 0.00296729 18.85934188 0.00372748 18.85561440 0.00000000 18.92490144 0.06928704 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 18.85561440 Difference in potential energy from amber=>gromacs conversion: 0.00296716 Difference in potential energy from amber=>lammps conversion: 0.00296729 Difference in potential energy from amber=>desmond conversion: 0.00372748 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.06928704 ======================================================================= INFO 2017-03-18 23:15:08 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4149784.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4149784.inpcrd') INFO 2017-03-18 23:15:08 Beginning InterMol conversion INFO 2017-03-18 23:15:08 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:15:09 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:15:09 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4177472.inpcrd INFO 2017-03-18 23:15:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4177472/mobley_4177472_converted.input INFO 2017-03-18 23:15:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4177472/mobley_4177472_converted.cms WARNING 2017-03-18 23:15:24 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:15:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4177472/mobley_4177472_converted.inp INFO 2017-03-18 23:15:24 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4177472/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4177472/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4177472/mobley_4177472_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4177472/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -2.18847201 -2.18847201 0.00000000 0.00000000 0.00000000 0.00000000 -10.07837736 -10.07837736 coulomb total -10.06419360 -10.07856416 -0.01437056 -10.07856397 -0.01437037 -10.07860634 -0.01441274 -10.07837736 -0.01418376 coulomb-14 -7.89478960 -7.89009216 0.00469744 0.00000000 7.89478960 -7.89009227 0.00469733 0.00000000 7.89478960 proper 18.42968320 18.42947450 -0.00020870 18.42947609 -0.00020711 18.42943220 -0.00025100 18.42947400 -0.00020920 vdw (SR) 0.00000000 13.79774544 13.79774544 0.00000000 0.00000000 0.00000000 0.00000000 29.30180720 29.30180720 vdw total 29.30180720 29.30149250 -0.00031470 29.30149298 -0.00031422 29.30179059 -0.00001661 29.30180720 0.00000000 vdw-14 15.50381200 15.50374707 -0.00006493 0.00000000 -15.50381200 15.50374447 -0.00006753 0.00000000 -15.50381200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 10.28510880 10.28490802 -0.00020078 10.28490797 -0.00020083 10.28425664 -0.00085216 10.28489960 -0.00020920 bond 2.44136400 2.44144139 0.00007739 2.44144140 0.00007740 2.44128978 -0.00007422 2.44144768 0.00008368 bonded 31.15615600 31.15582390 -0.00033210 31.15582546 -0.00033054 31.15497862 -0.00117738 31.15582128 -0.00033472 dihedral 18.42968320 18.42947450 -0.00020870 18.42947609 -0.00020711 18.42943220 -0.00025100 18.42947400 -0.00020920 nonbonded 19.23761360 19.22292834 -0.01468526 19.22292902 -0.01468458 19.22318425 -0.01442935 19.22342984 -0.01418376 potential 50.39376960 50.37875225 -0.01501735 50.37875322 -0.01501638 50.37808253 -0.01568707 50.37925112 -0.01451848 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 50.39376960 Difference in potential energy from amber=>gromacs conversion: -0.01501735 Difference in potential energy from amber=>lammps conversion: -0.01501638 Difference in potential energy from amber=>desmond conversion: -0.01568707 Difference in potential energy from amber=>charmm conversion: -0.01451848 ======================================================================= INFO 2017-03-18 23:15:24 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4177472.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4177472.inpcrd') INFO 2017-03-18 23:15:25 Beginning InterMol conversion INFO 2017-03-18 23:15:25 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:15:25 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:15:25 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4188615.inpcrd INFO 2017-03-18 23:15:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4188615/mobley_4188615_converted.input INFO 2017-03-18 23:15:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4188615/mobley_4188615_converted.cms WARNING 2017-03-18 23:15:40 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:15:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4188615/mobley_4188615_converted.inp INFO 2017-03-18 23:15:40 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4188615/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4188615/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4188615/mobley_4188615_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4188615/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -112.60224238 -112.60224238 0.00000000 0.00000000 0.00000000 0.00000000 22.24390128 22.24390128 coulomb total 22.21160080 22.23246091 0.02086011 22.23246055 0.02085975 22.23247603 0.02087523 22.24390128 0.03230048 coulomb-14 134.79383600 134.83470329 0.04086729 0.00000000 -134.79383600 134.83463837 0.04080237 0.00000000 -134.79383600 improper 0.00000000 0.01715110 0.01715110 0.00000000 0.00000000 0.00000000 0.00000000 0.01715440 0.01715440 proper 33.49501200 33.47787960 -0.01713240 33.49503208 0.00002008 33.49505945 0.00004745 33.47789944 -0.01711256 vdw (SR) 0.00000000 -4.97678226 -4.97678226 0.00000000 0.00000000 0.00000000 0.00000000 18.86105360 18.86105360 vdw total 18.86105360 18.86100217 -0.00005143 18.86100214 -0.00005146 18.86094385 -0.00010975 18.86105360 0.00000000 vdw-14 23.83792160 23.83778443 -0.00013717 0.00000000 -23.83792160 23.83773445 -0.00018715 0.00000000 -23.83792160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 8.35712160 8.35713240 0.00001080 8.35713248 0.00001088 8.35697876 -0.00014284 8.35716344 0.00004184 bond 7.87177760 7.87168859 -0.00008901 7.87168848 -0.00008912 7.87284967 0.00107207 7.87169392 -0.00008368 bonded 49.72391120 49.72385169 -0.00005951 49.72385304 -0.00005816 49.72488787 0.00097667 49.72391120 0.00000000 dihedral 33.49501200 33.49503070 0.00001870 33.49503208 0.00002008 33.49505945 0.00004745 33.49505384 0.00004184 nonbonded 41.07265440 41.09346307 0.02080867 41.09346311 0.02080871 41.09341988 0.02076548 41.10495488 0.03230048 potential 90.79656560 90.81731476 0.02074916 90.81731406 0.02074846 90.81820734 0.02164174 90.82878240 0.03221680 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 90.79656560 Difference in potential energy from amber=>gromacs conversion: 0.02074916 Difference in potential energy from amber=>lammps conversion: 0.02074846 Difference in potential energy from amber=>desmond conversion: 0.02164174 Difference in potential energy from amber=>charmm conversion: 0.03221680 ======================================================================= INFO 2017-03-18 23:15:40 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4188615.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4188615.inpcrd') INFO 2017-03-18 23:15:41 Beginning InterMol conversion INFO 2017-03-18 23:15:41 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:15:41 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4193752.inpcrd INFO 2017-03-18 23:15:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4193752/mobley_4193752_converted.input INFO 2017-03-18 23:15:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4193752/mobley_4193752_converted.cms INFO 2017-03-18 23:15:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4193752/mobley_4193752_converted.rst7 WARNING 2017-03-18 23:15:56 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:15:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4193752/mobley_4193752_converted.inp INFO 2017-03-18 23:15:56 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4193752/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4193752/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4193752/mobley_4193752_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_4193752/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4193752/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -21.70296232 -21.70296232 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 19.73596984 19.73596984 coulomb total 19.73341760 19.73447779 0.00106019 19.73447741 0.00105981 19.73464096 0.00122336 19.73341760 0.00000000 19.73596984 0.00255224 coulomb-14 41.43582560 41.43744011 0.00161451 0.00000000 -41.43582560 41.43744313 0.00161753 41.43582560 0.00000000 0.00000000 -41.43582560 improper 0.00000000 0.00006909 0.00006909 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00083680 0.00056555 -0.00027125 0.00063462 -0.00020218 0.00063070 -0.00020610 0.00083680 0.00000000 0.00058576 -0.00025104 vdw (SR) 0.00000000 2.19618624 2.19618624 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 26.24154592 26.24154592 vdw total 26.24162960 26.24146670 -0.00016290 26.24146684 -0.00016276 26.24164547 0.00001587 26.24162960 0.00000000 26.24154592 -0.00008368 vdw-14 24.04544800 24.04528047 -0.00016753 0.00000000 -24.04544800 24.04541520 -0.00003280 24.04544800 0.00000000 0.00000000 -24.04544800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.24515840 1.24533682 0.00017842 1.24533681 0.00017841 1.24505311 -0.00010529 1.24515840 0.00000000 1.24532576 0.00016736 bond 11.91896080 11.91891209 -0.00004871 11.91891227 -0.00004853 11.91579594 -0.00316486 11.91896080 0.00000000 11.91891896 -0.00004184 bonded 13.16495600 13.16488356 -0.00007244 13.16488369 -0.00007231 13.16147975 -0.00347625 13.16495600 0.00000000 13.16491416 -0.00004184 dihedral 0.00083680 0.00063464 -0.00020216 0.00063462 -0.00020218 0.00063070 -0.00020610 0.00083680 0.00000000 0.00066944 -0.00016736 nonbonded 45.97504720 45.97594450 0.00089730 45.97594258 0.00089538 45.97628643 0.00123923 45.97504720 0.00000000 45.97751576 0.00246856 potential 59.14000320 59.14082805 0.00082485 59.14082745 0.00082425 59.13770911 -0.00229409 59.14000320 0.00000000 59.14234624 0.00234304 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 59.14000320 Difference in potential energy from amber=>gromacs conversion: 0.00082485 Difference in potential energy from amber=>lammps conversion: 0.00082425 Difference in potential energy from amber=>desmond conversion: -0.00229409 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00234304 ======================================================================= INFO 2017-03-18 23:15:56 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4193752.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4193752.inpcrd') INFO 2017-03-18 23:15:57 Beginning InterMol conversion INFO 2017-03-18 23:15:57 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:15:57 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:15:57 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4218209.inpcrd INFO 2017-03-18 23:15:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4218209/mobley_4218209_converted.input INFO 2017-03-18 23:15:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4218209/mobley_4218209_converted.cms WARNING 2017-03-18 23:16:13 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:16:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4218209/mobley_4218209_converted.inp INFO 2017-03-18 23:16:13 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4218209/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4218209/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4218209/mobley_4218209_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4218209/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -11.68211243 -11.68211243 0.00000000 0.00000000 0.00000000 0.00000000 -114.75452616 -114.75452616 coulomb total -114.72862720 -114.72440851 0.00421869 -114.72440554 0.00422166 -114.72475457 0.00387263 -114.75452616 -0.02589896 coulomb-14 -103.03434720 -103.04229609 -0.00794889 0.00000000 103.03434720 -103.04217044 -0.00782324 0.00000000 103.03434720 improper 0.00000000 0.11618256 0.11618256 0.00000000 0.00000000 0.00000000 0.00000000 0.11618968 0.11618968 proper 0.22509920 0.10888859 -0.11621061 0.22506970 -0.00002950 0.22511324 0.00001404 0.10886768 -0.11623152 vdw (SR) 0.00000000 13.30147530 13.30147530 0.00000000 0.00000000 0.00000000 0.00000000 39.69523976 39.69523976 vdw total 39.69528160 39.69514243 -0.00013917 39.69514269 -0.00013891 39.69523888 -0.00004272 39.69523976 -0.00004184 vdw-14 26.39350880 26.39366713 0.00015833 0.00000000 -26.39350880 26.39365746 0.00014866 0.00000000 -26.39350880 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.73170960 3.73155073 -0.00015887 3.73155073 -0.00015887 3.73162076 -0.00008884 3.73162592 -0.00008368 bond 5.87559120 5.87552997 -0.00006123 5.87553011 -0.00006109 5.87584416 0.00025296 5.87554936 -0.00004184 bonded 9.83240000 9.83215185 -0.00024815 9.83215055 -0.00024945 9.83257816 0.00017816 9.83223264 -0.00016736 dihedral 0.22509920 0.22507114 -0.00002806 0.22506970 -0.00002950 0.22511324 0.00001404 0.22505736 -0.00004184 nonbonded -75.03334560 -75.02926608 0.00407952 -75.02926620 0.00407940 -75.02951569 0.00382991 -75.05928640 -0.02594080 potential -65.20094560 -65.19711424 0.00383136 -65.19711306 0.00383254 -65.19700009 0.00394551 -65.22705376 -0.02610816 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -65.20094560 Difference in potential energy from amber=>gromacs conversion: 0.00383136 Difference in potential energy from amber=>lammps conversion: 0.00383254 Difference in potential energy from amber=>desmond conversion: 0.00394551 Difference in potential energy from amber=>charmm conversion: -0.02610816 ======================================================================= INFO 2017-03-18 23:16:13 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4218209.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4218209.inpcrd') INFO 2017-03-18 23:16:13 Beginning InterMol conversion INFO 2017-03-18 23:16:13 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:16:13 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4219614.inpcrd INFO 2017-03-18 23:16:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4219614/mobley_4219614_converted.input INFO 2017-03-18 23:16:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4219614/mobley_4219614_converted.cms INFO 2017-03-18 23:16:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4219614/mobley_4219614_converted.rst7 WARNING 2017-03-18 23:16:29 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:16:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4219614/mobley_4219614_converted.inp INFO 2017-03-18 23:16:29 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4219614/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4219614/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4219614/mobley_4219614_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_4219614/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4219614/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -5.34263344 -5.34263344 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 9.30927448 9.30927448 coulomb total 9.31776800 9.31576587 -0.00200213 9.31576596 -0.00200204 9.31577047 -0.00199753 9.31776800 0.00000000 9.30927448 -0.00849352 coulomb-14 14.65906240 14.65839931 -0.00066309 0.00000000 -14.65906240 14.65840421 -0.00065819 14.65906240 0.00000000 0.00000000 -14.65906240 improper 0.00000000 0.00002677 0.00002677 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00031366 -0.00010474 0.00034040 -0.00007800 0.00034615 -0.00007225 0.00041840 0.00000000 0.00029288 -0.00012552 vdw (SR) 0.00000000 -2.72659505 -2.72659505 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 19.53505416 19.53505416 vdw total 19.53509600 19.53500523 -0.00009077 19.53500521 -0.00009079 19.53499784 -0.00009816 19.53509600 0.00000000 19.53505416 -0.00004184 vdw-14 22.26180880 22.26160028 -0.00020852 0.00000000 -22.26180880 22.26159073 -0.00021807 22.26180880 0.00000000 0.00000000 -22.26180880 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.75474560 2.75475980 0.00001420 2.75475978 0.00001418 2.75497570 0.00023010 2.75474560 0.00000000 2.75478744 0.00004184 bond 1.06148080 1.06153245 0.00005165 1.06153243 0.00005163 1.06182565 0.00034485 1.06148080 0.00000000 1.06152264 0.00004184 bonded 3.81664480 3.81663267 -0.00001213 3.81663261 -0.00001219 3.81714750 0.00050270 3.81664480 0.00000000 3.81664480 0.00000000 dihedral 0.00041840 0.00034042 -0.00007798 0.00034040 -0.00007800 0.00034615 -0.00007225 0.00041840 0.00000000 0.00033472 -0.00008368 nonbonded 28.85286400 28.85077110 -0.00209290 28.85077116 -0.00209284 28.85076831 -0.00209569 28.85286400 0.00000000 28.84432864 -0.00853536 potential 32.66950880 32.66740377 -0.00210503 32.66740383 -0.00210497 32.66781851 -0.00169029 32.66950880 0.00000000 32.66101528 -0.00849352 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 32.66950880 Difference in potential energy from amber=>gromacs conversion: -0.00210503 Difference in potential energy from amber=>lammps conversion: -0.00210497 Difference in potential energy from amber=>desmond conversion: -0.00169029 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.00849352 ======================================================================= INFO 2017-03-18 23:16:29 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4219614.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4219614.inpcrd') INFO 2017-03-18 23:16:29 Beginning InterMol conversion INFO 2017-03-18 23:16:29 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:16:29 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:16:29 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4252724.inpcrd INFO 2017-03-18 23:16:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4252724/mobley_4252724_converted.input INFO 2017-03-18 23:16:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4252724/mobley_4252724_converted.cms WARNING 2017-03-18 23:16:45 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:16:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4252724/mobley_4252724_converted.inp INFO 2017-03-18 23:16:45 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4252724/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4252724/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4252724/mobley_4252724_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4252724/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 12.21190805 12.21190805 0.00000000 0.00000000 0.00000000 0.00000000 -3.53347168 -3.53347168 coulomb total -3.53422480 -3.53408568 0.00013912 -3.53408564 0.00013916 -3.53413020 0.00009460 -3.53347168 0.00075312 coulomb-14 -15.74564720 -15.74599374 -0.00034654 0.00000000 15.74564720 -15.74597552 -0.00032832 0.00000000 15.74564720 improper 0.00000000 0.00004272 0.00004272 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.11171280 0.11157159 -0.00014121 0.11161434 -0.00009846 0.11161207 -0.00010073 0.11158728 -0.00012552 vdw (SR) 0.00000000 -2.96734406 -2.96734406 0.00000000 0.00000000 0.00000000 0.00000000 20.70205544 20.70205544 vdw total 20.70201360 20.70196806 -0.00004554 20.70196799 -0.00004561 20.70206688 0.00005328 20.70205544 0.00004184 vdw-14 23.66930640 23.66931212 0.00000572 0.00000000 -23.66930640 23.66951945 0.00021305 0.00000000 -23.66930640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.52588080 2.52593303 0.00005223 2.52593302 0.00005222 2.52598743 0.00010663 2.52588080 0.00000000 bond 1.11796480 1.11802897 0.00006417 1.11802898 0.00006418 1.11756753 -0.00039727 1.11804848 0.00008368 bonded 3.75555840 3.75557630 0.00001790 3.75557634 0.00001794 3.75516703 -0.00039137 3.75555840 0.00000000 dihedral 0.11171280 0.11161431 -0.00009849 0.11161434 -0.00009846 0.11161207 -0.00010073 0.11162912 -0.00008368 nonbonded 17.16778880 17.16788238 0.00009358 17.16788252 0.00009372 17.16793668 0.00014788 17.16858376 0.00079496 potential 20.92334720 20.92345868 0.00011148 20.92345891 0.00011171 20.92301478 -0.00033242 20.92410032 0.00075312 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 20.92334720 Difference in potential energy from amber=>gromacs conversion: 0.00011148 Difference in potential energy from amber=>lammps conversion: 0.00011171 Difference in potential energy from amber=>desmond conversion: -0.00033242 Difference in potential energy from amber=>charmm conversion: 0.00075312 ======================================================================= INFO 2017-03-18 23:16:45 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4252724.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4252724.inpcrd') INFO 2017-03-18 23:16:45 Beginning InterMol conversion INFO 2017-03-18 23:16:45 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:16:45 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:16:45 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4287564.inpcrd INFO 2017-03-18 23:16:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4287564/mobley_4287564_converted.input INFO 2017-03-18 23:16:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4287564/mobley_4287564_converted.cms WARNING 2017-03-18 23:17:01 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:17:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4287564/mobley_4287564_converted.inp INFO 2017-03-18 23:17:01 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4287564/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4287564/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4287564/mobley_4287564_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4287564/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 43.20008941 43.20008941 0.00000000 0.00000000 0.00000000 0.00000000 -130.00867888 -130.00867888 coulomb total -129.98390960 -129.98650847 -0.00259887 -129.98650786 -0.00259826 -129.98672208 -0.00281248 -130.00867888 -0.02476928 coulomb-14 -173.17534160 -173.18659788 -0.01125628 0.00000000 173.17534160 -173.18686141 -0.01151981 0.00000000 173.17534160 improper 0.00000000 0.00010469 0.00010469 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00083680 0.00080141 -0.00003539 0.00090617 0.00006937 0.00090976 0.00007296 0.00079496 -0.00004184 vdw (SR) 0.00000000 -1.43566500 -1.43566500 0.00000000 0.00000000 0.00000000 0.00000000 20.20909656 20.20909656 vdw total 20.20913840 20.20914305 0.00000465 20.20914300 0.00000460 20.20960945 0.00047105 20.20909656 -0.00004184 vdw-14 21.64466880 21.64480805 0.00013925 0.00000000 -21.64466880 21.64526916 0.00060036 0.00000000 -21.64466880 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.73175760 1.73173465 -0.00002295 1.73173463 -0.00002297 1.73165738 -0.00010022 1.73175760 0.00000000 bond 1.20457360 1.20469391 0.00012031 1.20469393 0.00012033 1.20436270 -0.00021090 1.20469912 0.00012552 bonded 2.93716800 2.93733466 0.00016666 2.93733473 0.00016673 2.93692985 -0.00023815 2.93737720 0.00020920 dihedral 0.00083680 0.00090610 0.00006930 0.00090617 0.00006937 0.00090976 0.00007296 0.00092048 0.00008368 nonbonded -109.77477120 -109.77736541 -0.00259421 -109.77736528 -0.00259408 -109.77711263 -0.00234143 -109.79958232 -0.02481112 potential -106.83760320 -106.84003075 -0.00242755 -106.84002992 -0.00242672 -106.84022699 -0.00262379 -106.86220512 -0.02460192 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -106.83760320 Difference in potential energy from amber=>gromacs conversion: -0.00242755 Difference in potential energy from amber=>lammps conversion: -0.00242672 Difference in potential energy from amber=>desmond conversion: -0.00262379 Difference in potential energy from amber=>charmm conversion: -0.02460192 ======================================================================= INFO 2017-03-18 23:17:01 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4287564.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4287564.inpcrd') INFO 2017-03-18 23:17:01 Beginning InterMol conversion INFO 2017-03-18 23:17:01 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:17:01 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4291494.inpcrd INFO 2017-03-18 23:17:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4291494/mobley_4291494_converted.input INFO 2017-03-18 23:17:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4291494/mobley_4291494_converted.cms INFO 2017-03-18 23:17:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4291494/mobley_4291494_converted.rst7 WARNING 2017-03-18 23:17:17 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:17:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4291494/mobley_4291494_converted.inp INFO 2017-03-18 23:17:17 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4291494/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4291494/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4291494/mobley_4291494_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_4291494/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4291494/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 22.69877110 22.69877110 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -92.99308192 -92.99308192 coulomb total -92.92245600 -92.92022881 0.00222719 -92.92022593 0.00223007 -92.92033818 0.00211782 -92.92245600 0.00000000 -92.99308192 -0.07062592 coulomb-14 -115.61856400 -115.61899991 -0.00043591 0.00000000 115.61856400 -115.61916817 -0.00060417 -115.61856400 0.00000000 0.00000000 115.61856400 improper 0.00000000 0.00016723 0.00016723 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00016736 0.00016736 proper 0.00125520 0.00126297 0.00000777 0.00143022 0.00017502 0.00143596 0.00018076 0.00125520 0.00000000 0.00125520 0.00000000 vdw (SR) 0.00000000 -1.05387209 -1.05387209 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 17.97475688 17.97475688 vdw total 17.97488240 17.97479895 -0.00008345 17.97479914 -0.00008326 17.97519314 0.00031074 17.97488240 0.00000000 17.97475688 -0.00012552 vdw-14 19.02883200 19.02867104 -0.00016096 0.00000000 -19.02883200 19.02906618 0.00023418 19.02883200 0.00000000 0.00000000 -19.02883200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.82966320 1.82985093 0.00018773 1.82985094 0.00018774 1.82986851 0.00020531 1.82966320 0.00000000 1.82987240 0.00020920 bond 0.77780560 0.77775689 -0.00004871 0.77775690 -0.00004870 0.77743260 -0.00037300 0.77780560 0.00000000 0.77776376 -0.00004184 bonded 2.60872400 2.60903802 0.00031402 2.60903805 0.00031405 2.60873708 0.00001308 2.60872400 0.00000000 2.60905872 0.00033472 dihedral 0.00125520 0.00143020 0.00017500 0.00143022 0.00017502 0.00143596 0.00018076 0.00125520 0.00000000 0.00142256 0.00016736 nonbonded -74.94757360 -74.94542985 0.00214375 -74.94542721 0.00214639 -74.94514504 0.00242856 -74.94757360 0.00000000 -75.01832504 -0.07075144 potential -72.33884960 -72.33639184 0.00245776 -72.33638941 0.00246019 -72.33644087 0.00240873 -72.33884960 0.00000000 -72.40926632 -0.07041672 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -72.33884960 Difference in potential energy from amber=>gromacs conversion: 0.00245776 Difference in potential energy from amber=>lammps conversion: 0.00246019 Difference in potential energy from amber=>desmond conversion: 0.00240873 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.07041672 ======================================================================= INFO 2017-03-18 23:17:17 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4291494.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4291494.inpcrd') INFO 2017-03-18 23:17:17 Beginning InterMol conversion INFO 2017-03-18 23:17:17 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:17:17 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:17:17 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_430089.inpcrd INFO 2017-03-18 23:17:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_430089/mobley_430089_converted.input INFO 2017-03-18 23:17:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_430089/mobley_430089_converted.cms WARNING 2017-03-18 23:17:33 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:17:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_430089/mobley_430089_converted.inp INFO 2017-03-18 23:17:33 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_430089/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_430089/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_430089/mobley_430089_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_430089/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 2.07085287 2.07085287 0.00000000 0.00000000 0.00000000 0.00000000 1.68782560 1.68782560 coulomb total 1.68489680 1.68854163 0.00364483 1.68854161 0.00364481 1.68852814 0.00363134 1.68782560 0.00292880 coulomb-14 -0.38325440 -0.38231124 0.00094316 0.00000000 0.38325440 -0.38231727 0.00093713 0.00000000 0.38325440 proper 0.03640080 0.03621446 -0.00018634 0.03621445 -0.00018635 0.03621089 -0.00018991 0.03623344 -0.00016736 vdw (SR) 0.00000000 -1.22258062 -1.22258062 0.00000000 0.00000000 0.00000000 0.00000000 1.59393664 1.59393664 vdw total 1.59410400 1.59388995 -0.00021405 1.59388999 -0.00021401 1.59389997 -0.00020403 1.59393664 -0.00016736 vdw-14 2.81666880 2.81647058 -0.00019822 0.00000000 -2.81666880 2.81647980 -0.00018900 0.00000000 -2.81666880 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.64726480 0.78780872 0.14054392 0.78780871 0.14054391 0.78775688 0.14049208 0.78780536 0.14054056 bond 2.07526400 2.07518193 -0.00008207 2.07518195 -0.00008205 2.07451430 -0.00074970 2.07518032 -0.00008368 bonded 2.75892960 2.89920511 0.14027551 2.89920511 0.14027551 2.89848207 0.13955247 2.89921912 0.14028952 dihedral 0.03640080 0.03621446 -0.00018634 0.03621445 -0.00018635 0.03621089 -0.00018991 0.03623344 -0.00016736 nonbonded 3.27900080 3.28243158 0.00343078 3.28243160 0.00343080 3.28242811 0.00342731 3.28176224 0.00276144 potential 6.03793040 6.18163669 0.14370629 6.18163657 0.14370617 6.18087659 0.14294619 6.18098136 0.14305096 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 6.03793040 Difference in potential energy from amber=>gromacs conversion: 0.14370629 Difference in potential energy from amber=>lammps conversion: 0.14370617 Difference in potential energy from amber=>desmond conversion: 0.14294619 Difference in potential energy from amber=>charmm conversion: 0.14305096 ======================================================================= INFO 2017-03-18 23:17:33 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_430089.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_430089.inpcrd') INFO 2017-03-18 23:17:33 Beginning InterMol conversion INFO 2017-03-18 23:17:33 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:17:33 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:17:33 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4305650.inpcrd INFO 2017-03-18 23:17:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4305650/mobley_4305650_converted.input INFO 2017-03-18 23:17:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4305650/mobley_4305650_converted.cms WARNING 2017-03-18 23:17:49 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:17:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4305650/mobley_4305650_converted.inp INFO 2017-03-18 23:17:49 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4305650/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4305650/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4305650/mobley_4305650_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4305650/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -19.87038180 -19.87038180 0.00000000 0.00000000 0.00000000 0.00000000 -6.43038960 -6.43038960 coulomb total -6.44377840 -6.44076407 0.00301433 -6.44076383 0.00301457 -6.44075324 0.00302516 -6.43038960 0.01338880 coulomb-14 13.43440560 13.42961773 -0.00478787 0.00000000 -13.43440560 13.42963764 -0.00476796 0.00000000 -13.43440560 proper 0.03723760 0.03708998 -0.00014762 0.03708998 -0.00014762 0.03708904 -0.00014856 0.03711208 -0.00012552 vdw (SR) 0.00000000 -0.49625226 -0.49625226 0.00000000 0.00000000 0.00000000 0.00000000 3.12963200 3.12963200 vdw total 3.12963200 3.12959341 -0.00003859 3.12959342 -0.00003858 3.12955573 -0.00007627 3.12963200 0.00000000 vdw-14 3.62585440 3.62584567 -0.00000873 0.00000000 -3.62585440 3.62580828 -0.00004612 0.00000000 -3.62585440 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.89446720 3.89697419 0.00250699 3.89697421 0.00250701 3.89674702 0.00227982 3.89697760 0.00251040 bond 4.51955680 4.51955657 -0.00000023 4.51955638 -0.00000042 4.51962128 0.00006448 4.51955680 0.00000000 bonded 8.45126160 8.45362074 0.00235914 8.45362057 0.00235897 8.45345733 0.00219573 8.45364648 0.00238488 dihedral 0.03723760 0.03708998 -0.00014762 0.03708998 -0.00014762 0.03708904 -0.00014856 0.03711208 -0.00012552 nonbonded -3.31414640 -3.31117066 0.00297574 -3.31117057 0.00297583 -3.31119751 0.00294889 -3.30075760 0.01338880 potential 5.13711520 5.14245008 0.00533488 5.14245022 0.00533502 5.14224265 0.00512745 5.15284704 0.01573184 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 5.13711520 Difference in potential energy from amber=>gromacs conversion: 0.00533488 Difference in potential energy from amber=>lammps conversion: 0.00533502 Difference in potential energy from amber=>desmond conversion: 0.00512745 Difference in potential energy from amber=>charmm conversion: 0.01573184 ======================================================================= INFO 2017-03-18 23:17:49 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4305650.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4305650.inpcrd') INFO 2017-03-18 23:17:49 Beginning InterMol conversion INFO 2017-03-18 23:17:49 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:17:50 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:17:50 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4338603.inpcrd INFO 2017-03-18 23:17:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4338603/mobley_4338603_converted.input INFO 2017-03-18 23:17:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4338603/mobley_4338603_converted.cms WARNING 2017-03-18 23:18:05 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:18:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4338603/mobley_4338603_converted.inp INFO 2017-03-18 23:18:05 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4338603/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4338603/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4338603/mobley_4338603_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4338603/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 467.96179949 467.96179949 0.00000000 0.00000000 0.00000000 0.00000000 -862.71034048 -862.71034048 coulomb total -862.44206240 -862.47126942 -0.02920702 -862.47126672 -0.02920432 -862.47133785 -0.02927545 -862.71034048 -0.26827808 coulomb-14 -1330.38773520 -1330.43306890 -0.04533370 0.00000000 1330.38773520 -1330.43311068 -0.04537548 0.00000000 1330.38773520 improper 0.00000000 0.00033038 0.00033038 0.00000000 0.00000000 0.00000000 0.00000000 0.00033472 0.00033472 proper 50.20841840 50.20822458 -0.00019382 50.20855647 0.00013807 50.20853974 0.00012134 50.20820920 -0.00020920 vdw (SR) 0.00000000 -2.42687631 -2.42687631 0.00000000 0.00000000 0.00000000 0.00000000 13.18696384 13.18696384 vdw total 13.18713120 13.18701001 -0.00012119 13.18700986 -0.00012134 13.18726633 0.00013513 13.18696384 -0.00016736 vdw-14 15.61385120 15.61388633 0.00003513 0.00000000 -15.61385120 15.61413638 0.00028518 0.00000000 -15.61385120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 14.63186640 14.63180844 -0.00005796 14.63180824 -0.00005816 14.63222585 0.00035945 14.63178272 -0.00008368 bond 19.49367440 19.49359642 -0.00007798 19.49359658 -0.00007782 19.49374829 0.00007389 19.49359072 -0.00008368 bonded 84.33395920 84.33395982 0.00000062 84.33396129 0.00000209 84.33451387 0.00055467 84.33391736 -0.00004184 dihedral 50.20841840 50.20855496 0.00013656 50.20855647 0.00013807 50.20853974 0.00012134 50.20854392 0.00012552 nonbonded -849.25493120 -849.28425940 -0.02932820 -849.28426104 -0.02932984 -849.28407152 -0.02914032 -849.52337664 -0.26844544 potential -764.92097200 -764.95029958 -0.02932758 -764.95030184 -0.02932984 -764.94956127 -0.02858927 -765.18945928 -0.26848728 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -764.92097200 Difference in potential energy from amber=>gromacs conversion: -0.02932758 Difference in potential energy from amber=>lammps conversion: -0.02932984 Difference in potential energy from amber=>desmond conversion: -0.02858927 Difference in potential energy from amber=>charmm conversion: -0.26848728 ======================================================================= INFO 2017-03-18 23:18:05 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4338603.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4338603.inpcrd') INFO 2017-03-18 23:18:05 Beginning InterMol conversion INFO 2017-03-18 23:18:05 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:18:06 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4371692.inpcrd INFO 2017-03-18 23:18:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4371692/mobley_4371692_converted.input INFO 2017-03-18 23:18:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4371692/mobley_4371692_converted.cms INFO 2017-03-18 23:18:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4371692/mobley_4371692_converted.rst7 WARNING 2017-03-18 23:18:21 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:18:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4371692/mobley_4371692_converted.inp INFO 2017-03-18 23:18:21 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4371692/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4371692/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4371692/mobley_4371692_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_4371692/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4371692/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 130.20736934 130.20736934 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -47.14234136 -47.14234136 coulomb total -47.19133600 -47.19152552 -0.00018952 -47.19152428 -0.00018828 -47.19384807 -0.00251207 -47.19133600 0.00000000 -47.14234136 0.04899464 coulomb-14 -177.39281360 -177.39889486 -0.00608126 0.00000000 177.39281360 -177.39956909 -0.00675549 -177.39281360 0.00000000 0.00000000 177.39281360 improper 0.00000000 0.11810991 0.11810991 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.11811432 0.11811432 proper 0.22593600 0.10768620 -0.11824980 0.22579496 -0.00014104 0.22580864 -0.00012736 0.22593600 0.00000000 0.10769616 -0.11823984 vdw (SR) 0.00000000 21.85686391 21.85686391 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 76.21833808 76.21833808 vdw total 76.21825440 76.21810779 -0.00014661 76.21810796 -0.00014644 76.21810524 -0.00014916 76.21783600 -0.00041840 76.21833808 0.00008368 vdw-14 54.36103840 54.36124388 0.00020548 0.00000000 -54.36103840 54.36087815 -0.00016025 54.36103840 0.00000000 0.00000000 -54.36103840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 11.32901680 11.32892054 -0.00009626 11.32892057 -0.00009623 11.32788440 -0.00113240 11.32901680 0.00000000 11.32889128 -0.00012552 bond 8.97426160 8.97445612 0.00019452 8.97445616 0.00019456 8.97381655 -0.00044505 8.97426160 0.00000000 8.97447080 0.00020920 bonded 20.52921440 20.52917278 -0.00004162 20.52917168 -0.00004272 20.52750959 -0.00170481 20.52921440 0.00000000 20.52917256 -0.00004184 dihedral 0.22593600 0.22579611 -0.00013989 0.22579496 -0.00014104 0.22580864 -0.00012736 0.22593600 0.00000000 0.22581048 -0.00012552 nonbonded 29.02691840 29.02658227 -0.00033613 29.02658284 -0.00033556 29.02425717 -0.00266123 29.02650000 -0.00041840 29.07599672 0.04907832 potential 49.55613280 49.55575504 -0.00037776 49.55575624 -0.00037656 49.55155969 -0.00457311 49.55571440 -0.00041840 49.60512744 0.04899464 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 49.55613280 Difference in potential energy from amber=>gromacs conversion: -0.00037776 Difference in potential energy from amber=>lammps conversion: -0.00037656 Difference in potential energy from amber=>desmond conversion: -0.00457311 Difference in potential energy from amber=>amber conversion: -0.00041840 Difference in potential energy from amber=>charmm conversion: 0.04899464 ======================================================================= INFO 2017-03-18 23:18:21 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4371692.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4371692.inpcrd') INFO 2017-03-18 23:18:22 Beginning InterMol conversion INFO 2017-03-18 23:18:22 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:18:22 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:18:22 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4375719.inpcrd INFO 2017-03-18 23:18:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4375719/mobley_4375719_converted.input INFO 2017-03-18 23:18:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4375719/mobley_4375719_converted.cms WARNING 2017-03-18 23:18:37 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:18:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4375719/mobley_4375719_converted.inp INFO 2017-03-18 23:18:38 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4375719/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4375719/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4375719/mobley_4375719_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4375719/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 8.06562438 8.06562438 0.00000000 0.00000000 0.00000000 0.00000000 3.79267048 3.79267048 coulomb total 3.80158240 3.80137631 -0.00020609 3.80137625 -0.00020615 3.80132354 -0.00025886 3.79267048 -0.00891192 coulomb-14 -4.26391440 -4.26424808 -0.00033368 0.00000000 4.26391440 -4.26425494 -0.00034054 0.00000000 4.26391440 proper 10.24368720 10.24348391 -0.00020329 10.24348386 -0.00020334 10.24348821 -0.00019899 10.24347800 -0.00020920 vdw (SR) 0.00000000 -3.88846563 -3.88846563 0.00000000 0.00000000 0.00000000 0.00000000 7.48910896 7.48910896 vdw total 7.48894160 7.48892920 -0.00001240 7.48892947 -0.00001213 7.48899183 0.00005023 7.48910896 0.00016736 vdw-14 11.37755120 11.37739483 -0.00015637 0.00000000 -11.37755120 11.37746212 -0.00008908 0.00000000 -11.37755120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.46686240 3.46691436 0.00005196 3.46691437 0.00005197 3.46699243 0.00013003 3.46686240 0.00000000 bond 1.32339920 1.32324730 -0.00015190 1.32324732 -0.00015188 1.32318633 -0.00021287 1.32323184 -0.00016736 bonded 15.03394880 15.03364558 -0.00030322 15.03364554 -0.00030326 15.03366697 -0.00028183 15.03357224 -0.00037656 dihedral 10.24368720 10.24348391 -0.00020329 10.24348386 -0.00020334 10.24348821 -0.00019899 10.24347800 -0.00020920 nonbonded 11.29052400 11.29030551 -0.00021849 11.29030560 -0.00021840 11.29031536 -0.00020864 11.28177944 -0.00874456 potential 26.32447280 26.32395108 -0.00052172 26.32395106 -0.00052174 26.32387645 -0.00059635 26.31535168 -0.00912112 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 26.32447280 Difference in potential energy from amber=>gromacs conversion: -0.00052172 Difference in potential energy from amber=>lammps conversion: -0.00052174 Difference in potential energy from amber=>desmond conversion: -0.00059635 Difference in potential energy from amber=>charmm conversion: -0.00912112 ======================================================================= INFO 2017-03-18 23:18:38 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4375719.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4375719.inpcrd') INFO 2017-03-18 23:18:38 Beginning InterMol conversion INFO 2017-03-18 23:18:38 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:18:38 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:18:38 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4395315.inpcrd INFO 2017-03-18 23:18:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4395315/mobley_4395315_converted.input INFO 2017-03-18 23:18:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4395315/mobley_4395315_converted.cms WARNING 2017-03-18 23:18:54 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:18:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4395315/mobley_4395315_converted.inp INFO 2017-03-18 23:18:54 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4395315/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4395315/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4395315/mobley_4395315_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4395315/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 37.62271530 37.62271530 0.00000000 0.00000000 0.00000000 0.00000000 -83.95890544 -83.95890544 coulomb total -83.95154160 -83.95427259 -0.00273099 -83.95426957 -0.00272797 -83.95484566 -0.00330406 -83.95890544 -0.00736384 coulomb-14 -121.57281440 -121.57698789 -0.00417349 0.00000000 121.57281440 -121.57701723 -0.00420283 0.00000000 121.57281440 improper 0.00000000 0.00003469 0.00003469 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00030534 -0.00011306 0.00034002 -0.00007838 0.00034141 -0.00007699 0.00029288 -0.00012552 vdw (SR) 0.00000000 0.70225300 0.70225300 0.00000000 0.00000000 0.00000000 0.00000000 20.69695096 20.69695096 vdw total 20.69699280 20.69691674 -0.00007606 20.69691665 -0.00007615 20.69691906 -0.00007374 20.69695096 -0.00004184 vdw-14 19.99449920 19.99466374 0.00016454 0.00000000 -19.99449920 19.99464911 0.00014991 0.00000000 -19.99449920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.15269200 1.15268999 -0.00000201 1.15268999 -0.00000201 1.15276126 0.00006926 1.15269200 0.00000000 bond 1.20624720 1.20617650 -0.00007070 1.20617649 -0.00007071 1.20610887 -0.00013833 1.20616352 -0.00008368 bonded 2.35935760 2.35920652 -0.00015108 2.35920650 -0.00015110 2.35921154 -0.00014606 2.35919024 -0.00016736 dihedral 0.00041840 0.00034003 -0.00007837 0.00034002 -0.00007838 0.00034141 -0.00007699 0.00033472 -0.00008368 nonbonded -63.25454880 -63.25735585 -0.00280705 -63.25735626 -0.00280746 -63.25792660 -0.00337780 -63.26195448 -0.00740568 potential -60.89519120 -60.89814934 -0.00295814 -60.89814929 -0.00295809 -60.89878233 -0.00359113 -60.90268056 -0.00748936 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -60.89519120 Difference in potential energy from amber=>gromacs conversion: -0.00295814 Difference in potential energy from amber=>lammps conversion: -0.00295809 Difference in potential energy from amber=>desmond conversion: -0.00359113 Difference in potential energy from amber=>charmm conversion: -0.00748936 ======================================================================= INFO 2017-03-18 23:18:54 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4395315.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4395315.inpcrd') INFO 2017-03-18 23:18:54 Beginning InterMol conversion INFO 2017-03-18 23:18:54 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:18:54 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:18:54 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4463913.inpcrd INFO 2017-03-18 23:18:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4463913/mobley_4463913_converted.input INFO 2017-03-18 23:18:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4463913/mobley_4463913_converted.cms WARNING 2017-03-18 23:19:10 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:19:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4463913/mobley_4463913_converted.inp INFO 2017-03-18 23:19:10 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4463913/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4463913/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4463913/mobley_4463913_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4463913/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 287.79045746 287.79045746 0.00000000 0.00000000 0.00000000 0.00000000 -395.68313936 -395.68313936 coulomb total -395.61853840 -395.64122210 -0.02268370 -395.64121568 -0.02267728 -395.64127593 -0.02273753 -395.68313936 -0.06460096 coulomb-14 -683.40033440 -683.43167956 -0.03134516 0.00000000 683.40033440 -683.43150102 -0.03116662 0.00000000 683.40033440 improper 0.00000000 0.00003980 0.00003980 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 39.92079920 39.92056019 -0.00023901 39.92059837 -0.00020083 39.92069954 -0.00009966 39.92046448 -0.00033472 vdw (SR) 0.00000000 -4.72419935 -4.72419935 0.00000000 0.00000000 0.00000000 0.00000000 10.64556040 10.64556040 vdw total 10.64576960 10.64538614 -0.00038346 10.64538635 -0.00038325 10.64517949 -0.00059011 10.64556040 -0.00020920 vdw-14 15.36992400 15.36958549 -0.00033851 0.00000000 -15.36992400 15.36950363 -0.00042037 0.00000000 -15.36992400 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.37727680 5.37746977 0.00019297 5.37746968 0.00019288 5.37710735 -0.00016945 5.37756968 0.00029288 bond 2.46061040 2.46060111 -0.00000929 2.46060111 -0.00000929 2.46041162 -0.00019878 2.46061040 0.00000000 bonded 47.75868640 47.75867087 -0.00001553 47.75866916 -0.00001724 47.75821851 -0.00046789 47.75868640 0.00000000 dihedral 39.92079920 39.92059999 -0.00019921 39.92059837 -0.00020083 39.92069954 -0.00009966 39.92050632 -0.00029288 nonbonded -384.97276880 -384.99583596 -0.02306716 -384.99583101 -0.02306221 -384.99609644 -0.02332764 -385.03757896 -0.06481016 potential -337.21408240 -337.23716509 -0.02308269 -337.23716134 -0.02307894 -337.23795630 -0.02387390 -337.27889256 -0.06481016 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -337.21408240 Difference in potential energy from amber=>gromacs conversion: -0.02308269 Difference in potential energy from amber=>lammps conversion: -0.02307894 Difference in potential energy from amber=>desmond conversion: -0.02387390 Difference in potential energy from amber=>charmm conversion: -0.06481016 ======================================================================= INFO 2017-03-18 23:19:10 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4463913.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4463913.inpcrd') INFO 2017-03-18 23:19:10 Beginning InterMol conversion INFO 2017-03-18 23:19:10 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:19:10 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4465023.inpcrd INFO 2017-03-18 23:19:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4465023/mobley_4465023_converted.input INFO 2017-03-18 23:19:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4465023/mobley_4465023_converted.cms INFO 2017-03-18 23:19:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4465023/mobley_4465023_converted.rst7 WARNING 2017-03-18 23:19:26 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:19:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4465023/mobley_4465023_converted.inp INFO 2017-03-18 23:19:26 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4465023/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4465023/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4465023/mobley_4465023_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_4465023/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4465023/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 5.66078464 5.66078464 coulomb total 5.66220720 5.66256825 0.00036105 5.66256828 0.00036108 5.66259715 0.00038995 5.66220720 0.00000000 5.66078464 -0.00142256 coulomb-14 5.66220720 5.66256825 0.00036105 0.00000000 -5.66220720 5.66259715 0.00038995 5.66220720 0.00000000 0.00000000 -5.66220720 improper 0.00000000 0.00004860 0.00004860 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00037936 -0.00003904 0.00042795 0.00000955 0.00042745 0.00000905 0.00041840 0.00000000 0.00037656 -0.00004184 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 2.36985944 2.36985944 vdw total 2.36981760 2.36984510 0.00002750 2.36984509 0.00002749 2.36980751 -0.00001009 2.36981760 0.00000000 2.36985944 0.00004184 vdw-14 2.36981760 2.36984510 0.00002750 0.00000000 -2.36981760 2.36980751 -0.00001009 2.36981760 0.00000000 0.00000000 -2.36981760 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.76985600 0.77004281 0.00018681 0.77004282 0.00018682 0.76996920 0.00011320 0.76985600 0.00000000 0.77006520 0.00020920 bond 0.37572320 0.37586360 0.00014040 0.37586360 0.00014040 0.37574378 0.00002058 0.37572320 0.00000000 0.37584872 0.00012552 bonded 1.14599760 1.14633438 0.00033678 1.14633436 0.00033676 1.14614042 0.00014282 1.14599760 0.00000000 1.14633232 0.00033472 dihedral 0.00041840 0.00042797 0.00000957 0.00042795 0.00000955 0.00042745 0.00000905 0.00041840 0.00000000 0.00041840 0.00000000 nonbonded 8.03202480 8.03241335 0.00038855 8.03241349 0.00038869 8.03240466 0.00037986 8.03202480 0.00000000 8.03064408 -0.00138072 potential 9.17802240 9.17874773 0.00072533 9.17874749 0.00072509 9.17852691 0.00050451 9.17802240 0.00000000 9.17697640 -0.00104600 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 9.17802240 Difference in potential energy from amber=>gromacs conversion: 0.00072533 Difference in potential energy from amber=>lammps conversion: 0.00072509 Difference in potential energy from amber=>desmond conversion: 0.00050451 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.00104600 ======================================================================= INFO 2017-03-18 23:19:26 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4465023.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4465023.inpcrd') INFO 2017-03-18 23:19:26 Beginning InterMol conversion INFO 2017-03-18 23:19:26 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:19:26 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4479135.inpcrd INFO 2017-03-18 23:19:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4479135/mobley_4479135_converted.input INFO 2017-03-18 23:19:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4479135/mobley_4479135_converted.cms INFO 2017-03-18 23:19:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4479135/mobley_4479135_converted.rst7 WARNING 2017-03-18 23:19:42 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:19:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4479135/mobley_4479135_converted.inp INFO 2017-03-18 23:19:42 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4479135/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4479135/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4479135/mobley_4479135_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_4479135/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4479135/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -37.14662360 -37.14662360 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -9.07358976 -9.07358976 coulomb total -9.13199840 -9.10356364 0.02843476 -9.10356352 0.02843488 -9.10355528 0.02844312 -9.13199840 0.00000000 -9.07358976 0.05840864 coulomb-14 28.04158640 28.04305995 0.00147355 0.00000000 -28.04158640 28.04309385 0.00150745 28.04158640 0.00000000 0.00000000 -28.04158640 improper 0.00000000 0.00012119 0.00012119 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 35.15773360 35.15778789 0.00005429 35.15788046 0.00014686 35.15788326 0.00014966 35.15773360 0.00000000 35.15777544 0.00004184 vdw (SR) 0.00000000 -9.03544158 -9.03544158 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 27.38235536 27.38235536 vdw total 27.38260640 27.38237841 -0.00022799 27.38237837 -0.00022803 27.38267502 0.00006862 27.38260640 0.00000000 27.38235536 -0.00025104 vdw-14 36.41795440 36.41781999 -0.00013441 0.00000000 -36.41795440 36.41811963 0.00016523 36.41795440 0.00000000 0.00000000 -36.41795440 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 7.79060800 7.79053665 -0.00007135 7.79053645 -0.00007155 7.79088590 0.00027790 7.79060800 0.00000000 7.79048248 -0.00012552 bond 2.38822720 2.38840352 0.00017632 2.38840351 0.00017631 2.38825447 0.00002727 2.38822720 0.00000000 2.38839456 0.00016736 bonded 45.33656880 45.33684926 0.00028046 45.33682043 0.00025163 45.33702363 0.00045483 45.33656880 0.00000000 45.33677800 0.00020920 dihedral 35.15773360 35.15790909 0.00017549 35.15788046 0.00014686 35.15788326 0.00014966 35.15773360 0.00000000 35.15790096 0.00016736 nonbonded 18.25060800 18.27881477 0.02820677 18.27881485 0.02820685 18.27911974 0.02851174 18.25060800 0.00000000 18.30876560 0.05815760 potential 63.58717680 63.61566403 0.02848723 63.61563637 0.02845957 63.61601502 0.02883822 63.58717680 0.00000000 63.64550176 0.05832496 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 63.58717680 Difference in potential energy from amber=>gromacs conversion: 0.02848723 Difference in potential energy from amber=>lammps conversion: 0.02845957 Difference in potential energy from amber=>desmond conversion: 0.02883822 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.05832496 ======================================================================= INFO 2017-03-18 23:19:42 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4479135.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4479135.inpcrd') INFO 2017-03-18 23:19:42 Beginning InterMol conversion INFO 2017-03-18 23:19:42 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:19:42 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4483973.inpcrd INFO 2017-03-18 23:19:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4483973/mobley_4483973_converted.input INFO 2017-03-18 23:19:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4483973/mobley_4483973_converted.cms INFO 2017-03-18 23:19:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4483973/mobley_4483973_converted.rst7 WARNING 2017-03-18 23:19:58 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:19:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4483973/mobley_4483973_converted.inp INFO 2017-03-18 23:19:58 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4483973/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4483973/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4483973/mobley_4483973_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_4483973/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4483973/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 5.88912851 5.88912851 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -4.84000936 -4.84000936 coulomb total -4.82666240 -4.82672347 -0.00006107 -4.82672349 -0.00006109 -4.82669073 -0.00002833 -4.82666240 0.00000000 -4.84000936 -0.01334696 coulomb-14 -10.71564240 -10.71585198 -0.00020958 0.00000000 10.71564240 -10.71583244 -0.00019004 -10.71564240 0.00000000 0.00000000 10.71564240 improper 0.00000000 0.00001365 0.00001365 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00000000 0.00011705 0.00011705 0.00013069 0.00013069 0.00013367 0.00013367 0.00000000 0.00000000 0.00012552 0.00012552 vdw (SR) 0.00000000 -0.86058352 -0.86058352 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 15.01466056 15.01466056 vdw total 15.01470240 15.01470391 0.00000151 15.01470407 0.00000167 15.01476659 0.00006419 15.01470240 0.00000000 15.01466056 -0.00004184 vdw-14 15.87535120 15.87528743 -0.00006377 0.00000000 -15.87535120 15.87534944 -0.00000176 15.87535120 0.00000000 0.00000000 -15.87535120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.19957680 0.19951174 -0.00006506 0.19951174 -0.00006506 0.19945414 -0.00012266 0.19957680 0.00000000 0.19953496 -0.00004184 bond 0.76818240 0.76799492 -0.00018748 0.76799491 -0.00018749 0.76781749 -0.00036491 0.76818240 0.00000000 0.76801504 -0.00016736 bonded 0.96775920 0.96763736 -0.00012184 0.96763735 -0.00012185 0.96740529 -0.00035391 0.96775920 0.00000000 0.96767552 -0.00008368 dihedral 0.00000000 0.00013070 0.00013070 0.00013069 0.00013069 0.00013367 0.00013367 0.00000000 0.00000000 0.00012552 0.00012552 nonbonded 10.18804000 10.18798044 -0.00005956 10.18798059 -0.00005941 10.18807587 0.00003587 10.18804000 0.00000000 10.17465120 -0.01338880 potential 11.15579920 11.15561780 -0.00018140 11.15561803 -0.00018117 11.15545348 -0.00034572 11.15579920 0.00000000 11.14232672 -0.01347248 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 11.15579920 Difference in potential energy from amber=>gromacs conversion: -0.00018140 Difference in potential energy from amber=>lammps conversion: -0.00018117 Difference in potential energy from amber=>desmond conversion: -0.00034572 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.01347248 ======================================================================= INFO 2017-03-18 23:19:58 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4483973.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4483973.inpcrd') INFO 2017-03-18 23:19:58 Beginning InterMol conversion INFO 2017-03-18 23:19:58 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:19:58 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:19:58 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4494568.inpcrd INFO 2017-03-18 23:19:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4494568/mobley_4494568_converted.input INFO 2017-03-18 23:19:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4494568/mobley_4494568_converted.cms WARNING 2017-03-18 23:20:14 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:20:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4494568/mobley_4494568_converted.inp INFO 2017-03-18 23:20:14 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4494568/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4494568/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4494568/mobley_4494568_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4494568/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 7.96582068 7.96582068 0.00000000 0.00000000 0.00000000 0.00000000 -14.29212560 -14.29212560 coulomb total -14.30509600 -14.29290025 0.01219575 -14.29290006 0.01219594 -14.29289956 0.01219644 -14.29212560 0.01297040 coulomb-14 -22.25636960 -22.25872094 -0.00235134 0.00000000 22.25636960 -22.25871021 -0.00234061 0.00000000 22.25636960 improper 0.00000000 0.00005737 0.00005737 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00083680 0.00070972 -0.00012708 0.00076708 -0.00006972 0.00077160 -0.00006520 0.00071128 -0.00012552 vdw (SR) 0.00000000 -1.98360337 -1.98360337 0.00000000 0.00000000 0.00000000 0.00000000 15.46573760 15.46573760 vdw total 15.46573760 15.46573935 0.00000175 15.46573927 0.00000167 15.46582951 0.00009191 15.46573760 0.00000000 vdw-14 17.44937200 17.44934271 -0.00002929 0.00000000 -17.44937200 17.44943279 0.00006079 0.00000000 -17.44937200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.08867680 1.08851240 -0.00016440 1.08851241 -0.00016439 1.08840386 -0.00027294 1.08855128 -0.00012552 bond 1.43050960 1.43059367 0.00008407 1.43059366 0.00008406 1.43066609 0.00015649 1.43059328 0.00008368 bonded 2.52002320 2.51987316 -0.00015004 2.51987315 -0.00015005 2.51984154 -0.00018166 2.51989768 -0.00012552 dihedral 0.00083680 0.00076709 -0.00006971 0.00076708 -0.00006972 0.00077160 -0.00006520 0.00075312 -0.00008368 nonbonded 1.16064160 1.17283909 0.01219749 1.17283926 0.01219766 1.17292995 0.01228835 1.17361200 0.01297040 potential 3.68066480 3.69271225 0.01204745 3.69271242 0.01204762 3.69270685 0.01204205 3.69350968 0.01284488 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 3.68066480 Difference in potential energy from amber=>gromacs conversion: 0.01204745 Difference in potential energy from amber=>lammps conversion: 0.01204762 Difference in potential energy from amber=>desmond conversion: 0.01204205 Difference in potential energy from amber=>charmm conversion: 0.01284488 ======================================================================= INFO 2017-03-18 23:20:14 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4494568.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4494568.inpcrd') INFO 2017-03-18 23:20:14 Beginning InterMol conversion INFO 2017-03-18 23:20:14 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:20:15 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:20:15 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4506634.inpcrd INFO 2017-03-18 23:20:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4506634/mobley_4506634_converted.input INFO 2017-03-18 23:20:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4506634/mobley_4506634_converted.cms WARNING 2017-03-18 23:20:30 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:20:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4506634/mobley_4506634_converted.inp INFO 2017-03-18 23:20:30 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4506634/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4506634/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4506634/mobley_4506634_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4506634/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -2.79081168 -2.79081168 coulomb total -2.77984960 -2.78864006 -0.00879046 -2.78864002 -0.00879042 -2.78866506 -0.00881546 -2.79081168 -0.01096208 coulomb-14 -2.77984960 -2.78864006 -0.00879046 0.00000000 2.77984960 -2.78866506 -0.00881546 0.00000000 2.77984960 proper 0.01004160 0.01015930 0.00011770 0.01015929 0.00011769 0.01016191 0.00012031 0.01016712 0.00012552 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 3.67664816 3.67664816 vdw total 3.67648080 3.67670614 0.00022534 3.67670615 0.00022535 3.67675819 0.00027739 3.67664816 0.00016736 vdw-14 3.67648080 3.67670614 0.00022534 0.00000000 -3.67648080 3.67675819 0.00027739 0.00000000 -3.67648080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.69619360 1.69633128 0.00013768 1.69633130 0.00013770 1.69643303 0.00023943 1.69640280 0.00020920 bond 1.67067120 1.67063231 -0.00003889 1.67063229 -0.00003891 1.67105981 0.00038861 1.67062936 -0.00004184 bonded 3.37690640 3.37712290 0.00021650 3.37712288 0.00021648 3.37765476 0.00074836 3.37719928 0.00029288 dihedral 0.01004160 0.01015930 0.00011770 0.01015929 0.00011769 0.01016191 0.00012031 0.01016712 0.00012552 nonbonded 0.89663120 0.88806608 -0.00856512 0.88806609 -0.00856511 0.88809313 -0.00853807 0.88583648 -0.01079472 potential 4.27353760 4.26518897 -0.00834863 4.26518885 -0.00834875 4.26570858 -0.00782902 4.26303576 -0.01050184 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 4.27353760 Difference in potential energy from amber=>gromacs conversion: -0.00834863 Difference in potential energy from amber=>lammps conversion: -0.00834875 Difference in potential energy from amber=>desmond conversion: -0.00782902 Difference in potential energy from amber=>charmm conversion: -0.01050184 ======================================================================= INFO 2017-03-18 23:20:30 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4506634.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4506634.inpcrd') INFO 2017-03-18 23:20:30 Beginning InterMol conversion INFO 2017-03-18 23:20:30 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:20:31 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4553008.inpcrd INFO 2017-03-18 23:20:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4553008/mobley_4553008_converted.input INFO 2017-03-18 23:20:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4553008/mobley_4553008_converted.cms INFO 2017-03-18 23:20:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4553008/mobley_4553008_converted.rst7 WARNING 2017-03-18 23:20:46 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:20:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4553008/mobley_4553008_converted.inp INFO 2017-03-18 23:20:46 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4553008/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4553008/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4553008/mobley_4553008_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_4553008/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4553008/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -11.87112651 -11.87112651 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -9.21852352 -9.21852352 coulomb total -9.23576160 -9.21963640 0.01612520 -9.21963646 0.01612514 -9.21963570 0.01612590 -9.23576160 0.00000000 -9.21852352 0.01723808 coulomb-14 2.64512480 2.65149010 0.00636530 0.00000000 -2.64512480 2.65148420 0.00635940 2.64512480 0.00000000 0.00000000 -2.64512480 improper 0.00000000 0.00001214 0.00001214 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00000000 0.00010834 0.00010834 0.00012046 0.00012046 0.00012120 0.00012120 0.00000000 0.00000000 0.00012552 0.00012552 vdw (SR) 0.00000000 -1.59983302 -1.59983302 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 14.06740296 14.06740296 vdw total 14.06744480 14.06742545 -0.00001935 14.06742555 -0.00001925 14.06747964 0.00003484 14.06744480 0.00000000 14.06740296 -0.00004184 vdw-14 15.66740640 15.66725846 -0.00014794 0.00000000 -15.66740640 15.66731042 -0.00009598 15.66740640 0.00000000 0.00000000 -15.66740640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.40794000 0.40796933 0.00002933 0.40796933 0.00002933 0.40795996 0.00001996 0.40794000 0.00000000 0.40798184 0.00004184 bond 0.90123360 0.90109810 -0.00013550 0.90109808 -0.00013552 0.90081956 -0.00041404 0.90123360 0.00000000 0.90110808 -0.00012552 bonded 1.30917360 1.30918791 0.00001431 1.30918787 0.00001427 1.30890072 -0.00027288 1.30917360 0.00000000 1.30921544 0.00004184 dihedral 0.00000000 0.00012048 0.00012048 0.00012046 0.00012046 0.00012120 0.00012120 0.00000000 0.00000000 0.00012552 0.00012552 nonbonded 4.83168320 4.84778904 0.01610584 4.84778909 0.01610589 4.84784393 0.01616073 4.83168320 0.00000000 4.84887944 0.01719624 potential 6.14085680 6.15697695 0.01612015 6.15697692 0.01612012 6.15668876 0.01583196 6.14085680 0.00000000 6.15809488 0.01723808 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 6.14085680 Difference in potential energy from amber=>gromacs conversion: 0.01612015 Difference in potential energy from amber=>lammps conversion: 0.01612012 Difference in potential energy from amber=>desmond conversion: 0.01583196 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.01723808 ======================================================================= INFO 2017-03-18 23:20:46 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4553008.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4553008.inpcrd') INFO 2017-03-18 23:20:47 Beginning InterMol conversion INFO 2017-03-18 23:20:47 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:20:47 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:20:47 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4561957.inpcrd INFO 2017-03-18 23:20:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4561957/mobley_4561957_converted.input INFO 2017-03-18 23:20:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4561957/mobley_4561957_converted.cms WARNING 2017-03-18 23:21:02 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:21:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4561957/mobley_4561957_converted.inp INFO 2017-03-18 23:21:02 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4561957/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4561957/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4561957/mobley_4561957_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4561957/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 1.99615130 1.99615130 0.00000000 0.00000000 0.00000000 0.00000000 -7.73035840 -7.73035840 coulomb total -7.75797280 -7.73065898 0.02731382 -7.73065881 0.02731399 -7.73066992 0.02730288 -7.73035840 0.02761440 coulomb-14 -9.71775840 -9.72681028 -0.00905188 0.00000000 9.71775840 -9.72682007 -0.00906167 0.00000000 9.71775840 proper 8.91652240 8.91638951 -0.00013289 8.91639186 -0.00013054 8.91641031 -0.00011209 8.91639688 -0.00012552 vdw (SR) 0.00000000 4.86787628 4.86787628 0.00000000 0.00000000 0.00000000 0.00000000 14.45471584 14.45471584 vdw total 14.45488320 14.45452290 -0.00036030 14.45452296 -0.00036024 14.45452392 -0.00035928 14.45471584 -0.00016736 vdw-14 9.58679920 9.58664661 -0.00015259 0.00000000 -9.58679920 9.58659050 -0.00020870 0.00000000 -9.58679920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 7.02158880 7.02179739 0.00020859 7.02179758 0.00020878 7.02182557 0.00023677 7.02179800 0.00020920 bond 0.71337200 0.71342291 0.00005091 0.71342292 0.00005092 0.71320451 -0.00016749 0.71341384 0.00004184 bonded 16.65148320 16.65160981 0.00012661 16.65161236 0.00012916 16.65144040 -0.00004280 16.65160872 0.00012552 dihedral 8.91652240 8.91638951 -0.00013289 8.91639186 -0.00013054 8.91641031 -0.00011209 8.91639688 -0.00012552 nonbonded 6.69691040 6.72386392 0.02695352 6.72386415 0.02695375 6.72385400 0.02694360 6.72435744 0.02744704 potential 23.34839360 23.37547373 0.02708013 23.37547663 0.02708303 23.37524651 0.02685291 23.37596616 0.02757256 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 23.34839360 Difference in potential energy from amber=>gromacs conversion: 0.02708013 Difference in potential energy from amber=>lammps conversion: 0.02708303 Difference in potential energy from amber=>desmond conversion: 0.02685291 Difference in potential energy from amber=>charmm conversion: 0.02757256 ======================================================================= INFO 2017-03-18 23:21:02 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4561957.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4561957.inpcrd') INFO 2017-03-18 23:21:03 Beginning InterMol conversion INFO 2017-03-18 23:21:03 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:21:03 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:21:03 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4584540.inpcrd INFO 2017-03-18 23:21:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4584540/mobley_4584540_converted.input INFO 2017-03-18 23:21:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4584540/mobley_4584540_converted.cms WARNING 2017-03-18 23:21:18 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:21:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4584540/mobley_4584540_converted.inp INFO 2017-03-18 23:21:19 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4584540/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4584540/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4584540/mobley_4584540_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4584540/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 73.46066891 73.46066891 0.00000000 0.00000000 0.00000000 0.00000000 -191.78393264 -191.78393264 coulomb total -191.78075280 -191.78013005 0.00062275 -191.78012938 0.00062342 -191.78031055 0.00044225 -191.78393264 -0.00317984 coulomb-14 -265.28819360 -265.24079896 0.04739464 0.00000000 265.28819360 -265.24103741 0.04715619 0.00000000 265.28819360 improper 0.00000000 0.00016493 0.00016493 0.00000000 0.00000000 0.00000000 0.00000000 0.00016736 0.00016736 proper 0.00167360 0.00159657 -0.00007703 0.00176154 0.00008794 0.00176216 0.00008856 0.00158992 -0.00008368 vdw (SR) 0.00000000 -2.53190896 -2.53190896 0.00000000 0.00000000 0.00000000 0.00000000 21.34509440 21.34509440 vdw total 21.34509440 21.34512476 0.00003036 21.34512494 0.00003054 21.34555715 0.00046275 21.34509440 0.00000000 vdw-14 23.87683280 23.87703372 0.00020092 0.00000000 -23.87683280 23.87746776 0.00063496 0.00000000 -23.87683280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.11584880 2.11604142 0.00019262 2.11604143 0.00019263 2.11592546 0.00007666 2.11605800 0.00020920 bond 1.87359520 1.87356761 -0.00002759 1.87356763 -0.00002757 1.87304599 -0.00054921 1.87355336 -0.00004184 bonded 3.99111760 3.99137053 0.00025293 3.99137060 0.00025300 3.99073361 -0.00038399 3.99136864 0.00025104 dihedral 0.00167360 0.00176151 0.00008791 0.00176154 0.00008794 0.00176216 0.00008856 0.00175728 0.00008368 nonbonded -170.43565840 -170.43500529 0.00065311 -170.43500151 0.00065689 -170.43475340 0.00090500 -170.43883824 -0.00317984 potential -166.44454080 -166.44363476 0.00090604 -166.44363287 0.00090793 -166.44408140 0.00045940 -166.44742776 -0.00288696 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -166.44454080 Difference in potential energy from amber=>gromacs conversion: 0.00090604 Difference in potential energy from amber=>lammps conversion: 0.00090793 Difference in potential energy from amber=>desmond conversion: 0.00045940 Difference in potential energy from amber=>charmm conversion: -0.00288696 ======================================================================= INFO 2017-03-18 23:21:19 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4584540.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4584540.inpcrd') INFO 2017-03-18 23:21:19 Beginning InterMol conversion INFO 2017-03-18 23:21:19 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:21:19 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:21:19 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4587267.inpcrd INFO 2017-03-18 23:21:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4587267/mobley_4587267_converted.input INFO 2017-03-18 23:21:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4587267/mobley_4587267_converted.cms WARNING 2017-03-18 23:21:35 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:21:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4587267/mobley_4587267_converted.inp INFO 2017-03-18 23:21:35 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4587267/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4587267/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4587267/mobley_4587267_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4587267/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -421.40999083 -421.40999083 0.00000000 0.00000000 0.00000000 0.00000000 215.84004984 215.84004984 coulomb total 215.84879440 215.85592166 0.00712726 215.85591975 0.00712535 215.85653062 0.00773622 215.84004984 -0.00874456 coulomb-14 637.24412000 637.26591250 0.02179250 0.00000000 -637.24412000 637.26549606 0.02137606 0.00000000 -637.24412000 proper 53.48867440 53.48861659 -0.00005781 53.48861582 -0.00005858 53.48857691 -0.00009749 53.48905096 0.00037656 vdw (SR) 0.00000000 -4.31128359 -4.31128359 0.00000000 0.00000000 0.00000000 0.00000000 11.03224568 11.03224568 vdw total 11.03237120 11.03189905 -0.00047215 11.03189924 -0.00047196 11.03188661 -0.00048459 11.03224568 -0.00012552 vdw-14 15.34356480 15.34318264 -0.00038216 0.00000000 -15.34356480 15.34311535 -0.00044945 0.00000000 -15.34356480 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 11.89260160 11.89280352 0.00020192 11.89280369 0.00020209 11.89300933 0.00040773 11.89264344 0.00004184 bond 0.73429200 0.73445849 0.00016649 0.73445848 0.00016648 0.73435083 0.00005883 0.73445936 0.00016736 bonded 66.11556800 66.11587860 0.00031060 66.11587799 0.00030999 66.11593707 0.00036907 66.11615376 0.00058576 dihedral 53.48867440 53.48861659 -0.00005781 53.48861582 -0.00005858 53.48857691 -0.00009749 53.48905096 0.00037656 nonbonded 226.88116560 226.88782072 0.00665512 226.88781816 0.00665256 226.88841723 0.00725163 226.87229552 -0.00887008 potential 292.99673360 293.00369932 0.00696572 293.00369578 0.00696218 293.00426815 0.00753455 292.98849112 -0.00824248 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 292.99673360 Difference in potential energy from amber=>gromacs conversion: 0.00696572 Difference in potential energy from amber=>lammps conversion: 0.00696218 Difference in potential energy from amber=>desmond conversion: 0.00753455 Difference in potential energy from amber=>charmm conversion: -0.00824248 ======================================================================= INFO 2017-03-18 23:21:35 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4587267.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4587267.inpcrd') INFO 2017-03-18 23:21:35 Beginning InterMol conversion INFO 2017-03-18 23:21:35 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:21:35 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:21:35 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4603202.inpcrd INFO 2017-03-18 23:21:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4603202/mobley_4603202_converted.input INFO 2017-03-18 23:21:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4603202/mobley_4603202_converted.cms WARNING 2017-03-18 23:21:51 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:21:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4603202/mobley_4603202_converted.inp INFO 2017-03-18 23:21:51 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4603202/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4603202/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4603202/mobley_4603202_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4603202/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 2.49215363 2.49215363 0.00000000 0.00000000 0.00000000 0.00000000 21.97729680 21.97729680 coulomb total 21.97646000 21.97877204 0.00231204 21.97877166 0.00231166 21.97874826 0.00228826 21.97729680 0.00083680 coulomb-14 19.48865360 19.48661840 -0.00203520 0.00000000 -19.48865360 19.48656926 -0.00208434 0.00000000 -19.48865360 proper 6.32160560 6.32148689 -0.00011871 6.32148677 -0.00011883 6.32149071 -0.00011489 6.32148008 -0.00012552 vdw (SR) 0.00000000 -2.92734967 -2.92734967 0.00000000 0.00000000 0.00000000 0.00000000 2.14911160 2.14911160 vdw total 2.14890240 2.14901766 0.00011526 2.14901767 0.00011527 2.14894237 0.00003997 2.14911160 0.00020920 vdw-14 5.07644720 5.07636733 -0.00007987 0.00000000 -5.07644720 5.07627503 -0.00017217 0.00000000 -5.07644720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.55812160 1.55812473 0.00000313 1.55812474 0.00000314 1.55816523 0.00004363 1.55820528 0.00008368 bond 1.62506560 1.62520105 0.00013545 1.62520104 0.00013544 1.62536301 0.00029741 1.62519112 0.00012552 bonded 9.50479280 9.50481268 0.00001988 9.50481255 0.00001975 9.50501895 0.00022615 9.50487648 0.00008368 dihedral 6.32160560 6.32148689 -0.00011871 6.32148677 -0.00011883 6.32149071 -0.00011489 6.32148008 -0.00012552 nonbonded 24.12536240 24.12778969 0.00242729 24.12778954 0.00242714 24.12769063 0.00232823 24.12640840 0.00104600 potential 33.63015520 33.63260237 0.00244717 33.63260200 0.00244680 33.63265631 0.00250111 33.63128488 0.00112968 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 33.63015520 Difference in potential energy from amber=>gromacs conversion: 0.00244717 Difference in potential energy from amber=>lammps conversion: 0.00244680 Difference in potential energy from amber=>desmond conversion: 0.00250111 Difference in potential energy from amber=>charmm conversion: 0.00112968 ======================================================================= INFO 2017-03-18 23:21:51 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4603202.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4603202.inpcrd') INFO 2017-03-18 23:21:51 Beginning InterMol conversion INFO 2017-03-18 23:21:51 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:21:51 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:21:51 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4609460.inpcrd INFO 2017-03-18 23:21:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4609460/mobley_4609460_converted.input INFO 2017-03-18 23:21:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4609460/mobley_4609460_converted.cms WARNING 2017-03-18 23:22:07 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:22:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4609460/mobley_4609460_converted.inp INFO 2017-03-18 23:22:07 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4609460/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4609460/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4609460/mobley_4609460_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4609460/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 20.18690572 20.18690572 0.00000000 0.00000000 0.00000000 0.00000000 -130.47247528 -130.47247528 coulomb total -130.45000720 -130.45433393 -0.00432673 -130.45433346 -0.00432626 -130.45446178 -0.00445458 -130.47247528 -0.02246808 coulomb-14 -150.63613360 -150.64123965 -0.00510605 0.00000000 150.63613360 -150.64117239 -0.00503879 0.00000000 150.63613360 improper 0.00000000 0.00003777 0.00003777 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 18.22843280 18.22855494 0.00012214 18.22857255 0.00013975 18.22856422 0.00013142 18.22851648 0.00008368 vdw (SR) 0.00000000 -2.84639399 -2.84639399 0.00000000 0.00000000 0.00000000 0.00000000 25.96134344 25.96134344 vdw total 25.96130160 25.96121930 -0.00008230 25.96121918 -0.00008242 25.96111201 -0.00018959 25.96134344 0.00004184 vdw-14 28.80767680 28.80761329 -0.00006351 0.00000000 -28.80767680 28.80756505 -0.00011175 0.00000000 -28.80767680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.64761120 3.64754087 -0.00007033 3.64754087 -0.00007033 3.64748643 -0.00012477 3.64756936 -0.00004184 bond 3.42251200 3.42246371 -0.00004829 3.42246372 -0.00004828 3.42244215 -0.00006985 3.42247016 -0.00004184 bonded 25.29855600 25.29859729 0.00004129 25.29857713 0.00002113 25.29849280 -0.00006320 25.29859784 0.00004184 dihedral 18.22843280 18.22859271 0.00015991 18.22857255 0.00013975 18.22856422 0.00013142 18.22855832 0.00012552 nonbonded -104.48870560 -104.49311463 -0.00440903 -104.49311135 -0.00440575 -104.49334977 -0.00464417 -104.51113184 -0.02242624 potential -79.19014960 -79.19451734 -0.00436774 -79.19453443 -0.00438483 -79.19495325 -0.00480365 -79.21257584 -0.02242624 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -79.19014960 Difference in potential energy from amber=>gromacs conversion: -0.00436774 Difference in potential energy from amber=>lammps conversion: -0.00438483 Difference in potential energy from amber=>desmond conversion: -0.00480365 Difference in potential energy from amber=>charmm conversion: -0.02242624 ======================================================================= INFO 2017-03-18 23:22:07 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4609460.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4609460.inpcrd') INFO 2017-03-18 23:22:07 Beginning InterMol conversion INFO 2017-03-18 23:22:07 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:22:07 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:22:07 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4613090.inpcrd INFO 2017-03-18 23:22:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4613090/mobley_4613090_converted.input INFO 2017-03-18 23:22:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4613090/mobley_4613090_converted.cms WARNING 2017-03-18 23:22:23 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:22:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4613090/mobley_4613090_converted.inp INFO 2017-03-18 23:22:23 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4613090/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4613090/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4613090/mobley_4613090_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4613090/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 13.27654664 13.27654664 0.00000000 0.00000000 0.00000000 0.00000000 7.86625472 7.86625472 coulomb total 7.90524960 7.89625549 -0.00899411 7.89625526 -0.00899434 7.89627860 -0.00897100 7.86625472 -0.03899488 coulomb-14 -5.37685840 -5.38029116 -0.00343276 0.00000000 5.37685840 -5.38020719 -0.00334879 0.00000000 5.37685840 improper 0.00000000 0.00010869 0.00010869 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00125520 0.00103548 -0.00021972 0.00114412 -0.00011108 0.00114119 -0.00011401 0.00104600 -0.00020920 vdw (SR) 0.00000000 -7.52641585 -7.52641585 0.00000000 0.00000000 0.00000000 0.00000000 9.50219872 9.50219872 vdw total 9.50186400 9.50221170 0.00034770 9.50221169 0.00034769 9.50228596 0.00042196 9.50219872 0.00033472 vdw-14 17.02846160 17.02862755 0.00016595 0.00000000 -17.02846160 17.02869921 0.00023761 0.00000000 -17.02846160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 11.96080080 11.96098543 0.00018463 11.96098531 0.00018451 11.96128686 0.00048606 11.96092632 0.00012552 bond 10.18134560 10.18118030 -0.00016530 10.18118033 -0.00016527 10.18227842 0.00093282 10.18117824 -0.00016736 bonded 22.14340160 22.14330991 -0.00009169 22.14330977 -0.00009183 22.14470647 0.00130487 22.14327608 -0.00012552 dihedral 0.00125520 0.00114417 -0.00011103 0.00114412 -0.00011108 0.00114119 -0.00011401 0.00117152 -0.00008368 nonbonded 17.40711360 17.39846719 -0.00864641 17.39846695 -0.00864665 17.39856456 -0.00854904 17.36845344 -0.03866016 potential 39.55051520 39.54177710 -0.00873810 39.54177692 -0.00873828 39.54316776 -0.00734744 39.51172952 -0.03878568 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 39.55051520 Difference in potential energy from amber=>gromacs conversion: -0.00873810 Difference in potential energy from amber=>lammps conversion: -0.00873828 Difference in potential energy from amber=>desmond conversion: -0.00734744 Difference in potential energy from amber=>charmm conversion: -0.03878568 ======================================================================= INFO 2017-03-18 23:22:23 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4613090.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4613090.inpcrd') INFO 2017-03-18 23:22:23 Beginning InterMol conversion INFO 2017-03-18 23:22:23 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:22:23 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:22:23 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4620651.inpcrd INFO 2017-03-18 23:22:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4620651/mobley_4620651_converted.input INFO 2017-03-18 23:22:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4620651/mobley_4620651_converted.cms WARNING 2017-03-18 23:22:39 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:22:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4620651/mobley_4620651_converted.inp INFO 2017-03-18 23:22:39 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4620651/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4620651/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4620651/mobley_4620651_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4620651/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -153.89575802 -153.89575802 0.00000000 0.00000000 0.00000000 0.00000000 -9.23509216 -9.23509216 coulomb total -9.20438160 -9.20458077 -0.00019917 -9.20458076 -0.00019916 -9.20460712 -0.00022552 -9.23509216 -0.03071056 coulomb-14 144.67769920 144.69117725 0.01347805 0.00000000 -144.67769920 144.69115076 0.01345156 0.00000000 -144.67769920 improper 0.00000000 0.00002781 0.00002781 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 27.03784480 27.03772940 -0.00011540 27.03775735 -0.00008745 27.03773702 -0.00010778 27.04562704 0.00778224 vdw (SR) 0.00000000 -1.36409278 -1.36409278 0.00000000 0.00000000 0.00000000 0.00000000 6.20989280 6.20989280 vdw total 6.20989280 6.20982759 -0.00006521 6.20982753 -0.00006527 6.20983960 -0.00005320 6.20989280 0.00000000 vdw-14 7.57387680 7.57392037 0.00004357 0.00000000 -7.57387680 7.57394605 0.00006925 0.00000000 -7.57387680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.84846720 2.84830708 -0.00016012 2.84830708 -0.00016012 2.84821725 -0.00024995 2.84834168 -0.00012552 bond 1.84054160 1.84067863 0.00013703 1.84067863 0.00013703 1.83980350 -0.00073810 1.84066712 0.00012552 bonded 31.72685360 31.72674292 -0.00011068 31.72674306 -0.00011054 31.72575777 -0.00109583 31.73467768 0.00782408 dihedral 27.03784480 27.03775721 -0.00008759 27.03775735 -0.00008745 27.03773702 -0.00010778 27.04566888 0.00782408 nonbonded -2.99448880 -2.99475318 -0.00026438 -2.99475298 -0.00026418 -2.99476751 -0.00027871 -3.02519936 -0.03071056 potential 28.73236480 28.73198973 -0.00037507 28.73198991 -0.00037489 28.73094772 -0.00141708 28.70952016 -0.02284464 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 28.73236480 Difference in potential energy from amber=>gromacs conversion: -0.00037507 Difference in potential energy from amber=>lammps conversion: -0.00037489 Difference in potential energy from amber=>desmond conversion: -0.00141708 Difference in potential energy from amber=>charmm conversion: -0.02284464 ======================================================================= INFO 2017-03-18 23:22:39 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4620651.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4620651.inpcrd') INFO 2017-03-18 23:22:39 Beginning InterMol conversion INFO 2017-03-18 23:22:39 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:22:39 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:22:39 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4630641.inpcrd INFO 2017-03-18 23:22:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4630641/mobley_4630641_converted.input INFO 2017-03-18 23:22:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4630641/mobley_4630641_converted.cms WARNING 2017-03-18 23:22:55 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:22:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4630641/mobley_4630641_converted.inp INFO 2017-03-18 23:22:55 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4630641/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4630641/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4630641/mobley_4630641_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4630641/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -21.26250615 -21.26250615 0.00000000 0.00000000 0.00000000 0.00000000 53.94539984 53.94539984 coulomb total 53.95728240 53.94253242 -0.01474998 53.94253380 -0.01474860 53.94256300 -0.01471940 53.94539984 -0.01188256 coulomb-14 75.20279760 75.20503857 0.00224097 0.00000000 -75.20279760 75.20507955 0.00228195 0.00000000 -75.20279760 proper 5.65383920 5.65388542 0.00004622 5.65388522 0.00004602 5.65390196 0.00006276 5.65388104 0.00004184 vdw (SR) 0.00000000 -1.81607534 -1.81607534 0.00000000 0.00000000 0.00000000 0.00000000 5.48355040 5.48355040 vdw total 5.48396880 5.48346319 -0.00050561 5.48346337 -0.00050543 5.48344172 -0.00052708 5.48355040 -0.00041840 vdw-14 7.29982480 7.29953852 -0.00028628 0.00000000 -7.29982480 7.29950820 -0.00031660 0.00000000 -7.29982480 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.59538320 0.59555014 0.00016694 0.59555014 0.00016694 0.59561444 0.00023124 0.59555056 0.00016736 bond 2.01292240 2.01309602 0.00017362 2.01309604 0.00017364 2.01322440 0.00030200 2.01308976 0.00016736 bonded 8.26214480 8.26253157 0.00038677 8.26253140 0.00038660 8.26274080 0.00059600 8.26252136 0.00037656 dihedral 5.65383920 5.65388542 0.00004622 5.65388522 0.00004602 5.65390196 0.00006276 5.65388104 0.00004184 nonbonded 59.44125120 59.42599561 -0.01525559 59.42599634 -0.01525486 59.42600472 -0.01524648 59.42895024 -0.01230096 potential 67.70339600 67.68852718 -0.01486882 67.68852606 -0.01486994 67.68870681 -0.01468919 67.69151344 -0.01188256 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 67.70339600 Difference in potential energy from amber=>gromacs conversion: -0.01486882 Difference in potential energy from amber=>lammps conversion: -0.01486994 Difference in potential energy from amber=>desmond conversion: -0.01468919 Difference in potential energy from amber=>charmm conversion: -0.01188256 ======================================================================= INFO 2017-03-18 23:22:55 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4630641.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4630641.inpcrd') INFO 2017-03-18 23:22:55 Beginning InterMol conversion INFO 2017-03-18 23:22:55 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:22:55 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:22:55 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4639255.inpcrd INFO 2017-03-18 23:22:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4639255/mobley_4639255_converted.input INFO 2017-03-18 23:22:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4639255/mobley_4639255_converted.cms WARNING 2017-03-18 23:23:11 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:23:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4639255/mobley_4639255_converted.inp INFO 2017-03-18 23:23:11 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4639255/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4639255/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4639255/mobley_4639255_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4639255/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -112.97580627 -112.97580627 0.00000000 0.00000000 0.00000000 0.00000000 69.19185400 69.19185400 coulomb total 69.14645760 69.13361083 -0.01284677 69.13360854 -0.01284906 69.13371732 -0.01274028 69.19185400 0.04539640 coulomb-14 182.10357920 182.10941710 0.00583790 0.00000000 -182.10357920 182.10954893 0.00596973 0.00000000 -182.10357920 proper 5.63542960 5.63527378 -0.00015582 5.63527396 -0.00015564 5.63527211 -0.00015749 5.63526224 -0.00016736 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 2.46454336 2.46454336 vdw total 2.46437600 2.46445913 0.00008313 2.46445918 0.00008318 2.46447181 0.00009581 2.46454336 0.00016736 vdw-14 2.46437600 2.46445913 0.00008313 0.00000000 -2.46437600 2.46447181 0.00009581 0.00000000 -2.46437600 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.16315200 1.16311122 -0.00004078 1.16311121 -0.00004079 1.16302308 -0.00012892 1.16306832 -0.00008368 bond 0.51505040 0.51494820 -0.00010220 0.51494818 -0.00010222 0.51526719 0.00021679 0.51496672 -0.00008368 bonded 7.31363200 7.31333320 -0.00029880 7.31333335 -0.00029865 7.31356239 -0.00006961 7.31329728 -0.00033472 dihedral 5.63542960 5.63527378 -0.00015582 5.63527396 -0.00015564 5.63527211 -0.00015749 5.63526224 -0.00016736 nonbonded 71.61083360 71.59806996 -0.01276364 71.59806822 -0.01276538 71.59818913 -0.01264447 71.65639736 0.04556376 potential 78.92446560 78.91140315 -0.01306245 78.91140315 -0.01306245 78.91173871 -0.01272689 78.96965280 0.04518720 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 78.92446560 Difference in potential energy from amber=>gromacs conversion: -0.01306245 Difference in potential energy from amber=>lammps conversion: -0.01306245 Difference in potential energy from amber=>desmond conversion: -0.01272689 Difference in potential energy from amber=>charmm conversion: 0.04518720 ======================================================================= INFO 2017-03-18 23:23:11 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4639255.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4639255.inpcrd') INFO 2017-03-18 23:23:11 Beginning InterMol conversion INFO 2017-03-18 23:23:11 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:23:12 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:23:12 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4678740.inpcrd INFO 2017-03-18 23:23:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4678740/mobley_4678740_converted.input INFO 2017-03-18 23:23:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4678740/mobley_4678740_converted.cms WARNING 2017-03-18 23:23:27 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:23:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4678740/mobley_4678740_converted.inp INFO 2017-03-18 23:23:27 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4678740/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4678740/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4678740/mobley_4678740_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4678740/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -51.53564932 -51.53564932 0.00000000 0.00000000 0.00000000 0.00000000 54.41317104 54.41317104 coulomb total 54.34430240 54.35252501 0.00822261 54.35252396 0.00822156 54.35310093 0.00879853 54.41317104 0.06886864 coulomb-14 105.87151760 105.88817433 0.01665673 0.00000000 -105.87151760 105.88815737 0.01663977 0.00000000 -105.87151760 improper 0.00000000 0.00008157 0.00008157 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00083680 0.00079254 -0.00004426 0.00087407 0.00003727 0.00087734 0.00004054 0.00079496 -0.00004184 vdw (SR) 0.00000000 1.35013390 1.35013390 0.00000000 0.00000000 0.00000000 0.00000000 26.56116168 26.56116168 vdw total 26.56128720 26.56133438 0.00004718 26.56133448 0.00004728 26.56138544 0.00009824 26.56116168 -0.00012552 vdw-14 25.21111040 25.21120047 0.00009007 0.00000000 -25.21111040 25.21132077 0.00021037 0.00000000 -25.21111040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.16603280 3.16585876 -0.00017404 3.16585875 -0.00017405 3.16594778 -0.00008502 3.16582360 -0.00020920 bond 6.15675600 6.15669404 -0.00006196 6.15669408 -0.00006192 6.15692897 0.00017297 6.15671416 -0.00004184 bonded 9.32362560 9.32342691 -0.00019869 9.32342690 -0.00019870 9.32375408 0.00012848 9.32341640 -0.00020920 dihedral 0.00083680 0.00087411 0.00003731 0.00087407 0.00003727 0.00087734 0.00004054 0.00087864 0.00004184 nonbonded 80.90558960 80.91385938 0.00826978 80.91385718 0.00826758 80.91448638 0.00889678 80.97433272 0.06874312 potential 90.22921520 90.23728630 0.00807110 90.23728614 0.00807094 90.23815934 0.00894414 90.29774912 0.06853392 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 90.22921520 Difference in potential energy from amber=>gromacs conversion: 0.00807110 Difference in potential energy from amber=>lammps conversion: 0.00807094 Difference in potential energy from amber=>desmond conversion: 0.00894414 Difference in potential energy from amber=>charmm conversion: 0.06853392 ======================================================================= INFO 2017-03-18 23:23:27 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4678740.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4678740.inpcrd') INFO 2017-03-18 23:23:28 Beginning InterMol conversion INFO 2017-03-18 23:23:28 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:23:28 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:23:28 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4683624.inpcrd INFO 2017-03-18 23:23:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4683624/mobley_4683624_converted.input INFO 2017-03-18 23:23:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4683624/mobley_4683624_converted.cms WARNING 2017-03-18 23:23:43 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:23:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4683624/mobley_4683624_converted.inp INFO 2017-03-18 23:23:43 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4683624/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4683624/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4683624/mobley_4683624_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4683624/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 24.99676562 24.99676562 0.00000000 0.00000000 0.00000000 0.00000000 -72.64536944 -72.64536944 coulomb total -72.66227280 -72.64959049 0.01268231 -72.64959110 0.01268170 -72.65016811 0.01210469 -72.64536944 0.01690336 coulomb-14 -97.64033440 -97.64635611 -0.00602171 0.00000000 97.64033440 -97.64635810 -0.00602370 0.00000000 97.64033440 improper 0.00000000 0.00007364 0.00007364 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.04476880 0.04460148 -0.00016732 0.04467506 -0.00009374 0.04468146 -0.00008734 0.04460144 -0.00016736 vdw (SR) 0.00000000 -4.56352840 -4.56352840 0.00000000 0.00000000 0.00000000 0.00000000 16.45583936 16.45583936 vdw total 16.45567200 16.45577225 0.00010025 16.45577242 0.00010042 16.45579898 0.00012698 16.45583936 0.00016736 vdw-14 21.01916080 21.01930065 0.00013985 0.00000000 -21.01916080 21.01933511 0.00017431 0.00000000 -21.01916080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.90876480 0.90889014 0.00012534 0.90889015 0.00012535 0.90889260 0.00012780 0.90884848 0.00008368 bond 1.86188000 1.86179465 -0.00008535 1.86179465 -0.00008535 1.86237438 0.00049438 1.86179632 -0.00008368 bonded 2.81541360 2.81535991 -0.00005369 2.81535986 -0.00005374 2.81594844 0.00053484 2.81532992 -0.00008368 dihedral 0.04476880 0.04467512 -0.00009368 0.04467506 -0.00009374 0.04468146 -0.00008734 0.04468512 -0.00008368 nonbonded -56.20660080 -56.19381824 0.01278256 -56.19381868 0.01278212 -56.19436913 0.01223167 -56.18953008 0.01707072 potential -53.39118720 -53.37845833 0.01272887 -53.37845947 0.01272773 -53.37850884 0.01267836 -53.37424200 0.01694520 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -53.39118720 Difference in potential energy from amber=>gromacs conversion: 0.01272887 Difference in potential energy from amber=>lammps conversion: 0.01272773 Difference in potential energy from amber=>desmond conversion: 0.01267836 Difference in potential energy from amber=>charmm conversion: 0.01694520 ======================================================================= INFO 2017-03-18 23:23:43 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4683624.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4683624.inpcrd') INFO 2017-03-18 23:23:44 Beginning InterMol conversion INFO 2017-03-18 23:23:44 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:23:44 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:23:44 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4687447.inpcrd INFO 2017-03-18 23:23:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4687447/mobley_4687447_converted.input INFO 2017-03-18 23:23:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4687447/mobley_4687447_converted.cms WARNING 2017-03-18 23:23:59 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:23:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4687447/mobley_4687447_converted.inp INFO 2017-03-18 23:23:59 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4687447/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4687447/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4687447/mobley_4687447_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4687447/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -68.14226484 -68.14226484 0.00000000 0.00000000 0.00000000 0.00000000 54.60299912 54.60299912 coulomb total 54.58990320 54.59158679 0.00168359 54.59158517 0.00168197 54.59155002 0.00164682 54.60299912 0.01309592 coulomb-14 122.72969040 122.73385163 0.00416123 0.00000000 -122.72969040 122.73379323 0.00410283 0.00000000 -122.72969040 proper 8.88137680 8.88157338 0.00019658 8.88157345 0.00019665 8.88162512 0.00024832 8.88158600 0.00020920 vdw (SR) 0.00000000 -2.64705164 -2.64705164 0.00000000 0.00000000 0.00000000 0.00000000 3.89074344 3.89074344 vdw total 3.89070160 3.89063359 -0.00006801 3.89063361 -0.00006799 3.89056968 -0.00013192 3.89074344 0.00004184 vdw-14 6.53791840 6.53768523 -0.00023317 0.00000000 -6.53791840 6.53762544 -0.00029296 0.00000000 -6.53791840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.51544480 1.51536577 -0.00007903 1.51536576 -0.00007904 1.51507019 -0.00037461 1.51536112 -0.00008368 bond 2.06522240 2.06502190 -0.00020050 2.06502190 -0.00020050 2.06512149 -0.00010091 2.06501320 -0.00020920 bonded 12.46204400 12.46196105 -0.00008295 12.46196111 -0.00008289 12.46181680 -0.00022720 12.46196032 -0.00008368 dihedral 8.88137680 8.88157338 0.00019658 8.88157345 0.00019665 8.88162512 0.00024832 8.88158600 0.00020920 nonbonded 58.48060480 58.48222038 0.00161558 58.48221982 0.00161502 58.48211971 0.00151491 58.49374256 0.01313776 potential 70.94264880 70.94418143 0.00153263 70.94418014 0.00153134 70.94388224 0.00123344 70.95570288 0.01305408 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 70.94264880 Difference in potential energy from amber=>gromacs conversion: 0.00153263 Difference in potential energy from amber=>lammps conversion: 0.00153134 Difference in potential energy from amber=>desmond conversion: 0.00123344 Difference in potential energy from amber=>charmm conversion: 0.01305408 ======================================================================= INFO 2017-03-18 23:23:59 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4687447.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4687447.inpcrd') INFO 2017-03-18 23:24:00 Beginning InterMol conversion INFO 2017-03-18 23:24:00 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:24:00 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:24:00 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_468867.inpcrd INFO 2017-03-18 23:24:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_468867/mobley_468867_converted.input INFO 2017-03-18 23:24:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_468867/mobley_468867_converted.cms WARNING 2017-03-18 23:24:16 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:24:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_468867/mobley_468867_converted.inp INFO 2017-03-18 23:24:16 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_468867/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_468867/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_468867/mobley_468867_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_468867/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 1.32896995 1.32896995 0.00000000 0.00000000 0.00000000 0.00000000 23.56684024 23.56684024 coulomb total 23.56930880 23.57247790 0.00316910 23.57247776 0.00316896 23.57247736 0.00316856 23.56684024 -0.00246856 coulomb-14 22.24172560 22.24350795 0.00178235 0.00000000 -22.24172560 22.24346878 0.00174318 0.00000000 -22.24172560 improper 0.00000000 0.01375589 0.01375589 0.00000000 0.00000000 0.00000000 0.00000000 0.01376536 0.01376536 proper 49.93394800 49.92010388 -0.01384412 49.93386432 -0.00008368 49.93394926 0.00000126 49.92499424 -0.00895376 vdw (SR) 0.00000000 -13.77505113 -13.77505113 0.00000000 0.00000000 0.00000000 0.00000000 3.87986504 3.87986504 vdw total 3.87982320 3.87976923 -0.00005397 3.87976931 -0.00005389 3.87997487 0.00015167 3.87986504 0.00004184 vdw-14 17.65480640 17.65482035 0.00001395 0.00000000 -17.65480640 17.65500217 0.00019577 0.00000000 -17.65480640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 198.08562240 198.08557019 -0.00005221 198.08557219 -0.00005021 198.08408813 -0.00153427 198.08503664 -0.00058576 bond 14.35404880 14.35416380 0.00011500 14.35416386 0.00011506 14.35244235 -0.00160645 14.35417432 0.00012552 bonded 262.37361920 262.37359376 -0.00002544 262.37360037 -0.00001883 262.37047974 -0.00313946 262.37797056 0.00435136 dihedral 49.93394800 49.93385977 -0.00008823 49.93386432 -0.00008368 49.93394926 0.00000126 49.93875960 0.00481160 nonbonded 27.44913200 27.45224712 0.00311512 27.45224699 0.00311499 27.45245223 0.00332023 27.44670528 -0.00242672 potential 289.82275120 289.82584089 0.00308969 289.82584318 0.00309198 289.82261355 -0.00013765 289.82471768 0.00196648 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 289.82275120 Difference in potential energy from amber=>gromacs conversion: 0.00308969 Difference in potential energy from amber=>lammps conversion: 0.00309198 Difference in potential energy from amber=>desmond conversion: -0.00013765 Difference in potential energy from amber=>charmm conversion: 0.00196648 ======================================================================= INFO 2017-03-18 23:24:16 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_468867.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_468867.inpcrd') INFO 2017-03-18 23:24:16 Beginning InterMol conversion INFO 2017-03-18 23:24:16 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:24:16 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:24:16 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4689084.inpcrd INFO 2017-03-18 23:24:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4689084/mobley_4689084_converted.input INFO 2017-03-18 23:24:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4689084/mobley_4689084_converted.cms WARNING 2017-03-18 23:24:32 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:24:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4689084/mobley_4689084_converted.inp INFO 2017-03-18 23:24:32 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4689084/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4689084/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4689084/mobley_4689084_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4689084/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -127.35922939 -127.35922939 0.00000000 0.00000000 0.00000000 0.00000000 -215.86921232 -215.86921232 coulomb total -215.91071760 -215.94046033 -0.02974273 -215.94045747 -0.02973987 -215.94048718 -0.02976958 -215.86921232 0.04150528 coulomb-14 -88.55728880 -88.58123094 -0.02394214 0.00000000 88.55728880 -88.58128948 -0.02400068 0.00000000 88.55728880 improper 0.00000000 0.00000520 0.00000520 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 41.13499600 41.13480854 -0.00018746 41.13481358 -0.00018242 41.13473291 -0.00026309 41.13482864 -0.00016736 vdw (SR) 0.00000000 -4.60723574 -4.60723574 0.00000000 0.00000000 0.00000000 0.00000000 11.79959128 11.79959128 vdw total 11.79929840 11.79942900 0.00013060 11.79942894 0.00013054 11.79958153 0.00028313 11.79959128 0.00029288 vdw-14 16.40671920 16.40666475 -0.00005445 0.00000000 -16.40671920 16.40680137 0.00008217 0.00000000 -16.40671920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.82626800 3.82642001 0.00015201 3.82642000 0.00015200 3.82617166 -0.00009634 3.82651904 0.00025104 bond 3.56686000 3.56677557 -0.00008443 3.56677557 -0.00008443 3.56701325 0.00015325 3.56677632 -0.00008368 bonded 48.52812400 48.52800933 -0.00011467 48.52800915 -0.00011485 48.52791783 -0.00020617 48.52812400 0.00000000 dihedral 41.13499600 41.13481375 -0.00018225 41.13481358 -0.00018242 41.13473291 -0.00026309 41.13482864 -0.00016736 nonbonded -204.11141920 -204.14103132 -0.02961212 -204.14102937 -0.02961017 -204.14090565 -0.02948645 -204.06962104 0.04179816 potential -155.58329520 -155.61302199 -0.02972679 -155.61301834 -0.02972314 -155.61305474 -0.02975954 -155.54153888 0.04175632 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -155.58329520 Difference in potential energy from amber=>gromacs conversion: -0.02972679 Difference in potential energy from amber=>lammps conversion: -0.02972314 Difference in potential energy from amber=>desmond conversion: -0.02975954 Difference in potential energy from amber=>charmm conversion: 0.04175632 ======================================================================= INFO 2017-03-18 23:24:32 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4689084.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4689084.inpcrd') INFO 2017-03-18 23:24:32 Beginning InterMol conversion INFO 2017-03-18 23:24:32 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:24:32 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:24:32 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4690963.inpcrd INFO 2017-03-18 23:24:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4690963/mobley_4690963_converted.input INFO 2017-03-18 23:24:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4690963/mobley_4690963_converted.cms WARNING 2017-03-18 23:24:48 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:24:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4690963/mobley_4690963_converted.inp INFO 2017-03-18 23:24:48 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4690963/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4690963/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4690963/mobley_4690963_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4690963/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -13.40768864 -13.40768864 0.00000000 0.00000000 0.00000000 0.00000000 15.23122440 15.23122440 coulomb total 15.23227040 15.22581972 -0.00645068 15.22581951 -0.00645089 15.22587562 -0.00639478 15.23122440 -0.00104600 coulomb-14 28.62107040 28.63350836 0.01243796 0.00000000 -28.62107040 28.63356696 0.01249656 0.00000000 -28.62107040 proper 11.99134400 11.99154943 0.00020543 11.99154943 0.00020543 11.99157215 0.00022815 11.99155320 0.00020920 vdw (SR) 0.00000000 -3.87689007 -3.87689007 0.00000000 0.00000000 0.00000000 0.00000000 4.36562744 4.36562744 vdw total 4.36558560 4.36547677 -0.00010883 4.36547682 -0.00010878 4.36543225 -0.00015335 4.36562744 0.00004184 vdw-14 8.24248000 8.24236683 -0.00011317 0.00000000 -8.24248000 8.24231908 -0.00016092 0.00000000 -8.24248000 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.00750720 1.00765539 0.00014819 1.00765540 0.00014820 1.00776734 0.00026014 1.00767456 0.00016736 bond 3.19197360 3.19207672 0.00010312 3.19207674 0.00010314 3.19223687 0.00026327 3.19205728 0.00008368 bonded 16.19082480 16.19128154 0.00045674 16.19128157 0.00045677 16.19157636 0.00075156 16.19128504 0.00046024 dihedral 11.99134400 11.99154943 0.00020543 11.99154943 0.00020543 11.99157215 0.00022815 11.99155320 0.00020920 nonbonded 19.59785600 19.59129649 -0.00655951 19.59129632 -0.00655968 19.59130786 -0.00654814 19.59685184 -0.00100416 potential 35.78868080 35.78257803 -0.00610277 35.78257802 -0.00610278 35.78281195 -0.00586885 35.78813688 -0.00054392 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 35.78868080 Difference in potential energy from amber=>gromacs conversion: -0.00610277 Difference in potential energy from amber=>lammps conversion: -0.00610278 Difference in potential energy from amber=>desmond conversion: -0.00586885 Difference in potential energy from amber=>charmm conversion: -0.00054392 ======================================================================= INFO 2017-03-18 23:24:48 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4690963.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4690963.inpcrd') INFO 2017-03-18 23:24:48 Beginning InterMol conversion INFO 2017-03-18 23:24:48 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:24:48 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:24:48 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4694328.inpcrd INFO 2017-03-18 23:24:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4694328/mobley_4694328_converted.input INFO 2017-03-18 23:24:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4694328/mobley_4694328_converted.cms WARNING 2017-03-18 23:25:04 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:25:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4694328/mobley_4694328_converted.inp INFO 2017-03-18 23:25:04 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4694328/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4694328/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4694328/mobley_4694328_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4694328/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -7.13625676 -7.13625676 0.00000000 0.00000000 0.00000000 0.00000000 -6.49720808 -6.49720808 coulomb total -6.49440480 -6.49828344 -0.00387864 -6.49828337 -0.00387857 -6.49824847 -0.00384367 -6.49720808 -0.00280328 coulomb-14 0.63931520 0.63797332 -0.00134188 0.00000000 -0.63931520 0.63796908 -0.00134612 0.00000000 -0.63931520 improper 0.00000000 0.00039955 0.00039955 0.00000000 0.00000000 0.00000000 0.00000000 0.00041840 0.00041840 proper 10.02277200 10.02241837 -0.00035363 10.02281802 0.00004602 10.02281530 0.00004330 10.02243728 -0.00033472 vdw (SR) 0.00000000 -3.26539966 -3.26539966 0.00000000 0.00000000 0.00000000 0.00000000 7.70617488 7.70617488 vdw total 7.70650960 7.70604563 -0.00046397 7.70604559 -0.00046401 7.70609692 -0.00041268 7.70617488 -0.00033472 vdw-14 10.97170320 10.97144528 -0.00025792 0.00000000 -10.97170320 10.97149940 -0.00020380 0.00000000 -10.97170320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.18400000 4.18419475 0.00019475 4.18419456 0.00019456 4.18387621 -0.00012379 4.18416736 0.00016736 bond 1.40624240 1.40609400 -0.00014840 1.40609399 -0.00014841 1.40562250 -0.00061990 1.40607504 -0.00016736 bonded 15.61301440 15.61310667 0.00009227 15.61310657 0.00009217 15.61231402 -0.00070038 15.61309808 0.00008368 dihedral 10.02277200 10.02281792 0.00004592 10.02281802 0.00004602 10.02281530 0.00004330 10.02285568 0.00008368 nonbonded 1.21210480 1.20776219 -0.00434261 1.20776239 -0.00434241 1.20784844 -0.00425636 1.20896680 -0.00313800 potential 16.82511920 16.82086886 -0.00425034 16.82086909 -0.00425011 16.82007689 -0.00504231 16.82206488 -0.00305432 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 16.82511920 Difference in potential energy from amber=>gromacs conversion: -0.00425034 Difference in potential energy from amber=>lammps conversion: -0.00425011 Difference in potential energy from amber=>desmond conversion: -0.00504231 Difference in potential energy from amber=>charmm conversion: -0.00305432 ======================================================================= INFO 2017-03-18 23:25:04 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4694328.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4694328.inpcrd') INFO 2017-03-18 23:25:04 Beginning InterMol conversion INFO 2017-03-18 23:25:04 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:25:04 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:25:04 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4699732.inpcrd INFO 2017-03-18 23:25:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4699732/mobley_4699732_converted.input INFO 2017-03-18 23:25:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4699732/mobley_4699732_converted.cms WARNING 2017-03-18 23:25:20 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:25:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4699732/mobley_4699732_converted.inp INFO 2017-03-18 23:25:20 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4699732/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4699732/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4699732/mobley_4699732_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4699732/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -1.53196810 -1.53196810 0.00000000 0.00000000 0.00000000 0.00000000 -3.09306384 -3.09306384 coulomb total -3.07189280 -3.07245855 -0.00056575 -3.07245852 -0.00056572 -3.07243989 -0.00054709 -3.09306384 -0.02117104 coulomb-14 -1.54138560 -1.54049046 0.00089514 0.00000000 1.54138560 -1.54046533 0.00092027 0.00000000 1.54138560 proper 5.82370960 5.82387687 0.00016727 5.82387445 0.00016485 5.82387834 0.00016874 5.82387696 0.00016736 vdw (SR) 0.00000000 0.23628028 0.23628028 0.00000000 0.00000000 0.00000000 0.00000000 2.30048872 2.30048872 vdw total 2.30078160 2.30043792 -0.00034368 2.30043797 -0.00034363 2.30054126 -0.00024034 2.30048872 -0.00029288 vdw-14 2.06438560 2.06415765 -0.00022795 0.00000000 -2.06438560 2.06424065 -0.00014495 0.00000000 -2.06438560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.86352960 2.86350260 -0.00002700 2.86350261 -0.00002699 2.86348018 -0.00004942 2.86352960 0.00000000 bond 0.30543200 0.30539753 -0.00003447 0.30539753 -0.00003447 0.30540527 -0.00002673 0.30539016 -0.00004184 bonded 8.99267120 8.99277701 0.00010581 8.99277460 0.00010340 8.99276379 0.00009259 8.99279672 0.00012552 dihedral 5.82370960 5.82387687 0.00016727 5.82387445 0.00016485 5.82387834 0.00016874 5.82387696 0.00016736 nonbonded -0.77111120 -0.77202063 -0.00090943 -0.77202055 -0.00090935 -0.77189863 -0.00078743 -0.79257512 -0.02146392 potential 8.22156000 8.22075638 -0.00080362 8.22075416 -0.00080584 8.22083006 -0.00072994 8.20022160 -0.02133840 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 8.22156000 Difference in potential energy from amber=>gromacs conversion: -0.00080362 Difference in potential energy from amber=>lammps conversion: -0.00080584 Difference in potential energy from amber=>desmond conversion: -0.00072994 Difference in potential energy from amber=>charmm conversion: -0.02133840 ======================================================================= INFO 2017-03-18 23:25:20 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4699732.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4699732.inpcrd') INFO 2017-03-18 23:25:20 Beginning InterMol conversion INFO 2017-03-18 23:25:20 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:25:21 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:25:21 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4715906.inpcrd INFO 2017-03-18 23:25:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4715906/mobley_4715906_converted.input INFO 2017-03-18 23:25:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4715906/mobley_4715906_converted.cms WARNING 2017-03-18 23:25:36 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:25:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4715906/mobley_4715906_converted.inp INFO 2017-03-18 23:25:36 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4715906/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4715906/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4715906/mobley_4715906_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4715906/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.03479740 0.03479740 0.00000000 0.00000000 0.00000000 0.00000000 -5.62526248 -5.62526248 coulomb total -5.61409120 -5.62583504 -0.01174384 -5.62583485 -0.01174365 -5.62586564 -0.01177444 -5.62526248 -0.01117128 coulomb-14 -5.66137040 -5.66063244 0.00073796 0.00000000 5.66137040 -5.66063205 0.00073835 0.00000000 5.66137040 proper 22.70029200 22.70013835 -0.00015365 22.70013594 -0.00015606 22.70010539 -0.00018661 22.70012464 -0.00016736 vdw (SR) 0.00000000 0.28615531 0.28615531 0.00000000 0.00000000 0.00000000 0.00000000 18.76339904 18.76339904 vdw total 18.76314800 18.76322774 0.00007974 18.76322833 0.00008033 18.76332650 0.00017850 18.76339904 0.00025104 vdw-14 18.47696240 18.47707243 0.00011003 0.00000000 -18.47696240 18.47709704 0.00013464 0.00000000 -18.47696240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 6.67640880 6.67649688 0.00008808 6.67649708 0.00008828 6.67636650 -0.00004230 6.67640880 0.00000000 bond 1.04851040 1.04844754 -0.00006286 1.04844756 -0.00006284 1.04877629 0.00026589 1.04842672 -0.00008368 bonded 30.42521120 30.42508277 -0.00012843 30.42508058 -0.00013062 30.42524819 0.00003699 30.42496016 -0.00025104 dihedral 22.70029200 22.70013835 -0.00015365 22.70013594 -0.00015606 22.70010539 -0.00018661 22.70012464 -0.00016736 nonbonded 13.14905680 13.13739270 -0.01166410 13.13739348 -0.01166332 13.13746086 -0.01159594 13.13813656 -0.01092024 potential 43.57426800 43.56247546 -0.01179254 43.56247330 -0.01179470 43.56263606 -0.01163194 43.56313856 -0.01112944 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 43.57426800 Difference in potential energy from amber=>gromacs conversion: -0.01179254 Difference in potential energy from amber=>lammps conversion: -0.01179470 Difference in potential energy from amber=>desmond conversion: -0.01163194 Difference in potential energy from amber=>charmm conversion: -0.01112944 ======================================================================= INFO 2017-03-18 23:25:36 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4715906.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4715906.inpcrd') INFO 2017-03-18 23:25:37 Beginning InterMol conversion INFO 2017-03-18 23:25:37 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:25:37 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:25:37 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4759887.inpcrd INFO 2017-03-18 23:25:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4759887/mobley_4759887_converted.input INFO 2017-03-18 23:25:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4759887/mobley_4759887_converted.cms WARNING 2017-03-18 23:25:52 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:25:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4759887/mobley_4759887_converted.inp INFO 2017-03-18 23:25:52 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4759887/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4759887/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4759887/mobley_4759887_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4759887/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 8.65630843 8.65630843 0.00000000 0.00000000 0.00000000 0.00000000 4.53382424 4.53382424 coulomb total 4.54089520 4.54100830 0.00011310 4.54100817 0.00011297 4.54096929 0.00007409 4.53382424 -0.00707096 coulomb-14 -4.11496400 -4.11530013 -0.00033613 0.00000000 4.11496400 -4.11529735 -0.00033335 0.00000000 4.11496400 proper 6.87807760 6.87825846 0.00018086 6.87825835 0.00018075 6.87825153 0.00017393 6.87824496 0.00016736 vdw (SR) 0.00000000 -3.24856529 -3.24856529 0.00000000 0.00000000 0.00000000 0.00000000 4.16994176 4.16994176 vdw total 4.17019280 4.16979808 -0.00039472 4.16979812 -0.00039468 4.16977560 -0.00041720 4.16994176 -0.00025104 vdw-14 7.41865040 7.41836337 -0.00028703 0.00000000 -7.41865040 7.41833187 -0.00031853 0.00000000 -7.41865040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.95469280 4.95475605 0.00006325 4.95475598 0.00006318 4.95469171 -0.00000109 4.95473464 0.00004184 bond 1.33762480 1.33780827 0.00018347 1.33780827 0.00018347 1.33772829 0.00010349 1.33779216 0.00016736 bonded 13.17039520 13.17082278 0.00042758 13.17082260 0.00042740 13.17067153 0.00027633 13.17077176 0.00037656 dihedral 6.87807760 6.87825846 0.00018086 6.87825835 0.00018075 6.87825153 0.00017393 6.87824496 0.00016736 nonbonded 8.71108800 8.71080638 -0.00028162 8.71080642 -0.00028158 8.71074489 -0.00034311 8.70376600 -0.00732200 potential 21.88148320 21.88162916 0.00014596 21.88162922 0.00014602 21.88131120 -0.00017200 21.87453776 -0.00694544 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 21.88148320 Difference in potential energy from amber=>gromacs conversion: 0.00014596 Difference in potential energy from amber=>lammps conversion: 0.00014602 Difference in potential energy from amber=>desmond conversion: -0.00017200 Difference in potential energy from amber=>charmm conversion: -0.00694544 ======================================================================= INFO 2017-03-18 23:25:52 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4759887.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4759887.inpcrd') INFO 2017-03-18 23:25:53 Beginning InterMol conversion INFO 2017-03-18 23:25:53 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:25:53 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:25:53 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4762983.inpcrd INFO 2017-03-18 23:25:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4762983/mobley_4762983_converted.input INFO 2017-03-18 23:25:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4762983/mobley_4762983_converted.cms WARNING 2017-03-18 23:26:08 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:26:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4762983/mobley_4762983_converted.inp INFO 2017-03-18 23:26:09 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4762983/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4762983/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4762983/mobley_4762983_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4762983/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 8.53656543 8.53656543 0.00000000 0.00000000 0.00000000 0.00000000 10.52962176 10.52962176 coulomb total 10.52401520 10.52437955 0.00036435 10.52437963 0.00036443 10.52435191 0.00033671 10.52962176 0.00560656 coulomb-14 1.98781840 1.98781411 -0.00000429 0.00000000 -1.98781840 1.98782315 0.00000475 0.00000000 -1.98781840 improper 0.00000000 0.00106636 0.00106636 0.00000000 0.00000000 0.00000000 0.00000000 0.00104600 0.00104600 proper 15.57410320 15.57300760 -0.00109560 15.57407559 -0.00002761 15.57407027 -0.00003293 15.57301536 -0.00108784 vdw (SR) 0.00000000 -2.24519815 -2.24519815 0.00000000 0.00000000 0.00000000 0.00000000 4.52700432 4.52700432 vdw total 4.52708800 4.52690864 -0.00017936 4.52690851 -0.00017949 4.52704108 -0.00004692 4.52700432 -0.00008368 vdw-14 6.77222240 6.77210680 -0.00011560 0.00000000 -6.77222240 6.77221780 -0.00000460 0.00000000 -6.77222240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.72922320 2.72919426 -0.00002894 2.72919425 -0.00002895 2.72915884 -0.00006436 2.72913952 -0.00008368 bond 1.17068320 1.17057164 -0.00011156 1.17057165 -0.00011155 1.17072130 0.00003810 1.17055768 -0.00012552 bonded 19.47400960 19.47383986 -0.00016974 19.47384149 -0.00016811 19.47395041 -0.00005919 19.47375856 -0.00025104 dihedral 15.57410320 15.57407396 -0.00002924 15.57407559 -0.00002761 15.57407027 -0.00003293 15.57406136 -0.00004184 nonbonded 15.05110320 15.05128819 0.00018499 15.05128813 0.00018493 15.05139299 0.00028979 15.05662608 0.00552288 potential 34.52511280 34.52512805 0.00001525 34.52512954 0.00001674 34.52528744 0.00017464 34.53042648 0.00531368 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 34.52511280 Difference in potential energy from amber=>gromacs conversion: 0.00001525 Difference in potential energy from amber=>lammps conversion: 0.00001674 Difference in potential energy from amber=>desmond conversion: 0.00017464 Difference in potential energy from amber=>charmm conversion: 0.00531368 ======================================================================= INFO 2017-03-18 23:26:09 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4762983.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4762983.inpcrd') INFO 2017-03-18 23:26:09 Beginning InterMol conversion INFO 2017-03-18 23:26:09 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:26:09 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:26:09 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4780078.inpcrd INFO 2017-03-18 23:26:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4780078/mobley_4780078_converted.input INFO 2017-03-18 23:26:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4780078/mobley_4780078_converted.cms WARNING 2017-03-18 23:26:25 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:26:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4780078/mobley_4780078_converted.inp INFO 2017-03-18 23:26:25 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4780078/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4780078/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4780078/mobley_4780078_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4780078/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -19.13273440 -19.13273440 0.00000000 0.00000000 0.00000000 0.00000000 -64.07444544 -64.07444544 coulomb total -64.04616160 -64.04838022 -0.00221862 -64.04837912 -0.00221752 -64.04888036 -0.00271876 -64.07444544 -0.02828384 coulomb-14 -44.91398480 -44.91564582 -0.00166102 0.00000000 44.91398480 -44.91542117 -0.00143637 0.00000000 44.91398480 improper 0.00000000 0.00007698 0.00007698 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00125520 0.00118039 -0.00007481 0.00125733 0.00000213 0.00125541 0.00000021 0.00117152 -0.00008368 vdw (SR) 0.00000000 -0.86851648 -0.86851648 0.00000000 0.00000000 0.00000000 0.00000000 21.38434032 21.38434032 vdw total 21.38400560 21.38425030 0.00024470 21.38425036 0.00024476 21.38445441 0.00044881 21.38434032 0.00033472 vdw-14 22.25260400 22.25276678 0.00016278 0.00000000 -22.25260400 22.25290458 0.00030058 0.00000000 -22.25260400 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.78366320 0.78385061 0.00018741 0.78385060 0.00018740 0.78383758 0.00017438 0.78387240 0.00020920 bond 1.98237920 1.98224486 -0.00013434 1.98224485 -0.00013435 1.98232473 -0.00005447 1.98225368 -0.00012552 bonded 2.76729760 2.76735283 0.00005523 2.76735279 0.00005519 2.76741772 0.00012012 2.76738128 0.00008368 dihedral 0.00125520 0.00125736 0.00000216 0.00125733 0.00000213 0.00125541 0.00000021 0.00125520 0.00000000 nonbonded -42.66215600 -42.66412992 -0.00197392 -42.66413085 -0.00197485 -42.66442595 -0.00226995 -42.69010512 -0.02794912 potential -39.89485840 -39.89677709 -0.00191869 -39.89677635 -0.00191795 -39.89707743 -0.00221903 -39.92276568 -0.02790728 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -39.89485840 Difference in potential energy from amber=>gromacs conversion: -0.00191869 Difference in potential energy from amber=>lammps conversion: -0.00191795 Difference in potential energy from amber=>desmond conversion: -0.00221903 Difference in potential energy from amber=>charmm conversion: -0.02790728 ======================================================================= INFO 2017-03-18 23:26:25 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4780078.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4780078.inpcrd') INFO 2017-03-18 23:26:25 Beginning InterMol conversion INFO 2017-03-18 23:26:25 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:26:25 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:26:25 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4792268.inpcrd INFO 2017-03-18 23:26:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4792268/mobley_4792268_converted.input INFO 2017-03-18 23:26:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4792268/mobley_4792268_converted.cms WARNING 2017-03-18 23:26:41 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:26:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4792268/mobley_4792268_converted.inp INFO 2017-03-18 23:26:41 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4792268/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4792268/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4792268/mobley_4792268_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4792268/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 25.52277734 25.52277734 0.00000000 0.00000000 0.00000000 0.00000000 -122.21719224 -122.21719224 coulomb total -122.20501680 -122.20595005 -0.00093325 -122.20594983 -0.00093303 -122.20652547 -0.00150867 -122.21719224 -0.01217544 coulomb-14 -147.72323280 -147.72872739 -0.00549459 0.00000000 147.72323280 -147.72892639 -0.00569359 0.00000000 147.72323280 improper 0.00000000 0.00030714 0.00030714 0.00000000 0.00000000 0.00000000 0.00000000 0.00029288 0.00029288 proper 5.03418880 5.03367840 -0.00051040 5.03398588 -0.00020292 5.03399232 -0.00019648 5.03368672 -0.00050208 vdw (SR) 0.00000000 -1.72819138 -1.72819138 0.00000000 0.00000000 0.00000000 0.00000000 5.10192776 5.10192776 vdw total 5.10196960 5.10183303 -0.00013657 5.10183320 -0.00013640 5.10182559 -0.00014401 5.10192776 -0.00004184 vdw-14 6.82996160 6.83002441 0.00006281 0.00000000 -6.82996160 6.82998106 0.00001946 0.00000000 -6.82996160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 7.28894640 7.28894882 0.00000242 7.28894891 0.00000251 7.28912736 0.00018096 7.28898824 0.00004184 bond 6.18562560 6.18558463 -0.00004097 6.18558460 -0.00004100 6.18533837 -0.00028723 6.18558376 -0.00004184 bonded 18.50876080 18.50851898 -0.00024182 18.50851938 -0.00024142 18.50845805 -0.00030275 18.50855160 -0.00020920 dihedral 5.03418880 5.03398553 -0.00020327 5.03398588 -0.00020292 5.03399232 -0.00019648 5.03397960 -0.00020920 nonbonded -117.10304720 -117.10411702 -0.00106982 -117.10411412 -0.00106692 -117.10469988 -0.00165268 -117.11526448 -0.01221728 potential -98.59428640 -98.59559804 -0.00131164 -98.59559599 -0.00130959 -98.59629472 -0.00200832 -98.60671288 -0.01242648 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -98.59428640 Difference in potential energy from amber=>gromacs conversion: -0.00131164 Difference in potential energy from amber=>lammps conversion: -0.00130959 Difference in potential energy from amber=>desmond conversion: -0.00200832 Difference in potential energy from amber=>charmm conversion: -0.01242648 ======================================================================= INFO 2017-03-18 23:26:41 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4792268.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4792268.inpcrd') INFO 2017-03-18 23:26:41 Beginning InterMol conversion INFO 2017-03-18 23:26:41 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:26:41 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4845722.inpcrd INFO 2017-03-18 23:26:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4845722/mobley_4845722_converted.input INFO 2017-03-18 23:26:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4845722/mobley_4845722_converted.cms INFO 2017-03-18 23:26:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4845722/mobley_4845722_converted.rst7 WARNING 2017-03-18 23:26:57 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:26:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4845722/mobley_4845722_converted.inp INFO 2017-03-18 23:26:57 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4845722/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4845722/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4845722/mobley_4845722_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_4845722/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4845722/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.24697394 0.24697394 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.25057976 0.25057976 coulomb total 0.24852960 0.25000827 0.00147867 0.25000826 0.00147866 0.25000810 0.00147850 0.24852960 0.00000000 0.25057976 0.00205016 coulomb-14 0.00251040 0.00303433 0.00052393 0.00000000 -0.00251040 0.00303446 0.00052406 0.00251040 0.00000000 0.00000000 -0.00251040 improper 0.00000000 0.00001287 0.00001287 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00000000 0.00010787 0.00010787 0.00012075 0.00012075 0.00012320 0.00012320 0.00000000 0.00000000 0.00012552 0.00012552 vdw (SR) 0.00000000 -4.37743941 -4.37743941 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 28.31990608 28.31990608 vdw total 28.32024080 28.31979917 -0.00044163 28.31979939 -0.00044141 28.31978056 -0.00046024 28.31982240 -0.00041840 28.31990608 -0.00033472 vdw-14 32.69754160 32.69723859 -0.00030301 0.00000000 -32.69754160 32.69721608 -0.00032552 32.69712320 -0.00041840 0.00000000 -32.69754160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.32384160 0.32380267 -0.00003893 0.32380268 -0.00003892 0.32379751 -0.00004409 0.32384160 0.00000000 0.32384160 0.00000000 bond 2.49491920 2.49479131 -0.00012789 2.49479130 -0.00012790 2.49500536 0.00008616 2.49491920 0.00000000 2.49479368 -0.00012552 bonded 2.81876080 2.81871473 -0.00004607 2.81871472 -0.00004608 2.81892606 0.00016526 2.81876080 0.00000000 2.81876080 -0.00000000 dihedral 0.00000000 0.00012074 0.00012074 0.00012075 0.00012075 0.00012320 0.00012320 0.00000000 0.00000000 0.00012552 0.00012552 nonbonded 28.56877040 28.56980744 0.00103704 28.56980761 0.00103721 28.56978866 0.00101826 28.56835200 -0.00041840 28.57048584 0.00171544 potential 31.38753120 31.38852217 0.00099097 31.38852239 0.00099119 31.38856419 0.00103299 31.38711280 -0.00041840 31.38928848 0.00175728 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 31.38753120 Difference in potential energy from amber=>gromacs conversion: 0.00099097 Difference in potential energy from amber=>lammps conversion: 0.00099119 Difference in potential energy from amber=>desmond conversion: 0.00103299 Difference in potential energy from amber=>amber conversion: -0.00041840 Difference in potential energy from amber=>charmm conversion: 0.00175728 ======================================================================= INFO 2017-03-18 23:26:57 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4845722.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4845722.inpcrd') INFO 2017-03-18 23:26:57 Beginning InterMol conversion INFO 2017-03-18 23:26:57 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:26:57 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:26:57 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4850657.inpcrd INFO 2017-03-18 23:26:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4850657/mobley_4850657_converted.input INFO 2017-03-18 23:26:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4850657/mobley_4850657_converted.cms WARNING 2017-03-18 23:27:13 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:27:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4850657/mobley_4850657_converted.inp INFO 2017-03-18 23:27:13 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4850657/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4850657/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4850657/mobley_4850657_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4850657/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -215.92326960 -215.92326960 coulomb total -215.91573840 -215.93668804 -0.02094964 -215.93668350 -0.02094510 -215.93665756 -0.02091916 -215.92326960 -0.00753120 coulomb-14 -215.91573840 -215.93668804 -0.02094964 0.00000000 215.91573840 -215.93665756 -0.02091916 0.00000000 215.91573840 proper 0.63931520 0.63936595 0.00005075 0.63936595 0.00005075 0.63936456 0.00004936 0.63914784 -0.00016736 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.80931112 -0.80931112 vdw total -0.80918560 -0.80930335 -0.00011775 -0.80930334 -0.00011774 -0.80930331 -0.00011771 -0.80931112 -0.00012552 vdw-14 -0.80918560 -0.80930335 -0.00011775 0.00000000 0.80918560 -0.80930331 -0.00011771 0.00000000 0.80918560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 6.68979760 6.68976727 -0.00003033 6.68976706 -0.00003054 6.68962037 -0.00017723 6.68983944 0.00004184 bond 1.90790400 1.90790798 0.00000398 1.90790797 0.00000397 1.90787336 -0.00003064 1.90790400 0.00000000 bonded 9.23701680 9.23704119 0.00002439 9.23704098 0.00002418 9.23685828 -0.00015852 9.23689128 -0.00012552 dihedral 0.63931520 0.63936595 0.00005075 0.63936595 0.00005075 0.63936456 0.00004936 0.63914784 -0.00016736 nonbonded -216.72492400 -216.74599138 -0.02106738 -216.74599044 -0.02106644 -216.74596087 -0.02103687 -216.73258072 -0.00765672 potential -207.48790720 -207.50895019 -0.02104299 -207.50894854 -0.02104134 -207.50913138 -0.02122418 -207.49568944 -0.00778224 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -207.48790720 Difference in potential energy from amber=>gromacs conversion: -0.02104299 Difference in potential energy from amber=>lammps conversion: -0.02104134 Difference in potential energy from amber=>desmond conversion: -0.02122418 Difference in potential energy from amber=>charmm conversion: -0.00778224 ======================================================================= INFO 2017-03-18 23:27:13 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4850657.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4850657.inpcrd') INFO 2017-03-18 23:27:13 Beginning InterMol conversion INFO 2017-03-18 23:27:13 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:27:13 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:27:13 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_486214.inpcrd INFO 2017-03-18 23:27:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_486214/mobley_486214_converted.input INFO 2017-03-18 23:27:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_486214/mobley_486214_converted.cms WARNING 2017-03-18 23:27:29 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:27:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_486214/mobley_486214_converted.inp INFO 2017-03-18 23:27:29 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_486214/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_486214/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_486214/mobley_486214_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_486214/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -172.43640258 -172.43640258 0.00000000 0.00000000 0.00000000 0.00000000 11.37207016 11.37207016 coulomb total 11.32148560 11.33789408 0.01640848 11.33789399 0.01640839 11.33803792 0.01655232 11.37207016 0.05058456 coulomb-14 183.77425040 183.77429665 0.00004625 0.00000000 -183.77425040 183.77430605 0.00005565 0.00000000 -183.77425040 improper 0.00000000 0.00001115 0.00001115 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 15.06658400 15.06640846 -0.00017554 15.06641957 -0.00016443 15.06642455 -0.00015945 15.06641664 -0.00016736 vdw (SR) 0.00000000 11.03604214 11.03604214 0.00000000 0.00000000 0.00000000 0.00000000 42.11848704 42.11848704 vdw total 42.11865440 42.11831454 -0.00033986 42.11831550 -0.00033890 42.11893063 0.00027623 42.11848704 -0.00016736 vdw-14 31.08251760 31.08227241 -0.00024519 0.00000000 -31.08251760 31.08242300 -0.00009460 0.00000000 -31.08251760 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.79203120 0.79187292 -0.00015828 0.79187292 -0.00015828 0.79185773 -0.00017347 0.79190568 -0.00012552 bond 1.65979280 1.65971961 -0.00007319 1.65971962 -0.00007318 1.65963992 -0.00015288 1.65970912 -0.00008368 bonded 17.51840800 17.51801214 -0.00039586 17.51801211 -0.00039589 17.51792219 -0.00048581 17.51803144 -0.00037656 dihedral 15.06658400 15.06641961 -0.00016439 15.06641957 -0.00016443 15.06642455 -0.00015945 15.06641664 -0.00016736 nonbonded 53.44014000 53.45620862 0.01606862 53.45621074 0.01607074 53.45696855 0.01682855 53.49055720 0.05041720 potential 70.95854800 70.97422077 0.01567277 70.97422126 0.01567326 70.97479112 0.01624312 71.00858864 0.05004064 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 70.95854800 Difference in potential energy from amber=>gromacs conversion: 0.01567277 Difference in potential energy from amber=>lammps conversion: 0.01567326 Difference in potential energy from amber=>desmond conversion: 0.01624312 Difference in potential energy from amber=>charmm conversion: 0.05004064 ======================================================================= INFO 2017-03-18 23:27:29 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_486214.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_486214.inpcrd') INFO 2017-03-18 23:27:29 Beginning InterMol conversion INFO 2017-03-18 23:27:29 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:27:29 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4883284.inpcrd INFO 2017-03-18 23:27:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4883284/mobley_4883284_converted.input INFO 2017-03-18 23:27:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4883284/mobley_4883284_converted.cms INFO 2017-03-18 23:27:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4883284/mobley_4883284_converted.rst7 WARNING 2017-03-18 23:27:45 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:27:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4883284/mobley_4883284_converted.inp INFO 2017-03-18 23:27:45 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4883284/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4883284/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4883284/mobley_4883284_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_4883284/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4883284/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 54.35452505 54.35452505 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -115.07527160 -115.07527160 coulomb total -115.10811600 -115.08179813 0.02631787 -115.08179864 0.02631736 -115.08216641 0.02594959 -115.10811600 0.00000000 -115.07527160 0.03284440 coulomb-14 -169.41936480 -169.43632318 -0.01695838 0.00000000 169.41936480 -169.43630247 -0.01693767 -169.41936480 0.00000000 0.00000000 169.41936480 improper 0.00000000 0.11000258 0.11000258 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.10999736 0.10999736 proper 0.21087360 0.10107226 -0.10980134 0.21107343 0.00019983 0.21108964 0.00021604 0.21087360 0.00000000 0.10108544 -0.10978816 vdw (SR) 0.00000000 -1.22552483 -1.22552483 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 14.73349576 14.73349576 vdw total 14.73353760 14.73350457 -0.00003303 14.73350455 -0.00003305 14.73357834 0.00004074 14.73353760 0.00000000 14.73349576 -0.00004184 vdw-14 15.95903120 15.95902940 -0.00000180 0.00000000 -15.95903120 15.95910421 0.00007301 15.95903120 0.00000000 0.00000000 -15.95903120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.40075520 3.40057658 -0.00017862 3.40057659 -0.00017861 3.40061214 -0.00014306 3.40075520 0.00000000 3.40062968 -0.00012552 bond 5.30740400 5.30725874 -0.00014526 5.30725882 -0.00014518 5.30740212 -0.00000188 5.30740400 0.00000000 5.30727848 -0.00012552 bonded 8.91903280 8.91891017 -0.00012263 8.91890883 -0.00012397 8.91910391 0.00007111 8.91903280 0.00000000 8.91899096 -0.00004184 dihedral 0.21087360 0.21107484 0.00020124 0.21107343 0.00019983 0.21108964 0.00021604 0.21087360 0.00000000 0.21108280 0.00020920 nonbonded -100.37457840 -100.34829356 0.02628484 -100.34829033 0.02628807 -100.34858807 0.02599033 -100.37457840 0.00000000 -100.34177584 0.03280256 potential -91.45554560 -91.42938339 0.02616221 -91.42938305 0.02616255 -91.42950355 0.02604205 -91.45554560 0.00000000 -91.42278488 0.03276072 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -91.45554560 Difference in potential energy from amber=>gromacs conversion: 0.02616221 Difference in potential energy from amber=>lammps conversion: 0.02616255 Difference in potential energy from amber=>desmond conversion: 0.02604205 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.03276072 ======================================================================= INFO 2017-03-18 23:27:45 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4883284.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4883284.inpcrd') INFO 2017-03-18 23:27:45 Beginning InterMol conversion INFO 2017-03-18 23:27:45 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:27:45 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:27:45 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4884177.inpcrd INFO 2017-03-18 23:27:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4884177/mobley_4884177_converted.input INFO 2017-03-18 23:27:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4884177/mobley_4884177_converted.cms WARNING 2017-03-18 23:28:01 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:28:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4884177/mobley_4884177_converted.inp INFO 2017-03-18 23:28:01 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4884177/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4884177/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4884177/mobley_4884177_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4884177/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -12.99862606 -12.99862606 0.00000000 0.00000000 0.00000000 0.00000000 -43.72167032 -43.72167032 coulomb total -43.69685920 -43.70489356 -0.00803436 -43.70489248 -0.00803328 -43.70496373 -0.00810453 -43.72167032 -0.02481112 coulomb-14 -30.70177360 -30.70626750 -0.00449390 0.00000000 30.70177360 -30.70629232 -0.00451872 0.00000000 30.70177360 improper 0.00000000 0.00011507 0.00011507 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.02133840 0.02130283 -0.00003557 0.02141789 0.00007949 0.02142573 0.00008733 0.02129656 -0.00004184 vdw (SR) 0.00000000 -3.27508147 -3.27508147 0.00000000 0.00000000 0.00000000 0.00000000 19.12067080 19.12067080 vdw total 19.12046160 19.12069113 0.00022953 19.12069130 0.00022970 19.12098245 0.00052085 19.12067080 0.00020920 vdw-14 22.39569680 22.39577260 0.00007580 0.00000000 -22.39569680 22.39608068 0.00038388 0.00000000 -22.39569680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.95685680 1.95684234 -0.00001446 1.95684232 -0.00001448 1.95686073 0.00000393 1.95681496 -0.00004184 bond 1.82924480 1.82941841 0.00017361 1.82941839 0.00017359 1.82911020 -0.00013460 1.82941216 0.00016736 bonded 3.80744000 3.80767865 0.00023865 3.80767861 0.00023861 3.80739667 -0.00004333 3.80764920 0.00020920 dihedral 0.02133840 0.02141790 0.00007950 0.02141789 0.00007949 0.02142573 0.00008733 0.02142208 0.00008368 nonbonded -24.57639760 -24.58420243 -0.00780483 -24.58420202 -0.00780442 -24.58398129 -0.00758369 -24.60099952 -0.02460192 potential -20.76895760 -20.77652378 -0.00756618 -20.77652311 -0.00756551 -20.77663603 -0.00767843 -20.79335032 -0.02439272 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -20.76895760 Difference in potential energy from amber=>gromacs conversion: -0.00756618 Difference in potential energy from amber=>lammps conversion: -0.00756551 Difference in potential energy from amber=>desmond conversion: -0.00767843 Difference in potential energy from amber=>charmm conversion: -0.02439272 ======================================================================= INFO 2017-03-18 23:28:01 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4884177.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4884177.inpcrd') INFO 2017-03-18 23:28:01 Beginning InterMol conversion INFO 2017-03-18 23:28:01 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:28:02 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:28:02 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4893032.inpcrd INFO 2017-03-18 23:28:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4893032/mobley_4893032_converted.input INFO 2017-03-18 23:28:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4893032/mobley_4893032_converted.cms WARNING 2017-03-18 23:28:17 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:28:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4893032/mobley_4893032_converted.inp INFO 2017-03-18 23:28:17 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4893032/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4893032/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4893032/mobley_4893032_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4893032/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.94657994 0.94657994 0.00000000 0.00000000 0.00000000 0.00000000 -3.60091776 -3.60091776 coulomb total -3.58819840 -3.59835892 -0.01016052 -3.59835887 -0.01016047 -3.59837894 -0.01018054 -3.60091776 -0.01271936 coulomb-14 -4.53796640 -4.54493885 -0.00697245 0.00000000 4.53796640 -4.54495786 -0.00699146 0.00000000 4.53796640 proper 1.73008400 1.72995251 -0.00013149 1.72995250 -0.00013150 1.72995143 -0.00013257 1.72995848 -0.00012552 vdw (SR) 0.00000000 -1.67834925 -1.67834925 0.00000000 0.00000000 0.00000000 0.00000000 2.92938576 2.92938576 vdw total 2.92963680 2.92932210 -0.00031470 2.92932216 -0.00031464 2.92932890 -0.00030790 2.92938576 -0.00025104 vdw-14 4.60783920 4.60767135 -0.00016785 0.00000000 -4.60783920 4.60767289 -0.00016631 0.00000000 -4.60783920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.77445840 0.83851943 0.06406103 0.83851941 0.06406101 0.83842779 0.06396939 0.83851544 0.06405704 bond 2.78779920 2.78773085 -0.00006835 2.78773088 -0.00006832 2.78859552 0.00079632 2.78771552 -0.00008368 bonded 5.29234160 5.35620279 0.06386119 5.35620279 0.06386119 5.35697475 0.06463315 5.35618944 0.06384784 dihedral 1.73008400 1.72995251 -0.00013149 1.72995250 -0.00013150 1.72995143 -0.00013257 1.72995848 -0.00012552 nonbonded -0.65856160 -0.66903681 -0.01047521 -0.66903675 -0.01047515 -0.66905004 -0.01048844 -0.67153200 -0.01297040 potential 4.63378000 4.68716598 0.05338598 4.68716617 0.05338617 4.68788402 0.05410402 4.68465744 0.05087744 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 4.63378000 Difference in potential energy from amber=>gromacs conversion: 0.05338598 Difference in potential energy from amber=>lammps conversion: 0.05338617 Difference in potential energy from amber=>desmond conversion: 0.05410402 Difference in potential energy from amber=>charmm conversion: 0.05087744 ======================================================================= INFO 2017-03-18 23:28:17 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4893032.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4893032.inpcrd') INFO 2017-03-18 23:28:17 Beginning InterMol conversion INFO 2017-03-18 23:28:17 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:28:18 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:28:18 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4924862.inpcrd INFO 2017-03-18 23:28:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4924862/mobley_4924862_converted.input INFO 2017-03-18 23:28:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4924862/mobley_4924862_converted.cms WARNING 2017-03-18 23:28:33 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:28:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4924862/mobley_4924862_converted.inp INFO 2017-03-18 23:28:33 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4924862/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4924862/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4924862/mobley_4924862_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4924862/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 11.69781741 11.69781741 0.00000000 0.00000000 0.00000000 0.00000000 -32.84063440 -32.84063440 coulomb total -32.81804080 -32.83928409 -0.02124329 -32.83928380 -0.02124300 -32.83927464 -0.02123384 -32.84063440 -0.02259360 coulomb-14 -44.52738320 -44.53710150 -0.00971830 0.00000000 44.52738320 -44.53704615 -0.00966295 0.00000000 44.52738320 improper 0.00000000 0.00000248 0.00000248 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 13.78125920 13.78132307 0.00006387 13.78132782 0.00006862 13.78134886 0.00008966 13.78134288 0.00008368 vdw (SR) 0.00000000 2.58922640 2.58922640 0.00000000 0.00000000 0.00000000 0.00000000 15.33766536 15.33766536 vdw total 15.33770720 15.33749609 -0.00021111 15.33749633 -0.00021087 15.33739344 -0.00031376 15.33766536 -0.00004184 vdw-14 12.74822960 12.74826969 0.00004009 0.00000000 -12.74822960 12.74827219 0.00004259 0.00000000 -12.74822960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.78816960 4.78831758 0.00014798 4.78831771 0.00014811 4.78880561 0.00063601 4.78833696 0.00016736 bond 1.56983680 1.56988339 0.00004659 1.56988341 0.00004661 1.56991478 0.00007798 1.56987864 0.00004184 bonded 20.13926560 20.13952652 0.00026092 20.13952894 0.00026334 20.14006925 0.00080365 20.13955848 0.00029288 dihedral 13.78125920 13.78132555 0.00006635 13.78132782 0.00006862 13.78134886 0.00008966 13.78134288 0.00008368 nonbonded -17.48033360 -17.50178800 -0.02145440 -17.50178748 -0.02145388 -17.50188120 -0.02154760 -17.50296904 -0.02263544 potential 2.65893200 2.63773852 -0.02119348 2.63774146 -0.02119054 2.63813169 -0.02080031 2.63658944 -0.02234256 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 2.65893200 Difference in potential energy from amber=>gromacs conversion: -0.02119348 Difference in potential energy from amber=>lammps conversion: -0.02119054 Difference in potential energy from amber=>desmond conversion: -0.02080031 Difference in potential energy from amber=>charmm conversion: -0.02234256 ======================================================================= INFO 2017-03-18 23:28:33 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4924862.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4924862.inpcrd') INFO 2017-03-18 23:28:34 Beginning InterMol conversion INFO 2017-03-18 23:28:34 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:28:34 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:28:34 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_49274.inpcrd INFO 2017-03-18 23:28:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_49274/mobley_49274_converted.input INFO 2017-03-18 23:28:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_49274/mobley_49274_converted.cms WARNING 2017-03-18 23:28:49 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:28:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_49274/mobley_49274_converted.inp INFO 2017-03-18 23:28:49 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_49274/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_49274/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_49274/mobley_49274_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_49274/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 6.76082701 6.76082701 0.00000000 0.00000000 0.00000000 0.00000000 1.76418360 1.76418360 coulomb total 1.75769840 1.76235021 0.00465181 1.76235017 0.00465177 1.76234557 0.00464717 1.76418360 0.00648520 coulomb-14 -4.99904320 -4.99847680 0.00056640 0.00000000 4.99904320 -4.99846049 0.00058271 0.00000000 4.99904320 proper 3.42000160 3.41997919 -0.00002241 3.41997917 -0.00002243 3.41996367 -0.00003793 3.41995976 -0.00004184 vdw (SR) 0.00000000 -2.61539545 -2.61539545 0.00000000 0.00000000 0.00000000 0.00000000 3.58024880 3.58024880 vdw total 3.58024880 3.58015098 -0.00009782 3.58015102 -0.00009778 3.58015948 -0.00008932 3.58024880 0.00000000 vdw-14 6.19566720 6.19554643 -0.00012077 0.00000000 -6.19566720 6.19554687 -0.00012033 0.00000000 -6.19566720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.95897280 1.09287215 0.13389935 1.09287214 0.13389934 1.09262698 0.13365418 1.09286080 0.13388800 bond 2.27191200 2.27196135 0.00004935 2.27196133 0.00004933 2.27237403 0.00046203 2.27195384 0.00004184 bonded 6.65088640 6.78481269 0.13392629 6.78481264 0.13392624 6.78496468 0.13407828 6.78477440 0.13388800 dihedral 3.42000160 3.41997919 -0.00002241 3.41997917 -0.00002243 3.41996367 -0.00003793 3.41995976 -0.00004184 nonbonded 5.33794720 5.34250119 0.00455399 5.34250107 0.00455387 5.34250505 0.00455785 5.34443240 0.00648520 potential 11.98883360 12.12731388 0.13848028 12.12731396 0.13848036 12.12740626 0.13857266 12.12920680 0.14037320 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 11.98883360 Difference in potential energy from amber=>gromacs conversion: 0.13848028 Difference in potential energy from amber=>lammps conversion: 0.13848036 Difference in potential energy from amber=>desmond conversion: 0.13857266 Difference in potential energy from amber=>charmm conversion: 0.14037320 ======================================================================= INFO 2017-03-18 23:28:49 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_49274.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_49274.inpcrd') INFO 2017-03-18 23:28:50 Beginning InterMol conversion INFO 2017-03-18 23:28:50 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:28:50 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:28:50 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4934872.inpcrd INFO 2017-03-18 23:28:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4934872/mobley_4934872_converted.input INFO 2017-03-18 23:28:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4934872/mobley_4934872_converted.cms WARNING 2017-03-18 23:29:06 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:29:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4934872/mobley_4934872_converted.inp INFO 2017-03-18 23:29:06 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4934872/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4934872/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4934872/mobley_4934872_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4934872/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 88.57600749 88.57600749 0.00000000 0.00000000 0.00000000 0.00000000 -131.05359104 -131.05359104 coulomb total -131.05124800 -131.06483489 -0.01358689 -131.06483345 -0.01358545 -131.06530791 -0.01405991 -131.05359104 -0.00234304 coulomb-14 -219.62945680 -219.64084238 -0.01138558 0.00000000 219.62945680 -219.64080255 -0.01134575 0.00000000 219.62945680 improper 0.00000000 0.00013620 0.00013620 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 52.81965280 52.81957788 -0.00007492 52.81969464 0.00004184 52.81953314 -0.00011966 52.81944360 -0.00020920 vdw (SR) 0.00000000 -6.32566535 -6.32566535 0.00000000 0.00000000 0.00000000 0.00000000 23.48516856 23.48516856 vdw total 23.48479200 23.48501878 0.00022678 23.48501877 0.00022677 23.48509475 0.00030275 23.48516856 0.00037656 vdw-14 29.81058160 29.81068413 0.00010253 0.00000000 -29.81058160 29.81072210 0.00014050 0.00000000 -29.81058160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 6.31198240 6.31203489 0.00005249 6.31203470 0.00005230 6.31184847 -0.00013393 6.31202424 0.00004184 bond 2.80118800 2.80113106 -0.00005694 2.80113106 -0.00005694 2.80063976 -0.00054824 2.80114616 -0.00004184 bonded 61.93282320 61.93288003 0.00005683 61.93286040 0.00003720 61.93202137 -0.00080183 61.93273952 -0.00008368 dihedral 52.81965280 52.81971408 0.00006128 52.81969464 0.00004184 52.81953314 -0.00011966 52.81956912 -0.00008368 nonbonded -107.56645600 -107.57981611 -0.01336011 -107.57981551 -0.01335951 -107.58021316 -0.01375716 -107.56842248 -0.00196648 potential -45.63363280 -45.64693607 -0.01330327 -45.64695466 -0.01332186 -45.64834500 -0.01471220 -45.63568296 -0.00205016 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -45.63363280 Difference in potential energy from amber=>gromacs conversion: -0.01330327 Difference in potential energy from amber=>lammps conversion: -0.01332186 Difference in potential energy from amber=>desmond conversion: -0.01471220 Difference in potential energy from amber=>charmm conversion: -0.00205016 ======================================================================= INFO 2017-03-18 23:29:06 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4934872.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4934872.inpcrd') INFO 2017-03-18 23:29:06 Beginning InterMol conversion INFO 2017-03-18 23:29:06 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:29:06 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:29:06 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4936555.inpcrd INFO 2017-03-18 23:29:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4936555/mobley_4936555_converted.input INFO 2017-03-18 23:29:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4936555/mobley_4936555_converted.cms WARNING 2017-03-18 23:29:22 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:29:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4936555/mobley_4936555_converted.inp INFO 2017-03-18 23:29:22 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4936555/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4936555/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4936555/mobley_4936555_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4936555/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 297.90868780 297.90868780 0.00000000 0.00000000 0.00000000 0.00000000 -357.74568168 -357.74568168 coulomb total -357.70020160 -357.70320081 -0.00299921 -357.70319734 -0.00299574 -357.70371993 -0.00351833 -357.74568168 -0.04548008 coulomb-14 -655.58552080 -655.61188861 -0.02636781 0.00000000 655.58552080 -655.61206410 -0.02654330 0.00000000 655.58552080 improper 0.00000000 0.00009562 0.00009562 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 41.87514560 41.87514152 -0.00000408 41.87517489 0.00002929 41.87531673 0.00017113 41.87506192 -0.00008368 vdw (SR) 0.00000000 33.42855646 33.42855646 0.00000000 0.00000000 0.00000000 0.00000000 86.13810000 86.13810000 vdw total 86.13810000 86.13765057 -0.00044943 86.13765231 -0.00044769 86.13839485 0.00029485 86.13810000 0.00000000 vdw-14 52.70919520 52.70909411 -0.00010109 0.00000000 -52.70919520 52.70908893 -0.00010627 0.00000000 -52.70919520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 6.91908080 6.91905571 -0.00002509 6.91905570 -0.00002510 6.91934774 0.00026694 6.91908080 0.00000000 bond 18.47361520 18.47382427 0.00020907 18.47382440 0.00020920 18.47525407 0.00163887 18.47382440 0.00020920 bonded 67.26784160 67.26811712 0.00027552 67.26805498 0.00021338 67.26991854 0.00207694 67.26805080 0.00020920 dihedral 41.87514560 41.87523714 0.00009154 41.87517489 0.00002929 41.87531673 0.00017113 41.87514560 0.00000000 nonbonded -271.56210160 -271.56555024 -0.00344864 -271.56554503 -0.00344343 -271.56532508 -0.00322348 -271.60758168 -0.04548008 potential -204.29426000 -204.29743312 -0.00317312 -204.29749005 -0.00323005 -204.29563570 -0.00137570 -204.33953088 -0.04527088 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -204.29426000 Difference in potential energy from amber=>gromacs conversion: -0.00317312 Difference in potential energy from amber=>lammps conversion: -0.00323005 Difference in potential energy from amber=>desmond conversion: -0.00137570 Difference in potential energy from amber=>charmm conversion: -0.04527088 ======================================================================= INFO 2017-03-18 23:29:22 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4936555.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4936555.inpcrd') INFO 2017-03-18 23:29:22 Beginning InterMol conversion INFO 2017-03-18 23:29:22 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:29:22 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:29:22 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4964807.inpcrd INFO 2017-03-18 23:29:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4964807/mobley_4964807_converted.input INFO 2017-03-18 23:29:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4964807/mobley_4964807_converted.cms WARNING 2017-03-18 23:29:38 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:29:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4964807/mobley_4964807_converted.inp INFO 2017-03-18 23:29:38 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4964807/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4964807/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4964807/mobley_4964807_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4964807/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -110.33280723 -110.33280723 0.00000000 0.00000000 0.00000000 0.00000000 -18.10002584 -18.10002584 coulomb total -18.09872880 -18.09909004 -0.00036124 -18.09908988 -0.00036108 -18.09899867 -0.00026987 -18.10002584 -0.00129704 coulomb-14 92.23042240 92.23371719 0.00329479 0.00000000 -92.23042240 92.23382483 0.00340243 0.00000000 -92.23042240 improper 0.00000000 0.00000260 0.00000260 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 14.41262480 14.41266736 0.00004256 14.41266831 0.00004351 14.41266568 0.00004088 14.41266664 0.00004184 vdw (SR) 0.00000000 -0.75786107 -0.75786107 0.00000000 0.00000000 0.00000000 0.00000000 14.98056096 14.98056096 vdw total 14.98081200 14.98044490 -0.00036710 14.98044506 -0.00036694 14.98042601 -0.00038599 14.98056096 -0.00025104 vdw-14 15.73853440 15.73830597 -0.00022843 0.00000000 -15.73853440 15.73830143 -0.00023297 0.00000000 -15.73853440 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.99320960 3.99301912 -0.00019048 3.99301910 -0.00019050 3.99297625 -0.00023335 3.99312592 -0.00008368 bond 2.78612560 2.78619324 0.00006764 2.78619326 0.00006766 2.78641694 0.00029134 2.78620928 0.00008368 bonded 21.19196000 21.19188232 -0.00007768 21.19188067 -0.00007933 21.19205887 0.00009887 21.19200184 0.00004184 dihedral 14.41262480 14.41266996 0.00004516 14.41266831 0.00004351 14.41266568 0.00004088 14.41266664 0.00004184 nonbonded -3.11791680 -3.11864514 -0.00072834 -3.11864469 -0.00072789 -3.11857266 -0.00065586 -3.11946488 -0.00154808 potential 18.07404320 18.07323718 -0.00080602 18.07323611 -0.00080709 18.07344175 -0.00060145 18.07249512 -0.00154808 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 18.07404320 Difference in potential energy from amber=>gromacs conversion: -0.00080602 Difference in potential energy from amber=>lammps conversion: -0.00080709 Difference in potential energy from amber=>desmond conversion: -0.00060145 Difference in potential energy from amber=>charmm conversion: -0.00154808 ======================================================================= INFO 2017-03-18 23:29:38 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4964807.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4964807.inpcrd') INFO 2017-03-18 23:29:38 Beginning InterMol conversion INFO 2017-03-18 23:29:38 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:29:38 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:29:38 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4983965.inpcrd INFO 2017-03-18 23:29:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4983965/mobley_4983965_converted.input INFO 2017-03-18 23:29:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4983965/mobley_4983965_converted.cms WARNING 2017-03-18 23:29:54 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:29:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4983965/mobley_4983965_converted.inp INFO 2017-03-18 23:29:54 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4983965/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4983965/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4983965/mobley_4983965_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4983965/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 8.72972667 8.72972667 0.00000000 0.00000000 0.00000000 0.00000000 -9.76980736 -9.76980736 coulomb total -9.77215040 -9.77256077 -0.00041037 -9.77256085 -0.00041045 -9.77257499 -0.00042459 -9.76980736 0.00234304 coulomb-14 -18.50164800 -18.50228744 -0.00063944 0.00000000 18.50164800 -18.50227970 -0.00063170 0.00000000 18.50164800 proper 0.02928800 0.02922469 -0.00006331 0.02922468 -0.00006332 0.02922154 -0.00006646 0.02924616 -0.00004184 vdw (SR) 0.00000000 -1.02578121 -1.02578121 0.00000000 0.00000000 0.00000000 0.00000000 -0.25518216 -0.25518216 vdw total -0.25522400 -0.25523029 -0.00000629 -0.25523032 -0.00000632 -0.25523749 -0.00001349 -0.25518216 0.00004184 vdw-14 0.77069280 0.77055091 -0.00014189 0.00000000 -0.77069280 0.77054336 -0.00014944 0.00000000 -0.77069280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.73426800 1.73436869 0.00010069 1.73436871 0.00010071 1.73451432 0.00024632 1.73430984 0.00004184 bond 1.04056080 1.04061473 0.00005393 1.04061473 0.00005393 1.04038443 -0.00017637 1.04060264 0.00004184 bonded 2.80411680 2.80420811 0.00009131 2.80420812 0.00009132 2.80412028 0.00000348 2.80415864 0.00004184 dihedral 0.02928800 0.02922469 -0.00006331 0.02922468 -0.00006332 0.02922154 -0.00006646 0.02924616 -0.00004184 nonbonded -10.02737440 -10.02779106 -0.00041666 -10.02779113 -0.00041673 -10.02781248 -0.00043808 -10.02498952 0.00238488 potential -7.22325760 -7.22358295 -0.00032535 -7.22358270 -0.00032510 -7.22372730 -0.00046970 -7.22083088 0.00242672 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -7.22325760 Difference in potential energy from amber=>gromacs conversion: -0.00032535 Difference in potential energy from amber=>lammps conversion: -0.00032510 Difference in potential energy from amber=>desmond conversion: -0.00046970 Difference in potential energy from amber=>charmm conversion: 0.00242672 ======================================================================= INFO 2017-03-18 23:29:54 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4983965.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4983965.inpcrd') INFO 2017-03-18 23:29:54 Beginning InterMol conversion INFO 2017-03-18 23:29:54 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:29:54 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5003962.inpcrd INFO 2017-03-18 23:29:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5003962/mobley_5003962_converted.input INFO 2017-03-18 23:29:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5003962/mobley_5003962_converted.cms INFO 2017-03-18 23:30:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5003962/mobley_5003962_converted.rst7 WARNING 2017-03-18 23:30:10 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:30:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5003962/mobley_5003962_converted.inp INFO 2017-03-18 23:30:10 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5003962/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5003962/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5003962/mobley_5003962_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_5003962/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5003962/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -132.61785874 -132.61785874 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 28.29174776 28.29174776 coulomb total 28.09137600 28.09432985 0.00295385 28.09432949 0.00295349 28.09401820 0.00264220 28.09137600 0.00000000 28.29174776 0.20037176 coulomb-14 160.70618480 160.71218858 0.00600378 0.00000000 -160.70618480 160.71210307 0.00591827 160.70618480 0.00000000 0.00000000 -160.70618480 improper 0.00000000 0.11291505 0.11291505 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.11292616 0.11292616 proper 0.21714960 0.10434269 -0.11280691 0.21725655 0.00010695 0.21729536 0.00014576 0.21714960 0.00000000 0.10434896 -0.11280064 vdw (SR) 0.00000000 -4.89170270 -4.89170270 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 45.18289048 45.18289048 vdw total 45.18301600 45.18284070 -0.00017530 45.18284027 -0.00017573 45.18245760 -0.00055840 45.18301600 0.00000000 45.18289048 -0.00012552 vdw-14 50.07453040 50.07454339 0.00001299 0.00000000 -50.07453040 50.07410070 -0.00042970 50.07453040 0.00000000 0.00000000 -50.07453040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 7.30317200 7.30303859 -0.00013341 7.30303853 -0.00013347 7.30270582 -0.00046618 7.30317200 0.00000000 7.30300464 -0.00016736 bond 8.33243600 8.33238187 -0.00005413 8.33238203 -0.00005397 8.33388333 0.00144733 8.33243600 0.00000000 8.33239416 -0.00004184 bonded 15.85275760 15.85267820 -0.00007940 15.85267710 -0.00008050 15.85388451 0.00112691 15.85275760 0.00000000 15.85267392 -0.00008368 dihedral 0.21714960 0.21725774 0.00010814 0.21725655 0.00010695 0.21729536 0.00014576 0.21714960 0.00000000 0.21727512 0.00012552 nonbonded 73.27439200 73.27717054 0.00277854 73.27717018 0.00277818 73.27647580 0.00208380 73.27439200 0.00000000 73.47463824 0.20024624 potential 89.12714960 89.12984875 0.00269915 89.12984828 0.00269868 89.13019346 0.00304386 89.12714960 0.00000000 89.32727032 0.20012072 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 89.12714960 Difference in potential energy from amber=>gromacs conversion: 0.00269915 Difference in potential energy from amber=>lammps conversion: 0.00269868 Difference in potential energy from amber=>desmond conversion: 0.00304386 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.20012072 ======================================================================= INFO 2017-03-18 23:30:10 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5003962.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5003962.inpcrd') INFO 2017-03-18 23:30:10 Beginning InterMol conversion INFO 2017-03-18 23:30:10 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:30:11 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:30:11 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5006685.inpcrd INFO 2017-03-18 23:30:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5006685/mobley_5006685_converted.input INFO 2017-03-18 23:30:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5006685/mobley_5006685_converted.cms WARNING 2017-03-18 23:30:26 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:30:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5006685/mobley_5006685_converted.inp INFO 2017-03-18 23:30:26 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5006685/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5006685/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5006685/mobley_5006685_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5006685/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -17.36625755 -17.36625755 0.00000000 0.00000000 0.00000000 0.00000000 15.47372904 15.47372904 coulomb total 15.46406400 15.46460965 0.00054565 15.46460959 0.00054559 15.46456474 0.00050074 15.47372904 0.00966504 coulomb-14 32.82975600 32.83086719 0.00111119 0.00000000 -32.82975600 32.83089689 0.00114089 0.00000000 -32.82975600 improper 0.00000000 0.00288933 0.00288933 0.00000000 0.00000000 0.00000000 0.00000000 0.00288696 0.00288696 proper 60.01236720 60.00958931 -0.00277789 60.01248017 0.00011297 60.01241741 0.00005021 60.01006600 -0.00230120 vdw (SR) 0.00000000 8.44027072 8.44027072 0.00000000 0.00000000 0.00000000 0.00000000 32.25240584 32.25240584 vdw total 32.25236400 32.25215782 -0.00020618 32.25215815 -0.00020585 32.25269370 0.00032970 32.25240584 0.00004184 vdw-14 23.81198080 23.81188710 -0.00009370 0.00000000 -23.81198080 23.81209268 0.00011188 0.00000000 -23.81198080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.83377520 4.83387745 0.00010225 4.83387729 0.00010209 4.83438853 0.00061333 4.83373336 -0.00004184 bond 1.99283920 1.99276087 -0.00007833 1.99276088 -0.00007832 1.99266760 -0.00017160 1.99275552 -0.00008368 bonded 66.83898160 66.83911697 0.00013537 66.83911833 0.00013673 66.83947354 0.00049194 66.83944184 0.00046024 dihedral 60.01236720 60.01247864 0.00011144 60.01248017 0.00011297 60.01241741 0.00005021 60.01295296 0.00058576 nonbonded 47.71642800 47.71676747 0.00033947 47.71676690 0.00033890 47.71725844 0.00083044 47.72613488 0.00970688 potential 114.55540960 114.55588444 0.00047484 114.55588658 0.00047698 114.55662547 0.00121587 114.56561856 0.01020896 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 114.55540960 Difference in potential energy from amber=>gromacs conversion: 0.00047484 Difference in potential energy from amber=>lammps conversion: 0.00047698 Difference in potential energy from amber=>desmond conversion: 0.00121587 Difference in potential energy from amber=>charmm conversion: 0.01020896 ======================================================================= INFO 2017-03-18 23:30:26 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5006685.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5006685.inpcrd') INFO 2017-03-18 23:30:27 Beginning InterMol conversion INFO 2017-03-18 23:30:27 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:30:27 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5026370.inpcrd INFO 2017-03-18 23:30:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5026370/mobley_5026370_converted.input INFO 2017-03-18 23:30:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5026370/mobley_5026370_converted.cms INFO 2017-03-18 23:30:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5026370/mobley_5026370_converted.rst7 WARNING 2017-03-18 23:30:42 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:30:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5026370/mobley_5026370_converted.inp INFO 2017-03-18 23:30:42 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5026370/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5026370/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5026370/mobley_5026370_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_5026370/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5026370/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -61.04022514 -61.04022514 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -82.13777760 -82.13777760 coulomb total -82.13192000 -82.13187890 0.00004110 -82.13187816 0.00004184 -82.13202196 -0.00010196 -82.13192000 0.00000000 -82.13777760 -0.00585760 coulomb-14 -21.09405440 -21.09165376 0.00240064 0.00000000 21.09405440 -21.09183173 0.00222267 -21.09405440 0.00000000 0.00000000 21.09405440 improper 0.00000000 0.00006341 0.00006341 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00083680 0.00073896 -0.00009784 0.00080238 -0.00003442 0.00080003 -0.00003677 0.00083680 0.00000000 0.00075312 -0.00008368 vdw (SR) 0.00000000 -2.07723073 -2.07723073 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 17.92254056 17.92254056 vdw total 17.92258240 17.92258120 -0.00000120 17.92258114 -0.00000126 17.92297262 0.00039022 17.92258240 0.00000000 17.92254056 -0.00004184 vdw-14 19.99993840 19.99981193 -0.00012647 0.00000000 -19.99993840 20.00020396 0.00026556 19.99993840 0.00000000 0.00000000 -19.99993840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.88698400 1.61066075 -0.27632325 1.61066076 -0.27632324 1.61056737 -0.27641663 1.88698400 0.00000000 1.61067264 -0.27631136 bond 2.26898320 2.26900082 0.00001762 2.26900081 0.00001761 2.26916698 0.00018378 2.26898320 0.00000000 2.26898320 0.00000000 bonded 4.15680400 3.88046395 -0.27634005 3.88046396 -0.27634004 3.88053438 -0.27626962 4.15680400 0.00000000 3.88049264 -0.27631136 dihedral 0.00083680 0.00080237 -0.00003443 0.00080238 -0.00003442 0.00080003 -0.00003677 0.00083680 0.00000000 0.00083680 0.00000000 nonbonded -64.20933760 -64.20929770 0.00003990 -64.20929576 0.00004184 -64.20904934 0.00028826 -64.20933760 0.00000000 -64.21523704 -0.00589944 potential -60.05253360 -60.32883376 -0.27630016 -60.32883241 -0.27629881 -60.32856254 -0.27602894 -60.05253360 0.00000000 -60.33474440 -0.28221080 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -60.05253360 Difference in potential energy from amber=>gromacs conversion: -0.27630016 Difference in potential energy from amber=>lammps conversion: -0.27629881 Difference in potential energy from amber=>desmond conversion: -0.27602894 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.28221080 ======================================================================= INFO 2017-03-18 23:30:42 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5026370.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5026370.inpcrd') INFO 2017-03-18 23:30:43 Beginning InterMol conversion INFO 2017-03-18 23:30:43 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:30:43 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:30:43 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5052949.inpcrd INFO 2017-03-18 23:30:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5052949/mobley_5052949_converted.input INFO 2017-03-18 23:30:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5052949/mobley_5052949_converted.cms WARNING 2017-03-18 23:30:59 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:30:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5052949/mobley_5052949_converted.inp INFO 2017-03-18 23:30:59 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5052949/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5052949/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5052949/mobley_5052949_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5052949/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -0.34985753 -0.34985753 0.00000000 0.00000000 0.00000000 0.00000000 -0.52546856 -0.52546856 coulomb total -0.51086640 -0.51613799 -0.00527159 -0.51613799 -0.00527159 -0.51619527 -0.00532887 -0.52546856 -0.01460216 coulomb-14 -0.16526800 -0.16628046 -0.00101246 0.00000000 0.16526800 -0.16629403 -0.00102603 0.00000000 0.16526800 proper 0.05439200 0.05453342 0.00014142 0.05453340 0.00014140 0.05454274 0.00015074 0.05451752 0.00012552 vdw (SR) 0.00000000 -2.40359436 -2.40359436 0.00000000 0.00000000 0.00000000 0.00000000 0.85202976 0.85202976 vdw total 0.85186240 0.85192381 0.00006141 0.85192382 0.00006142 0.85188649 0.00002409 0.85202976 0.00016736 vdw-14 3.25557040 3.25551817 -0.00005223 0.00000000 -3.25557040 3.25548458 -0.00008582 0.00000000 -3.25557040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.14973920 2.14975396 0.00001476 2.14975397 0.00001477 2.14973727 -0.00000193 2.14969736 -0.00004184 bond 1.07235920 1.07239677 0.00003757 1.07239677 0.00003757 1.07270238 0.00034318 1.07240104 0.00004184 bonded 3.27649040 3.27668414 0.00019374 3.27668414 0.00019374 3.27698239 0.00049199 3.27661592 0.00012552 dihedral 0.05439200 0.05453342 0.00014142 0.05453340 0.00014140 0.05454274 0.00015074 0.05451752 0.00012552 nonbonded 0.34099600 0.33578582 -0.00521018 0.33578582 -0.00521018 0.33569123 -0.00530477 0.32656120 -0.01443480 potential 3.61748640 3.61246996 -0.00501644 3.61246995 -0.00501645 3.61260857 -0.00487783 3.60317712 -0.01430928 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 3.61748640 Difference in potential energy from amber=>gromacs conversion: -0.00501644 Difference in potential energy from amber=>lammps conversion: -0.00501645 Difference in potential energy from amber=>desmond conversion: -0.00487783 Difference in potential energy from amber=>charmm conversion: -0.01430928 ======================================================================= INFO 2017-03-18 23:30:59 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5052949.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5052949.inpcrd') INFO 2017-03-18 23:30:59 Beginning InterMol conversion INFO 2017-03-18 23:30:59 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:30:59 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:30:59 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5056289.inpcrd INFO 2017-03-18 23:30:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5056289/mobley_5056289_converted.input INFO 2017-03-18 23:30:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5056289/mobley_5056289_converted.cms WARNING 2017-03-18 23:31:15 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:31:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5056289/mobley_5056289_converted.inp INFO 2017-03-18 23:31:15 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5056289/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5056289/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5056289/mobley_5056289_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5056289/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 15.86935638 15.86935638 0.00000000 0.00000000 0.00000000 0.00000000 -26.55283552 -26.55283552 coulomb total -26.54204080 -26.54742673 -0.00538593 -26.54742644 -0.00538564 -26.54748586 -0.00544506 -26.55283552 -0.01079472 coulomb-14 -42.41655520 -42.41678312 -0.00022792 0.00000000 42.41655520 -42.41683678 -0.00028158 0.00000000 42.41655520 proper 35.38032240 35.38037693 0.00005453 35.38037428 0.00005188 35.38037135 0.00004895 35.38120104 0.00087864 vdw (SR) 0.00000000 -1.21641428 -1.21641428 0.00000000 0.00000000 0.00000000 0.00000000 1.43364760 1.43364760 vdw total 1.43385680 1.43358363 -0.00027317 1.43358367 -0.00027313 1.43355789 -0.00029891 1.43364760 -0.00020920 vdw-14 2.65014560 2.64999791 -0.00014769 0.00000000 -2.65014560 2.64997510 -0.00017050 0.00000000 -2.65014560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 18.96146960 18.96143704 -0.00003256 18.96143696 -0.00003264 18.96119956 -0.00027004 18.96134408 -0.00012552 bond 2.33885600 2.33884159 -0.00001441 2.33884161 -0.00001439 2.33813343 -0.00072257 2.33885600 0.00000000 bonded 56.68064800 56.68065556 0.00000756 56.68065285 0.00000485 56.67970435 -0.00094365 56.68140112 0.00075312 dihedral 35.38032240 35.38037693 0.00005453 35.38037428 0.00005188 35.38037135 0.00004895 35.38120104 0.00087864 nonbonded -25.10818400 -25.11384310 -0.00565910 -25.11384286 -0.00565886 -25.11392797 -0.00574397 -25.11918792 -0.01100392 potential 31.57246400 31.56681246 -0.00565154 31.56681016 -0.00565384 31.56574433 -0.00671967 31.56221320 -0.01025080 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 31.57246400 Difference in potential energy from amber=>gromacs conversion: -0.00565154 Difference in potential energy from amber=>lammps conversion: -0.00565384 Difference in potential energy from amber=>desmond conversion: -0.00671967 Difference in potential energy from amber=>charmm conversion: -0.01025080 ======================================================================= INFO 2017-03-18 23:31:15 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5056289.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5056289.inpcrd') INFO 2017-03-18 23:31:15 Beginning InterMol conversion INFO 2017-03-18 23:31:15 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:31:15 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5063386.inpcrd INFO 2017-03-18 23:31:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5063386/mobley_5063386_converted.input INFO 2017-03-18 23:31:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5063386/mobley_5063386_converted.cms INFO 2017-03-18 23:31:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5063386/mobley_5063386_converted.rst7 WARNING 2017-03-18 23:31:31 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:31:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5063386/mobley_5063386_converted.inp INFO 2017-03-18 23:31:31 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5063386/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5063386/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5063386/mobley_5063386_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_5063386/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5063386/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 114.04089523 114.04089523 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -64.67518416 -64.67518416 coulomb total -64.69426320 -64.70286989 -0.00860669 -64.70286969 -0.00860649 -64.70365586 -0.00939266 -64.69426320 0.00000000 -64.67518416 0.01907904 coulomb-14 -178.73629600 -178.74376512 -0.00746912 0.00000000 178.73629600 -178.74387699 -0.00758099 -178.73629600 0.00000000 0.00000000 178.73629600 improper 0.00000000 0.00002712 0.00002712 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 20.08361840 20.08342751 -0.00019089 20.08345481 -0.00016359 20.08345342 -0.00016498 20.08361840 0.00000000 20.08340920 -0.00020920 vdw (SR) 0.00000000 -5.11325676 -5.11325676 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 13.46356808 13.46356808 vdw total 13.46369360 13.46358414 -0.00010946 13.46358398 -0.00010962 13.46369494 0.00000134 13.46369360 0.00000000 13.46356808 -0.00012552 vdw-14 18.57696000 18.57684090 -0.00011910 0.00000000 -18.57696000 18.57695071 -0.00000929 18.57696000 0.00000000 0.00000000 -18.57696000 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.37988320 1.38007484 0.00019164 1.38007483 0.00019163 1.37975842 -0.00012478 1.37988320 0.00000000 1.38009240 0.00020920 bond 11.14826800 11.14822869 -0.00003931 11.14822867 -0.00003933 11.14838913 0.00012113 11.14826800 0.00000000 11.14822616 -0.00004184 bonded 32.61176960 32.61175816 -0.00001144 32.61175830 -0.00001130 32.61160098 -0.00016862 32.61176960 0.00000000 32.61176960 0.00000000 dihedral 20.08361840 20.08345463 -0.00016377 20.08345481 -0.00016359 20.08345342 -0.00016498 20.08361840 0.00000000 20.08345104 -0.00016736 nonbonded -51.23056960 -51.23928575 -0.00871615 -51.23928487 -0.00871527 -51.23996092 -0.00939132 -51.23056960 0.00000000 -51.21161608 0.01895352 potential -18.61880000 -18.62752759 -0.00872759 -18.62752699 -0.00872699 -18.62842115 -0.00962115 -18.61880000 0.00000000 -18.59984648 0.01895352 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -18.61880000 Difference in potential energy from amber=>gromacs conversion: -0.00872759 Difference in potential energy from amber=>lammps conversion: -0.00872699 Difference in potential energy from amber=>desmond conversion: -0.00962115 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.01895352 ======================================================================= INFO 2017-03-18 23:31:31 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5063386.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5063386.inpcrd') INFO 2017-03-18 23:31:31 Beginning InterMol conversion INFO 2017-03-18 23:31:31 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:31:31 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:31:31 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5072416.inpcrd INFO 2017-03-18 23:31:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5072416/mobley_5072416_converted.input INFO 2017-03-18 23:31:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5072416/mobley_5072416_converted.cms WARNING 2017-03-18 23:31:47 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:31:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5072416/mobley_5072416_converted.inp INFO 2017-03-18 23:31:47 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5072416/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5072416/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5072416/mobley_5072416_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5072416/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -152.59162885 -152.59162885 0.00000000 0.00000000 0.00000000 0.00000000 -48.86163064 -48.86163064 coulomb total -48.85991520 -48.86169474 -0.00177954 -48.86169340 -0.00177820 -48.86175365 -0.00183845 -48.86163064 -0.00171544 coulomb-14 103.72638080 103.72993411 0.00355331 0.00000000 -103.72638080 103.73035769 0.00397689 0.00000000 -103.72638080 improper 0.00000000 0.11511660 0.11511660 0.00000000 0.00000000 0.00000000 0.00000000 0.11510184 0.11510184 proper 15.28415200 15.16923613 -0.11491587 15.28435116 0.00019916 15.28430149 0.00014949 15.16921752 -0.11493448 vdw (SR) 0.00000000 -4.29907595 -4.29907595 0.00000000 0.00000000 0.00000000 0.00000000 15.15114264 15.15114264 vdw total 15.15110080 15.15114954 0.00004874 15.15114933 0.00004853 15.15131293 0.00021213 15.15114264 0.00004184 vdw-14 19.45016080 19.45022548 0.00006468 0.00000000 -19.45016080 19.45037841 0.00021761 0.00000000 -19.45016080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.96392160 3.96372934 -0.00019226 3.96372935 -0.00019225 3.96378365 -0.00013795 3.96379608 -0.00012552 bond 6.34545440 6.34564210 0.00018770 6.34564226 0.00018786 6.34622057 0.00076617 6.34562176 0.00016736 bonded 25.59352800 25.59372417 0.00019617 25.59372277 0.00019477 25.59430572 0.00077772 25.59373720 0.00020920 dihedral 15.28415200 15.28435273 0.00020073 15.28435116 0.00019916 15.28430149 0.00014949 15.28431936 0.00016736 nonbonded -33.70881440 -33.71054521 -0.00173081 -33.71054448 -0.00173008 -33.71044072 -0.00162632 -33.71048800 -0.00167360 potential -8.11528640 -8.11682104 -0.00153464 -8.11682193 -0.00153553 -8.11619441 -0.00090801 -8.11666712 -0.00138072 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -8.11528640 Difference in potential energy from amber=>gromacs conversion: -0.00153464 Difference in potential energy from amber=>lammps conversion: -0.00153553 Difference in potential energy from amber=>desmond conversion: -0.00090801 Difference in potential energy from amber=>charmm conversion: -0.00138072 ======================================================================= INFO 2017-03-18 23:31:47 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5072416.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5072416.inpcrd') INFO 2017-03-18 23:31:47 Beginning InterMol conversion INFO 2017-03-18 23:31:47 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:31:47 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:31:47 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5076071.inpcrd INFO 2017-03-18 23:31:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5076071/mobley_5076071_converted.input INFO 2017-03-18 23:31:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5076071/mobley_5076071_converted.cms WARNING 2017-03-18 23:32:03 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:32:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5076071/mobley_5076071_converted.inp INFO 2017-03-18 23:32:03 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5076071/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5076071/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5076071/mobley_5076071_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5076071/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 1021.49373794 1021.49373794 0.00000000 0.00000000 0.00000000 0.00000000 -525.16697728 -525.16697728 coulomb total -525.05894640 -525.08867725 -0.02973085 -525.08865280 -0.02970640 -525.08793315 -0.02898675 -525.16697728 -0.10803088 coulomb-14 -1546.52731760 -1546.58241518 -0.05509758 0.00000000 1546.52731760 -1546.58280162 -0.05548402 0.00000000 1546.52731760 improper 0.00000000 0.11919966 0.11919966 0.00000000 0.00000000 0.00000000 0.00000000 0.11920216 0.11920216 proper 75.57224480 75.45295100 -0.11929380 75.57214857 -0.00009623 75.57212388 -0.00012092 75.45295896 -0.11928584 vdw (SR) 0.00000000 -5.05048440 -5.05048440 0.00000000 0.00000000 0.00000000 0.00000000 40.44200008 40.44200008 vdw total 40.44212560 40.44196941 -0.00015619 40.44196954 -0.00015606 40.44249116 0.00036556 40.44200008 -0.00012552 vdw-14 45.49221360 45.49245381 0.00024021 0.00000000 -45.49221360 45.49270480 0.00049120 0.00000000 -45.49221360 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 12.48296400 12.48285644 -0.00010756 12.48285647 -0.00010753 12.48322613 0.00026213 12.48296400 0.00000000 bond 39.02416800 39.02417128 0.00000328 39.02417135 0.00000335 39.02439364 0.00022564 39.02416800 0.00000000 bonded 127.07937680 127.07917838 -0.00019842 127.07917639 -0.00020041 127.07974365 0.00036685 127.07929312 -0.00008368 dihedral 75.57224480 75.57215066 -0.00009414 75.57214857 -0.00009623 75.57212388 -0.00012092 75.57216112 -0.00008368 nonbonded -484.61682080 -484.64670783 -0.02988703 -484.64669456 -0.02987376 -484.64544200 -0.02862120 -484.72497720 -0.10815640 potential -357.53744400 -357.56752945 -0.03008545 -357.56752278 -0.03007878 -357.56601946 -0.02857546 -357.64568408 -0.10824008 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -357.53744400 Difference in potential energy from amber=>gromacs conversion: -0.03008545 Difference in potential energy from amber=>lammps conversion: -0.03007878 Difference in potential energy from amber=>desmond conversion: -0.02857546 Difference in potential energy from amber=>charmm conversion: -0.10824008 ======================================================================= INFO 2017-03-18 23:32:03 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5076071.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5076071.inpcrd') INFO 2017-03-18 23:32:03 Beginning InterMol conversion INFO 2017-03-18 23:32:03 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:32:04 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:32:04 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5079234.inpcrd INFO 2017-03-18 23:32:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5079234/mobley_5079234_converted.input INFO 2017-03-18 23:32:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5079234/mobley_5079234_converted.cms WARNING 2017-03-18 23:32:19 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:32:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5079234/mobley_5079234_converted.inp INFO 2017-03-18 23:32:19 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5079234/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5079234/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5079234/mobley_5079234_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5079234/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 12.79803891 12.79803891 0.00000000 0.00000000 0.00000000 0.00000000 -5.98454256 -5.98454256 coulomb total -5.96722080 -5.98080302 -0.01358222 -5.98080290 -0.01358210 -5.98084303 -0.01362223 -5.98454256 -0.01732176 coulomb-14 -18.77486320 -18.77884193 -0.00397873 0.00000000 18.77486320 -18.77888306 -0.00401986 0.00000000 18.77486320 proper 10.08427680 10.08424329 -0.00003351 10.08424333 -0.00003347 10.08422316 -0.00005364 10.08423496 -0.00004184 vdw (SR) 0.00000000 -3.05504476 -3.05504476 0.00000000 0.00000000 0.00000000 0.00000000 5.05950200 5.05950200 vdw total 5.05929280 5.05938983 0.00009703 5.05938987 0.00009707 5.05940797 0.00011517 5.05950200 0.00020920 vdw-14 8.11444960 8.11443458 -0.00001502 0.00000000 -8.11444960 8.11444378 -0.00000582 0.00000000 -8.11444960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.68192000 3.68192305 0.00000305 3.68192305 0.00000305 3.68188628 -0.00003372 3.68187816 -0.00004184 bond 0.99370000 0.99386101 0.00016101 0.99386100 0.00016100 0.99394142 0.00024142 0.99386736 0.00016736 bonded 14.75989680 14.76002735 0.00013055 14.76002738 0.00013058 14.76005085 0.00015405 14.75998048 0.00008368 dihedral 10.08427680 10.08424329 -0.00003351 10.08424333 -0.00003347 10.08422316 -0.00005364 10.08423496 -0.00004184 nonbonded -0.90792800 -0.92141319 -0.01348519 -0.92141307 -0.01348507 -0.92143506 -0.01350706 -0.92504056 -0.01711256 potential 13.85196880 13.83861416 -0.01335464 13.83861431 -0.01335449 13.83854414 -0.01342466 13.83493992 -0.01702888 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 13.85196880 Difference in potential energy from amber=>gromacs conversion: -0.01335464 Difference in potential energy from amber=>lammps conversion: -0.01335449 Difference in potential energy from amber=>desmond conversion: -0.01342466 Difference in potential energy from amber=>charmm conversion: -0.01702888 ======================================================================= INFO 2017-03-18 23:32:19 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5079234.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5079234.inpcrd') INFO 2017-03-18 23:32:19 Beginning InterMol conversion INFO 2017-03-18 23:32:19 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:32:20 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:32:20 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5094777.inpcrd INFO 2017-03-18 23:32:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5094777/mobley_5094777_converted.input INFO 2017-03-18 23:32:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5094777/mobley_5094777_converted.cms WARNING 2017-03-18 23:32:35 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:32:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5094777/mobley_5094777_converted.inp INFO 2017-03-18 23:32:35 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5094777/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5094777/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5094777/mobley_5094777_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5094777/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -1.65895393 -1.65895393 0.00000000 0.00000000 0.00000000 0.00000000 -9.84951256 -9.84951256 coulomb total -9.85959600 -9.85338128 0.00621472 -9.85338109 0.00621491 -9.85338914 0.00620686 -9.84951256 0.01008344 coulomb-14 -8.19436400 -8.19442735 -0.00006335 0.00000000 8.19436400 -8.19441634 -0.00005234 0.00000000 8.19436400 improper 0.00000000 0.02559184 0.02559184 0.00000000 0.00000000 0.00000000 0.00000000 0.02560608 0.02560608 proper 10.62150240 10.59601968 -0.02548272 10.62161077 0.00010837 10.62150981 0.00000741 10.59710968 -0.02439272 vdw (SR) 0.00000000 -3.34696103 -3.34696103 0.00000000 0.00000000 0.00000000 0.00000000 12.84525656 12.84525656 vdw total 12.84529840 12.84525255 -0.00004585 12.84525238 -0.00004602 12.84541962 0.00012122 12.84525656 -0.00004184 vdw-14 16.19208000 16.19221358 0.00013358 0.00000000 -16.19208000 16.19238121 0.00030121 0.00000000 -16.19208000 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 48.18168880 48.18170322 0.00001442 48.18170135 0.00001255 48.18205616 0.00036736 48.18156328 -0.00012552 bond 2.19701840 2.19715348 0.00013508 2.19715346 0.00013506 2.19667705 -0.00034135 2.19714392 0.00012552 bonded 61.00020960 61.00046821 0.00025861 61.00046558 0.00025598 61.00024301 0.00003341 61.00142296 0.00121336 dihedral 10.62150240 10.62161152 0.00010912 10.62161077 0.00010837 10.62150981 0.00000741 10.62271576 0.00121336 nonbonded 2.98570240 2.99187127 0.00616887 2.99187133 0.00616893 2.99203048 0.00632808 2.99574400 0.01004160 potential 63.98591200 63.99233948 0.00642748 63.99233862 0.00642662 63.99221478 0.00630278 63.99712512 0.01121312 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 63.98591200 Difference in potential energy from amber=>gromacs conversion: 0.00642748 Difference in potential energy from amber=>lammps conversion: 0.00642662 Difference in potential energy from amber=>desmond conversion: 0.00630278 Difference in potential energy from amber=>charmm conversion: 0.01121312 ======================================================================= INFO 2017-03-18 23:32:35 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5094777.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5094777.inpcrd') INFO 2017-03-18 23:32:36 Beginning InterMol conversion INFO 2017-03-18 23:32:36 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:32:36 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:32:36 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5110043.inpcrd INFO 2017-03-18 23:32:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5110043/mobley_5110043_converted.input INFO 2017-03-18 23:32:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5110043/mobley_5110043_converted.cms WARNING 2017-03-18 23:32:51 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:32:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5110043/mobley_5110043_converted.inp INFO 2017-03-18 23:32:51 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5110043/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5110043/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5110043/mobley_5110043_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5110043/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 11.74782446 11.74782446 0.00000000 0.00000000 0.00000000 0.00000000 -27.98083472 -27.98083472 coulomb total -27.99054160 -27.99749098 -0.00694938 -27.99749081 -0.00694921 -27.99754235 -0.00700075 -27.98083472 0.00970688 coulomb-14 -39.74674480 -39.74531544 0.00142936 0.00000000 39.74674480 -39.74532216 0.00142264 0.00000000 39.74674480 improper 0.00000000 0.00013976 0.00013976 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00167360 0.00152050 -0.00015310 0.00166022 -0.00001338 0.00165343 -0.00002017 0.00150624 -0.00016736 vdw (SR) 0.00000000 -5.23030981 -5.23030981 0.00000000 0.00000000 0.00000000 0.00000000 29.50719976 29.50719976 vdw total 29.50724160 29.50719692 -0.00004468 29.50719683 -0.00004477 29.50730628 0.00006468 29.50719976 -0.00004184 vdw-14 34.73766000 34.73750673 -0.00015327 0.00000000 -34.73766000 34.73763895 -0.00002105 0.00000000 -34.73766000 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.65560880 1.65556272 -0.00004608 1.65556273 -0.00004607 1.65543599 -0.00017281 1.65556696 -0.00004184 bond 6.15842960 6.15849990 0.00007030 6.15849989 0.00007029 6.15854709 0.00011749 6.15851328 0.00008368 bonded 7.81571200 7.81572288 0.00001088 7.81572284 0.00001084 7.81563651 -0.00007549 7.81571200 0.00000000 dihedral 0.00167360 0.00166026 -0.00001334 0.00166022 -0.00001338 0.00165343 -0.00002017 0.00163176 -0.00004184 nonbonded 1.51670000 1.50970594 -0.00699406 1.50970628 -0.00699372 1.50976393 -0.00693607 1.52636504 0.00966504 potential 9.33241200 9.32542883 -0.00698317 9.32542932 -0.00698268 9.32529376 -0.00711824 9.34211888 0.00970688 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 9.33241200 Difference in potential energy from amber=>gromacs conversion: -0.00698317 Difference in potential energy from amber=>lammps conversion: -0.00698268 Difference in potential energy from amber=>desmond conversion: -0.00711824 Difference in potential energy from amber=>charmm conversion: 0.00970688 ======================================================================= INFO 2017-03-18 23:32:51 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5110043.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5110043.inpcrd') INFO 2017-03-18 23:32:52 Beginning InterMol conversion INFO 2017-03-18 23:32:52 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:32:52 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_511661.inpcrd INFO 2017-03-18 23:32:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_511661/mobley_511661_converted.input INFO 2017-03-18 23:32:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_511661/mobley_511661_converted.cms INFO 2017-03-18 23:33:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_511661/mobley_511661_converted.rst7 WARNING 2017-03-18 23:33:07 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:33:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_511661/mobley_511661_converted.inp INFO 2017-03-18 23:33:07 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_511661/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_511661/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_511661/mobley_511661_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_511661/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_511661/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 9.21942691 9.21942691 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 6.31922072 6.31922072 coulomb total 6.30528800 6.30541946 0.00013146 6.30541938 0.00013138 6.30546845 0.00018045 6.30528800 0.00000000 6.31922072 0.01393272 coulomb-14 -2.91373760 -2.91400744 -0.00026984 0.00000000 2.91373760 -2.91396124 -0.00022364 -2.91373760 0.00000000 0.00000000 2.91373760 improper 0.00000000 0.00004059 0.00004059 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00034319 -0.00007521 0.00038360 -0.00003480 0.00035936 -0.00005904 0.00041840 0.00000000 0.00033472 -0.00008368 vdw (SR) 0.00000000 -0.10421588 -0.10421588 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.78397392 1.78397392 vdw total 1.78405760 1.78395980 -0.00009780 1.78395982 -0.00009778 1.78392336 -0.00013424 1.78405760 0.00000000 1.78397392 -0.00008368 vdw-14 1.88823920 1.88817569 -0.00006351 0.00000000 -1.88823920 1.88814265 -0.00009655 1.88823920 0.00000000 0.00000000 -1.88823920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.40498720 1.40482390 -0.00016330 1.40482390 -0.00016330 1.40492625 -0.00006095 1.40498720 0.00000000 1.40481984 -0.00016736 bond 0.15104240 0.15087772 -0.00016468 0.15087772 -0.00016468 0.15089770 -0.00014470 0.15104240 0.00000000 0.15087504 -0.00016736 bonded 1.55644800 1.55608541 -0.00036259 1.55608522 -0.00036278 1.55618331 -0.00026469 1.55644800 0.00000000 1.55607144 -0.00037656 dihedral 0.00041840 0.00038378 -0.00003462 0.00038360 -0.00003480 0.00035936 -0.00005904 0.00041840 0.00000000 0.00037656 -0.00004184 nonbonded 8.08934560 8.08937926 0.00003366 8.08937907 0.00003347 8.08939180 0.00004620 8.08934560 0.00000000 8.10319464 0.01384904 potential 9.64579360 9.64546467 -0.00032893 9.64546432 -0.00032928 9.64556202 -0.00023158 9.64579360 0.00000000 9.65930792 0.01351432 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 9.64579360 Difference in potential energy from amber=>gromacs conversion: -0.00032893 Difference in potential energy from amber=>lammps conversion: -0.00032928 Difference in potential energy from amber=>desmond conversion: -0.00023158 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.01351432 ======================================================================= INFO 2017-03-18 23:33:07 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_511661.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_511661.inpcrd') INFO 2017-03-18 23:33:08 Beginning InterMol conversion INFO 2017-03-18 23:33:08 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:33:08 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:33:08 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5123639.inpcrd INFO 2017-03-18 23:33:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5123639/mobley_5123639_converted.input INFO 2017-03-18 23:33:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5123639/mobley_5123639_converted.cms WARNING 2017-03-18 23:33:24 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:33:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5123639/mobley_5123639_converted.inp INFO 2017-03-18 23:33:24 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5123639/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5123639/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5123639/mobley_5123639_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5123639/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 56.86505050 56.86505050 0.00000000 0.00000000 0.00000000 0.00000000 -44.20588464 -44.20588464 coulomb total -44.20605200 -44.19659210 0.00945990 -44.19659198 0.00946002 -44.19654512 0.00950688 -44.20588464 0.00016736 coulomb-14 -101.05029440 -101.06164261 -0.01134821 0.00000000 101.05029440 -101.06156233 -0.01126793 0.00000000 101.05029440 proper 13.93481200 13.93470875 -0.00010325 13.93471326 -0.00009874 13.93470472 -0.00010728 13.93472832 -0.00008368 vdw (SR) 0.00000000 -0.78136035 -0.78136035 0.00000000 0.00000000 0.00000000 0.00000000 8.33235232 8.33235232 vdw total 8.33243600 8.33218965 -0.00024635 8.33218998 -0.00024602 8.33209221 -0.00034379 8.33235232 -0.00008368 vdw-14 9.11358880 9.11355000 -0.00003880 0.00000000 -9.11358880 9.11341546 -0.00017334 0.00000000 -9.11358880 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 7.02660960 7.02649150 -0.00011810 7.02649161 -0.00011799 7.02624555 -0.00036405 7.02644224 -0.00016736 bond 0.63220240 0.63229647 0.00009407 0.63229646 0.00009406 0.63234633 0.00014393 0.63228608 0.00008368 bonded 21.59362400 21.59349671 -0.00012729 21.59350133 -0.00012267 21.59329661 -0.00032739 21.59345664 -0.00016736 dihedral 13.93481200 13.93470875 -0.00010325 13.93471326 -0.00009874 13.93470472 -0.00010728 13.93472832 -0.00008368 nonbonded -35.87361600 -35.86440246 0.00921354 -35.86440200 0.00921400 -35.86445291 0.00916309 -35.87353232 0.00008368 potential -14.27999200 -14.27090575 0.00908625 -14.27090059 0.00909141 -14.27121920 0.00877280 -14.28007568 -0.00008368 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -14.27999200 Difference in potential energy from amber=>gromacs conversion: 0.00908625 Difference in potential energy from amber=>lammps conversion: 0.00909141 Difference in potential energy from amber=>desmond conversion: 0.00877280 Difference in potential energy from amber=>charmm conversion: -0.00008368 ======================================================================= INFO 2017-03-18 23:33:24 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5123639.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5123639.inpcrd') INFO 2017-03-18 23:33:24 Beginning InterMol conversion INFO 2017-03-18 23:33:24 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:33:24 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:33:24 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5157661.inpcrd INFO 2017-03-18 23:33:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5157661/mobley_5157661_converted.input INFO 2017-03-18 23:33:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5157661/mobley_5157661_converted.cms WARNING 2017-03-18 23:33:40 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:33:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5157661/mobley_5157661_converted.inp INFO 2017-03-18 23:33:40 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5157661/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5157661/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5157661/mobley_5157661_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5157661/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 12.15304805 12.15304805 0.00000000 0.00000000 0.00000000 0.00000000 -2.78600008 -2.78600008 coulomb total -2.79574880 -2.78647668 0.00927212 -2.78647664 0.00927216 -2.78650003 0.00924877 -2.78600008 0.00974872 coulomb-14 -14.93771680 -14.93952474 -0.00180794 0.00000000 14.93771680 -14.93953345 -0.00181665 0.00000000 14.93771680 proper 0.08200640 0.08200045 -0.00000595 0.08200045 -0.00000595 0.08202325 0.00001685 0.08200640 0.00000000 vdw (SR) 0.00000000 -0.34859689 -0.34859689 0.00000000 0.00000000 0.00000000 0.00000000 4.61185584 4.61185584 vdw total 4.61202320 4.61177927 -0.00024393 4.61177927 -0.00024393 4.61180716 -0.00021604 4.61185584 -0.00016736 vdw-14 4.96055040 4.96037616 -0.00017424 0.00000000 -4.96055040 4.96040187 -0.00014853 0.00000000 -4.96055040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.07277760 1.07293043 0.00015283 1.07293044 0.00015284 1.07321233 0.00043473 1.07294496 0.00016736 bond 0.40333760 0.40354664 0.00020904 0.40354664 0.00020904 0.40382150 0.00048390 0.40354680 0.00020920 bonded 1.55812160 1.55847752 0.00035592 1.55847754 0.00035594 1.55905709 0.00093549 1.55849816 0.00037656 dihedral 0.08200640 0.08200045 -0.00000595 0.08200045 -0.00000595 0.08202325 0.00001685 0.08200640 0.00000000 nonbonded 1.81627440 1.82530258 0.00902818 1.82530272 0.00902832 1.82530713 0.00903273 1.82585576 0.00958136 potential 3.37439600 3.38378011 0.00938411 3.38378025 0.00938425 3.38434273 0.00994673 3.38431208 0.00991608 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 3.37439600 Difference in potential energy from amber=>gromacs conversion: 0.00938411 Difference in potential energy from amber=>lammps conversion: 0.00938425 Difference in potential energy from amber=>desmond conversion: 0.00994673 Difference in potential energy from amber=>charmm conversion: 0.00991608 ======================================================================= INFO 2017-03-18 23:33:40 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5157661.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5157661.inpcrd') INFO 2017-03-18 23:33:40 Beginning InterMol conversion INFO 2017-03-18 23:33:40 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:33:40 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:33:40 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5200358.inpcrd INFO 2017-03-18 23:33:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5200358/mobley_5200358_converted.input INFO 2017-03-18 23:33:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5200358/mobley_5200358_converted.cms WARNING 2017-03-18 23:33:56 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:33:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5200358/mobley_5200358_converted.inp INFO 2017-03-18 23:33:56 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5200358/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5200358/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5200358/mobley_5200358_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5200358/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -202.49311243 -202.49311243 0.00000000 0.00000000 0.00000000 0.00000000 27.33900912 27.33900912 coulomb total 27.33741920 27.34307058 0.00565138 27.34307011 0.00565091 27.34315337 0.00573417 27.33900912 0.00158992 coulomb-14 229.82544640 229.83618301 0.01073661 0.00000000 -229.82544640 229.83625702 0.01081062 0.00000000 -229.82544640 improper 0.00000000 0.00062408 0.00062408 0.00000000 0.00000000 0.00000000 0.00000000 0.00062760 0.00062760 proper 0.06987280 0.06924514 -0.00062766 0.06986883 -0.00000397 0.06986550 -0.00000730 0.06924520 -0.00062760 vdw (SR) 0.00000000 92.80764768 92.80764768 0.00000000 0.00000000 0.00000000 0.00000000 128.38365512 128.38365512 vdw total 128.38352960 128.38246351 -0.00106609 128.38246268 -0.00106692 128.38254243 -0.00098717 128.38365512 0.00012552 vdw-14 35.57487840 35.57481583 -0.00006257 0.00000000 -35.57487840 35.57463598 -0.00024242 0.00000000 -35.57487840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 8.32197600 8.32218216 0.00020616 8.32218227 0.00020627 8.32207077 0.00009477 8.32214336 0.00016736 bond 5.99148800 5.99150021 0.00001221 5.99150013 0.00001213 5.99175410 0.00026610 5.99148800 0.00000000 bonded 14.38333680 14.38355159 0.00021479 14.38355123 0.00021443 14.38369037 0.00035357 14.38350416 0.00016736 dihedral 0.06987280 0.06986923 -0.00000357 0.06986883 -0.00000397 0.06986550 -0.00000730 0.06987280 0.00000000 nonbonded 155.72094880 155.72553409 0.00458529 155.72553446 0.00458566 155.72569580 0.00474700 155.72266424 0.00171544 potential 170.10428560 170.10908568 0.00480008 170.10908465 0.00479905 170.10922690 0.00494130 170.10621024 0.00192464 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 170.10428560 Difference in potential energy from amber=>gromacs conversion: 0.00480008 Difference in potential energy from amber=>lammps conversion: 0.00479905 Difference in potential energy from amber=>desmond conversion: 0.00494130 Difference in potential energy from amber=>charmm conversion: 0.00192464 ======================================================================= INFO 2017-03-18 23:33:56 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5200358.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5200358.inpcrd') INFO 2017-03-18 23:33:56 Beginning InterMol conversion INFO 2017-03-18 23:33:56 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:33:56 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:33:56 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5220185.inpcrd INFO 2017-03-18 23:33:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5220185/mobley_5220185_converted.input INFO 2017-03-18 23:33:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5220185/mobley_5220185_converted.cms WARNING 2017-03-18 23:34:12 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:34:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5220185/mobley_5220185_converted.inp INFO 2017-03-18 23:34:12 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5220185/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5220185/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5220185/mobley_5220185_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5220185/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -19.14540641 -19.14540641 0.00000000 0.00000000 0.00000000 0.00000000 230.80274512 230.80274512 coulomb total 230.79153200 230.80073620 0.00920420 230.80073262 0.00920062 230.80041195 0.00887995 230.80274512 0.01121312 coulomb-14 249.93877120 249.94614261 0.00737141 0.00000000 -249.93877120 249.94580869 0.00703749 0.00000000 -249.93877120 improper 0.00000000 0.00008797 0.00008797 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.02050160 0.02046328 -0.00003832 0.02055118 0.00004958 0.02055288 0.00005128 0.02045976 -0.00004184 vdw (SR) 0.00000000 -3.24140483 -3.24140483 0.00000000 0.00000000 0.00000000 0.00000000 24.35293016 24.35293016 vdw total 24.35297200 24.35297963 0.00000763 24.35297953 0.00000753 24.35234028 -0.00063172 24.35293016 -0.00004184 vdw-14 27.59431680 27.59438446 0.00006766 0.00000000 -27.59431680 27.59374041 -0.00057639 0.00000000 -27.59431680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.96483040 0.96495312 0.00012272 0.96495312 0.00012272 0.96502448 0.00019408 0.96495592 0.00012552 bond 1.85309360 1.85310470 0.00001110 1.85310469 0.00001109 1.85353981 0.00044621 1.85309360 0.00000000 bonded 2.83842560 2.83860907 0.00018347 2.83860899 0.00018339 2.83911717 0.00069157 2.83859296 0.00016736 dihedral 0.02050160 0.02055125 0.00004965 0.02055118 0.00004958 0.02055288 0.00005128 0.02054344 0.00004184 nonbonded 255.14450400 255.15371582 0.00921182 255.15371298 0.00920898 255.15275223 0.00824823 255.15567528 0.01117128 potential 257.98292960 257.99232489 0.00939529 257.99232268 0.00939308 257.99180679 0.00887719 257.99431008 0.01138048 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 257.98292960 Difference in potential energy from amber=>gromacs conversion: 0.00939529 Difference in potential energy from amber=>lammps conversion: 0.00939308 Difference in potential energy from amber=>desmond conversion: 0.00887719 Difference in potential energy from amber=>charmm conversion: 0.01138048 ======================================================================= INFO 2017-03-18 23:34:12 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5220185.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5220185.inpcrd') INFO 2017-03-18 23:34:12 Beginning InterMol conversion INFO 2017-03-18 23:34:12 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:34:12 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:34:12 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_525934.inpcrd INFO 2017-03-18 23:34:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_525934/mobley_525934_converted.input INFO 2017-03-18 23:34:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_525934/mobley_525934_converted.cms WARNING 2017-03-18 23:34:28 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:34:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_525934/mobley_525934_converted.inp INFO 2017-03-18 23:34:28 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_525934/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_525934/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_525934/mobley_525934_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_525934/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 15.34540576 15.34540576 coulomb total 15.34356480 15.34424656 0.00068176 15.34424637 0.00068157 15.34422056 0.00065576 15.34540576 0.00184096 coulomb-14 15.34356480 15.34424656 0.00068176 0.00000000 -15.34356480 15.34422056 0.00065576 0.00000000 -15.34356480 proper 0.00000000 0.00000411 0.00000411 0.00000411 0.00000411 0.00000436 0.00000436 0.00000000 0.00000000 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.02539688 -0.02539688 vdw total -0.02552240 -0.02540498 0.00011742 -0.02540498 0.00011742 -0.02540471 0.00011769 -0.02539688 0.00012552 vdw-14 -0.02552240 -0.02540498 0.00011742 0.00000000 0.02552240 -0.02540471 0.00011769 0.00000000 0.02552240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.10836560 0.10850142 0.00013582 0.10850142 0.00013582 0.10849238 0.00012678 0.10849112 0.00012552 bond 0.32300480 0.32280084 -0.00020396 0.32280084 -0.00020396 0.32272690 -0.00027790 0.32279560 -0.00020920 bonded 0.43137040 0.43130637 -0.00006403 0.43130638 -0.00006402 0.43122364 -0.00014676 0.43128672 -0.00008368 dihedral 0.00000000 0.00000411 0.00000411 0.00000411 0.00000411 0.00000436 0.00000436 0.00000000 0.00000000 nonbonded 15.31804240 15.31884157 0.00079917 15.31884154 0.00079914 15.31881585 0.00077345 15.32000888 0.00196648 potential 15.74941280 15.75014795 0.00073515 15.75014793 0.00073513 15.75003262 0.00061982 15.75129560 0.00188280 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 15.74941280 Difference in potential energy from amber=>gromacs conversion: 0.00073515 Difference in potential energy from amber=>lammps conversion: 0.00073513 Difference in potential energy from amber=>desmond conversion: 0.00061982 Difference in potential energy from amber=>charmm conversion: 0.00188280 ======================================================================= INFO 2017-03-18 23:34:28 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_525934.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_525934.inpcrd') INFO 2017-03-18 23:34:28 Beginning InterMol conversion INFO 2017-03-18 23:34:28 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:34:28 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:34:28 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5263791.inpcrd INFO 2017-03-18 23:34:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5263791/mobley_5263791_converted.input INFO 2017-03-18 23:34:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5263791/mobley_5263791_converted.cms WARNING 2017-03-18 23:34:44 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:34:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5263791/mobley_5263791_converted.inp INFO 2017-03-18 23:34:44 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5263791/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5263791/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5263791/mobley_5263791_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5263791/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -18.08657746 -18.08657746 0.00000000 0.00000000 0.00000000 0.00000000 1.33172536 1.33172536 coulomb total 1.32883840 1.33506266 0.00622426 1.33506264 0.00622424 1.33486248 0.00602408 1.33172536 0.00288696 coulomb-14 19.42087280 19.42164012 0.00076732 0.00000000 -19.42087280 19.42166412 0.00079132 0.00000000 -19.42087280 improper 0.00000000 0.00004862 0.00004862 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.02092000 0.02102939 0.00010939 0.02107800 0.00015800 0.02106656 0.00014656 0.02104552 0.00012552 vdw (SR) 0.00000000 3.65226578 3.65226578 0.00000000 0.00000000 0.00000000 0.00000000 39.53800504 39.53800504 vdw total 39.53796320 39.53793064 -0.00003256 39.53793056 -0.00003264 39.53790982 -0.00005338 39.53800504 0.00004184 vdw-14 35.88574960 35.88566486 -0.00008474 0.00000000 -35.88574960 35.88578910 0.00003950 0.00000000 -35.88574960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.01791920 3.01796619 0.00004699 3.01796619 0.00004699 3.01795870 0.00003950 3.01796104 0.00004184 bond 5.39861520 5.39874174 0.00012654 5.39874156 0.00012636 5.39816178 -0.00045342 5.39874072 0.00012552 bonded 8.43745440 8.43778593 0.00033153 8.43778574 0.00033134 8.43718703 -0.00026737 8.43778912 0.00033472 dihedral 0.02092000 0.02107801 0.00015801 0.02107800 0.00015800 0.02106656 0.00014656 0.02108736 0.00016736 nonbonded 40.86680160 40.87299329 0.00619169 40.87299350 0.00619190 40.87277231 0.00597071 40.86973040 0.00292880 potential 49.30425600 49.31077923 0.00652323 49.31077886 0.00652286 49.30984959 0.00559359 49.30756136 0.00330536 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 49.30425600 Difference in potential energy from amber=>gromacs conversion: 0.00652323 Difference in potential energy from amber=>lammps conversion: 0.00652286 Difference in potential energy from amber=>desmond conversion: 0.00559359 Difference in potential energy from amber=>charmm conversion: 0.00330536 ======================================================================= INFO 2017-03-18 23:34:44 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5263791.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5263791.inpcrd') INFO 2017-03-18 23:34:44 Beginning InterMol conversion INFO 2017-03-18 23:34:44 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:34:44 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:34:44 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_52782.inpcrd INFO 2017-03-18 23:34:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_52782/mobley_52782_converted.input INFO 2017-03-18 23:34:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_52782/mobley_52782_converted.cms WARNING 2017-03-18 23:35:00 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:35:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_52782/mobley_52782_converted.inp INFO 2017-03-18 23:35:00 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_52782/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_52782/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_52782/mobley_52782_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_52782/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -91.88527750 -91.88527750 0.00000000 0.00000000 0.00000000 0.00000000 -20.68803904 -20.68803904 coulomb total -20.70075840 -20.70387158 -0.00311318 -20.70387130 -0.00311290 -20.70385791 -0.00309951 -20.68803904 0.01271936 coulomb-14 71.18406560 71.18140592 -0.00265968 0.00000000 -71.18406560 71.18145395 -0.00261165 0.00000000 -71.18406560 proper 5.63752160 5.63762034 0.00009874 5.63762034 0.00009874 5.63762038 0.00009878 5.63760528 0.00008368 vdw (SR) 0.00000000 -0.31257896 -0.31257896 0.00000000 0.00000000 0.00000000 0.00000000 25.36056288 25.36056288 vdw total 25.36047920 25.36038526 -0.00009394 25.36038590 -0.00009330 25.36045155 -0.00002765 25.36056288 0.00008368 vdw-14 25.67302400 25.67296422 -0.00005978 0.00000000 -25.67302400 25.67295074 -0.00007326 0.00000000 -25.67302400 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 6.85757600 6.85763748 0.00006148 6.85763750 0.00006150 6.85797683 0.00040083 6.85778520 0.00020920 bond 3.34845520 3.34826605 -0.00018915 3.34826604 -0.00018916 3.34849743 0.00004223 3.34824600 -0.00020920 bonded 15.84355280 15.84352388 -0.00002892 15.84352389 -0.00002891 15.84409464 0.00054184 15.84363648 0.00008368 dihedral 5.63752160 5.63762034 0.00009874 5.63762034 0.00009874 5.63762038 0.00009878 5.63760528 0.00008368 nonbonded 4.65972080 4.65651368 -0.00320712 4.65651418 -0.00320662 4.65659364 -0.00312716 4.67252384 0.01280304 potential 20.50327360 20.50003756 -0.00323604 20.50003811 -0.00323549 20.50062668 -0.00264692 20.51620216 0.01292856 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 20.50327360 Difference in potential energy from amber=>gromacs conversion: -0.00323604 Difference in potential energy from amber=>lammps conversion: -0.00323549 Difference in potential energy from amber=>desmond conversion: -0.00264692 Difference in potential energy from amber=>charmm conversion: 0.01292856 ======================================================================= INFO 2017-03-18 23:35:00 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_52782.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_52782.inpcrd') INFO 2017-03-18 23:35:00 Beginning InterMol conversion INFO 2017-03-18 23:35:00 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:35:01 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:35:01 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5282042.inpcrd INFO 2017-03-18 23:35:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5282042/mobley_5282042_converted.input INFO 2017-03-18 23:35:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5282042/mobley_5282042_converted.cms WARNING 2017-03-18 23:35:16 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:35:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5282042/mobley_5282042_converted.inp INFO 2017-03-18 23:35:16 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5282042/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5282042/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5282042/mobley_5282042_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5282042/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -29.97796776 -29.97796776 0.00000000 0.00000000 0.00000000 0.00000000 25.33621200 25.33621200 coulomb total 25.34625360 25.33099987 -0.01525373 25.33099957 -0.01525403 25.33081167 -0.01544193 25.33621200 -0.01004160 coulomb-14 55.30913280 55.30896763 -0.00016517 0.00000000 -55.30913280 55.30891523 -0.00021757 0.00000000 -55.30913280 improper 0.00000000 0.10195772 0.10195772 0.00000000 0.00000000 0.00000000 0.00000000 0.10196408 0.10196408 proper 39.51871680 39.41676180 -0.10195500 39.51874023 0.00002343 39.51874157 0.00002477 39.41692008 -0.10179672 vdw (SR) 0.00000000 -2.41353684 -2.41353684 0.00000000 0.00000000 0.00000000 0.00000000 57.81346600 57.81346600 vdw total 57.81367520 57.81326281 -0.00041239 57.81326517 -0.00041003 57.81315312 -0.00052208 57.81346600 -0.00020920 vdw-14 60.22700640 60.22679965 -0.00020675 0.00000000 -60.22700640 60.22681896 -0.00018744 0.00000000 -60.22700640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 26.91860080 26.91844961 -0.00015119 26.91844976 -0.00015104 26.91708251 -0.00151829 26.91826608 -0.00033472 bond 14.52559280 14.52543858 -0.00015422 14.52543841 -0.00015439 14.52496700 -0.00062580 14.52542544 -0.00016736 bonded 80.96291040 80.96260771 -0.00030269 80.96262840 -0.00028200 80.96079108 -0.00211932 80.96257568 -0.00033472 dihedral 39.51871680 39.51871952 0.00000272 39.51874023 0.00002343 39.51874157 0.00002477 39.51888416 0.00016736 nonbonded 83.15992880 83.14426268 -0.01566612 83.14426390 -0.01566490 83.14396479 -0.01596401 83.14967800 -0.01025080 potential 164.12283920 164.10687039 -0.01596881 164.10688979 -0.01594941 164.10440742 -0.01843178 164.11225368 -0.01058552 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 164.12283920 Difference in potential energy from amber=>gromacs conversion: -0.01596881 Difference in potential energy from amber=>lammps conversion: -0.01594941 Difference in potential energy from amber=>desmond conversion: -0.01843178 Difference in potential energy from amber=>charmm conversion: -0.01058552 ======================================================================= INFO 2017-03-18 23:35:16 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5282042.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5282042.inpcrd') INFO 2017-03-18 23:35:17 Beginning InterMol conversion INFO 2017-03-18 23:35:17 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:35:17 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:35:17 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5286200.inpcrd INFO 2017-03-18 23:35:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5286200/mobley_5286200_converted.input INFO 2017-03-18 23:35:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5286200/mobley_5286200_converted.cms WARNING 2017-03-18 23:35:32 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:35:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5286200/mobley_5286200_converted.inp INFO 2017-03-18 23:35:32 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5286200/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5286200/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5286200/mobley_5286200_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5286200/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.19768651 0.19768651 0.00000000 0.00000000 0.00000000 0.00000000 4.94117848 4.94117848 coulomb total 4.91661840 4.93166439 0.01504599 4.93166448 0.01504608 4.93166787 0.01504947 4.94117848 0.02456008 coulomb-14 4.72582800 4.73397787 0.00814987 0.00000000 -4.72582800 4.73400964 0.00818164 0.00000000 -4.72582800 proper 8.21863120 8.21852756 -0.00010364 8.21852744 -0.00010376 8.21852313 -0.00010807 8.21854752 -0.00008368 vdw (SR) 0.00000000 -1.59521114 -1.59521114 0.00000000 0.00000000 0.00000000 0.00000000 0.60040400 0.60040400 vdw total 0.60040400 0.60036603 -0.00003797 0.60036605 -0.00003795 0.60034039 -0.00006361 0.60040400 -0.00000000 vdw-14 2.19576320 2.19557717 -0.00018603 0.00000000 -2.19576320 2.19554915 -0.00021405 0.00000000 -2.19576320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.37146720 3.37161320 0.00014600 3.37161318 0.00014598 3.37166380 0.00019660 3.37167640 0.00020920 bond 0.45229040 0.45232040 0.00003000 0.45232040 0.00003000 0.45247837 0.00018797 0.45233224 0.00004184 bonded 12.04238880 12.04246116 0.00007236 12.04246102 0.00007222 12.04266530 0.00027650 12.04255616 0.00016736 dihedral 8.21863120 8.21852756 -0.00010364 8.21852744 -0.00010376 8.21852313 -0.00010807 8.21854752 -0.00008368 nonbonded 5.51702240 5.53203042 0.01500802 5.53203041 0.01500801 5.53200826 0.01498586 5.54158248 0.02456008 potential 17.55941120 17.57449158 0.01508038 17.57449159 0.01508039 17.57462548 0.01521428 17.58413864 0.02472744 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 17.55941120 Difference in potential energy from amber=>gromacs conversion: 0.01508038 Difference in potential energy from amber=>lammps conversion: 0.01508039 Difference in potential energy from amber=>desmond conversion: 0.01521428 Difference in potential energy from amber=>charmm conversion: 0.02472744 ======================================================================= INFO 2017-03-18 23:35:32 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5286200.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5286200.inpcrd') INFO 2017-03-18 23:35:33 Beginning InterMol conversion INFO 2017-03-18 23:35:33 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:35:33 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:35:33 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5310099.inpcrd INFO 2017-03-18 23:35:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5310099/mobley_5310099_converted.input INFO 2017-03-18 23:35:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5310099/mobley_5310099_converted.cms WARNING 2017-03-18 23:35:48 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:35:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5310099/mobley_5310099_converted.inp INFO 2017-03-18 23:35:48 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5310099/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5310099/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5310099/mobley_5310099_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5310099/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 7.38915633 7.38915633 0.00000000 0.00000000 0.00000000 0.00000000 10.36749176 10.36749176 coulomb total 10.37255440 10.36642235 -0.00613205 10.36642233 -0.00613207 10.36643122 -0.00612318 10.36749176 -0.00506264 coulomb-14 2.97858960 2.97726602 -0.00132358 0.00000000 -2.97858960 2.97729078 -0.00129882 0.00000000 -2.97858960 improper 0.00000000 0.00130679 0.00130679 0.00000000 0.00000000 0.00000000 0.00000000 0.00129704 0.00129704 proper 13.84569280 13.84439942 -0.00129338 13.84570577 0.00001297 13.84572288 0.00003008 13.84439576 -0.00129704 vdw (SR) 0.00000000 -1.60710476 -1.60710476 0.00000000 0.00000000 0.00000000 0.00000000 3.96254088 3.96254088 vdw total 3.96266640 3.96247376 -0.00019264 3.96247381 -0.00019259 3.96256316 -0.00010324 3.96254088 -0.00012552 vdw-14 5.56974080 5.56957853 -0.00016227 0.00000000 -5.56974080 5.56965202 -0.00008878 0.00000000 -5.56974080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.33093040 1.33072407 -0.00020633 1.33072409 -0.00020631 1.33052452 -0.00040588 1.33067936 -0.00025104 bond 1.14683440 1.14675903 -0.00007537 1.14675905 -0.00007535 1.14645178 -0.00038262 1.14675072 -0.00008368 bonded 16.32345760 16.32318932 -0.00026828 16.32318890 -0.00026870 16.32269918 -0.00075842 16.32312288 -0.00033472 dihedral 13.84569280 13.84570621 0.00001341 13.84570577 0.00001297 13.84572288 0.00003008 13.84569280 -0.00000000 nonbonded 14.33522080 14.32889611 -0.00632469 14.32889585 -0.00632495 14.32899438 -0.00622642 14.33003264 -0.00518816 potential 30.65867840 30.65208543 -0.00659297 30.65208483 -0.00659357 30.65165480 -0.00702360 30.65315552 -0.00552288 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 30.65867840 Difference in potential energy from amber=>gromacs conversion: -0.00659297 Difference in potential energy from amber=>lammps conversion: -0.00659357 Difference in potential energy from amber=>desmond conversion: -0.00702360 Difference in potential energy from amber=>charmm conversion: -0.00552288 ======================================================================= INFO 2017-03-18 23:35:48 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5310099.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5310099.inpcrd') INFO 2017-03-18 23:35:49 Beginning InterMol conversion INFO 2017-03-18 23:35:49 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:35:49 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:35:49 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5311804.inpcrd INFO 2017-03-18 23:35:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5311804/mobley_5311804_converted.input INFO 2017-03-18 23:35:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5311804/mobley_5311804_converted.cms WARNING 2017-03-18 23:36:05 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:36:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5311804/mobley_5311804_converted.inp INFO 2017-03-18 23:36:05 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5311804/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5311804/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5311804/mobley_5311804_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5311804/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -29.52522534 -29.52522534 0.00000000 0.00000000 0.00000000 0.00000000 14.24463720 14.24463720 coulomb total 14.26618480 14.24975562 -0.01642918 14.24975549 -0.01642931 14.24983657 -0.01634823 14.24463720 -0.02154760 coulomb-14 43.77928400 43.77498096 -0.00430304 0.00000000 -43.77928400 43.77503013 -0.00425387 0.00000000 -43.77928400 improper 0.00000000 0.00007041 0.00007041 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00627600 0.00614318 -0.00013282 0.00621354 -0.00006246 0.00621407 -0.00006193 0.00615048 -0.00012552 vdw (SR) 0.00000000 -2.48023448 -2.48023448 0.00000000 0.00000000 0.00000000 0.00000000 14.54153384 14.54153384 vdw total 14.54149200 14.54152985 0.00003785 14.54152966 0.00003766 14.54158375 0.00009175 14.54153384 0.00004184 vdw-14 17.02176720 17.02176433 -0.00000287 0.00000000 -17.02176720 17.02182268 0.00005548 0.00000000 -17.02176720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.79454160 0.79451002 -0.00003158 0.79451001 -0.00003159 0.79454612 0.00000452 0.79445792 -0.00008368 bond 1.51586320 1.51591844 0.00005524 1.51591843 0.00005523 1.51569248 -0.00017072 1.51590504 0.00004184 bonded 2.31668080 2.31664206 -0.00003874 2.31664198 -0.00003882 2.31645267 -0.00022813 2.31659712 -0.00008368 dihedral 0.00627600 0.00621359 -0.00006241 0.00621354 -0.00006246 0.00621407 -0.00006193 0.00623416 -0.00004184 nonbonded 28.80767680 28.79128547 -0.01639133 28.79128514 -0.01639166 28.79142032 -0.01625648 28.78617104 -0.02150576 potential 31.12435760 31.10792753 -0.01643007 31.10792745 -0.01643015 31.10782787 -0.01652973 31.10276816 -0.02158944 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 31.12435760 Difference in potential energy from amber=>gromacs conversion: -0.01643007 Difference in potential energy from amber=>lammps conversion: -0.01643015 Difference in potential energy from amber=>desmond conversion: -0.01652973 Difference in potential energy from amber=>charmm conversion: -0.02158944 ======================================================================= INFO 2017-03-18 23:36:05 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5311804.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5311804.inpcrd') INFO 2017-03-18 23:36:05 Beginning InterMol conversion INFO 2017-03-18 23:36:05 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:36:05 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:36:05 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5326154.inpcrd INFO 2017-03-18 23:36:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5326154/mobley_5326154_converted.input INFO 2017-03-18 23:36:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5326154/mobley_5326154_converted.cms WARNING 2017-03-18 23:36:20 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:36:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5326154/mobley_5326154_converted.inp INFO 2017-03-18 23:36:21 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5326154/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5326154/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5326154/mobley_5326154_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5326154/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 14.65348804 14.65348804 0.00000000 0.00000000 0.00000000 0.00000000 -62.14428256 -62.14428256 coulomb total -62.09516240 -62.12913443 -0.03397203 -62.12913230 -0.03396990 -62.12938940 -0.03422700 -62.14428256 -0.04912016 coulomb-14 -76.77221600 -76.78262247 -0.01040647 0.00000000 76.77221600 -76.78257809 -0.01036209 0.00000000 76.77221600 improper 0.00000000 0.00103230 0.00103230 0.00000000 0.00000000 0.00000000 0.00000000 0.00104600 0.00104600 proper 8.97007760 8.96909246 -0.00098514 8.97010354 0.00002594 8.97013542 0.00005782 8.96907344 -0.00100416 vdw (SR) 0.00000000 12.74681414 12.74681414 0.00000000 0.00000000 0.00000000 0.00000000 36.40527688 36.40527688 vdw total 36.40540240 36.40512660 -0.00027580 36.40512667 -0.00027573 36.40491099 -0.00049141 36.40527688 -0.00012552 vdw-14 23.65842800 23.65831246 -0.00011554 0.00000000 -23.65842800 23.65831390 -0.00011410 0.00000000 -23.65842800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.07440320 3.07451902 0.00011582 3.07451901 0.00011581 3.07457902 0.00017582 3.07457056 0.00016736 bond 5.02707600 5.02705774 -0.00001826 5.02705759 -0.00001841 5.02615782 -0.00091818 5.02707600 0.00000000 bonded 17.07155680 17.07170153 0.00014473 17.07168014 0.00012334 17.07087226 -0.00068454 17.07176600 0.00020920 dihedral 8.97007760 8.97012477 0.00004717 8.97010354 0.00002594 8.97013542 0.00005782 8.97011944 0.00004184 nonbonded -25.68976000 -25.72400783 -0.03424783 -25.72400688 -0.03424688 -25.72447841 -0.03471841 -25.73900568 -0.04924568 potential -8.61820320 -8.65230630 -0.03410310 -8.65232665 -0.03412345 -8.65366695 -0.03546375 -8.66723968 -0.04903648 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -8.61820320 Difference in potential energy from amber=>gromacs conversion: -0.03410310 Difference in potential energy from amber=>lammps conversion: -0.03412345 Difference in potential energy from amber=>desmond conversion: -0.03546375 Difference in potential energy from amber=>charmm conversion: -0.04903648 ======================================================================= INFO 2017-03-18 23:36:21 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5326154.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5326154.inpcrd') INFO 2017-03-18 23:36:21 Beginning InterMol conversion INFO 2017-03-18 23:36:21 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:36:21 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:36:21 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5346580.inpcrd INFO 2017-03-18 23:36:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5346580/mobley_5346580_converted.input INFO 2017-03-18 23:36:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5346580/mobley_5346580_converted.cms WARNING 2017-03-18 23:36:37 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:36:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5346580/mobley_5346580_converted.inp INFO 2017-03-18 23:36:37 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5346580/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5346580/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5346580/mobley_5346580_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5346580/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -80.00796799 -80.00796799 0.00000000 0.00000000 0.00000000 0.00000000 -7.44655768 -7.44655768 coulomb total -7.44584640 -7.44526614 0.00058026 -7.44526608 0.00058032 -7.44530164 0.00054476 -7.44655768 -0.00071128 coulomb-14 72.56143840 72.56270185 0.00126345 0.00000000 -72.56143840 72.56269486 0.00125646 0.00000000 -72.56143840 improper 0.00000000 0.00301773 0.00301773 0.00000000 0.00000000 0.00000000 0.00000000 0.00301248 0.00301248 proper 11.05705680 11.05401697 -0.00303983 11.05703337 -0.00002343 11.05703843 -0.00001837 11.05400248 -0.00305432 vdw (SR) 0.00000000 4.37488646 4.37488646 0.00000000 0.00000000 0.00000000 0.00000000 17.99801992 17.99801992 vdw total 17.99789440 17.99781656 -0.00007784 17.99781700 -0.00007740 17.99775319 -0.00014121 17.99801992 0.00012552 vdw-14 13.62310400 13.62293010 -0.00017390 0.00000000 -13.62310400 13.62301710 -0.00008690 0.00000000 -13.62310400 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.06852160 4.06838633 -0.00013527 4.06838633 -0.00013527 4.06816841 -0.00035319 4.06835424 -0.00016736 bond 2.77943120 2.77963513 0.00020393 2.77963513 0.00020393 2.77901444 -0.00041676 2.77964040 0.00020920 bonded 17.90500960 17.90505616 0.00004656 17.90505483 0.00004523 17.90422129 -0.00078831 17.90500960 0.00000000 dihedral 11.05705680 11.05703470 -0.00002210 11.05703337 -0.00002343 11.05703843 -0.00001837 11.05701496 -0.00004184 nonbonded 10.55204800 10.55255041 0.00050241 10.55255092 0.00050292 10.55245155 0.00040355 10.55146224 -0.00058576 potential 28.45705760 28.45760657 0.00054897 28.45760570 0.00054810 28.45662903 -0.00042857 28.45647184 -0.00058576 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 28.45705760 Difference in potential energy from amber=>gromacs conversion: 0.00054897 Difference in potential energy from amber=>lammps conversion: 0.00054810 Difference in potential energy from amber=>desmond conversion: -0.00042857 Difference in potential energy from amber=>charmm conversion: -0.00058576 ======================================================================= INFO 2017-03-18 23:36:37 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5346580.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5346580.inpcrd') INFO 2017-03-18 23:36:37 Beginning InterMol conversion INFO 2017-03-18 23:36:37 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:36:37 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:36:37 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5347550.inpcrd INFO 2017-03-18 23:36:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5347550/mobley_5347550_converted.input INFO 2017-03-18 23:36:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5347550/mobley_5347550_converted.cms WARNING 2017-03-18 23:36:53 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:36:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5347550/mobley_5347550_converted.inp INFO 2017-03-18 23:36:53 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5347550/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5347550/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5347550/mobley_5347550_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5347550/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -34.30594894 -34.30594894 0.00000000 0.00000000 0.00000000 0.00000000 3.83220928 3.83220928 coulomb total 3.83965680 3.83645122 -0.00320558 3.83645119 -0.00320561 3.83655081 -0.00310599 3.83220928 -0.00744752 coulomb-14 38.14343600 38.14240017 -0.00103583 0.00000000 -38.14343600 38.14235377 -0.00108223 0.00000000 -38.14343600 proper 0.02259360 0.02239037 -0.00020323 0.02239037 -0.00020323 0.02239030 -0.00020330 0.02238440 -0.00020920 vdw (SR) 0.00000000 2.39955603 2.39955603 0.00000000 0.00000000 0.00000000 0.00000000 14.96436888 14.96436888 vdw total 14.96449440 14.96447619 -0.00001821 14.96447641 -0.00001799 14.96444480 -0.00004960 14.96436888 -0.00012552 vdw-14 12.56497040 12.56492016 -0.00005024 0.00000000 -12.56497040 12.56485287 -0.00011753 0.00000000 -12.56497040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.64849600 1.64856085 0.00006485 1.64856085 0.00006485 1.64833663 -0.00015937 1.64857968 0.00008368 bond 1.53636480 1.53650375 0.00013895 1.53650375 0.00013895 1.53619095 -0.00017385 1.53649032 0.00012552 bonded 3.20745440 3.20745497 0.00000057 3.20745497 0.00000057 3.20691787 -0.00053653 3.20745440 -0.00000000 dihedral 0.02259360 0.02239037 -0.00020323 0.02239037 -0.00020323 0.02239030 -0.00020330 0.02238440 -0.00020920 nonbonded 18.80415120 18.80092741 -0.00322379 18.80092743 -0.00322377 18.80099561 -0.00315559 18.79657816 -0.00757304 potential 22.01160560 22.00838239 -0.00322321 22.00838266 -0.00322294 22.00786301 -0.00374259 22.00403256 -0.00757304 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 22.01160560 Difference in potential energy from amber=>gromacs conversion: -0.00322321 Difference in potential energy from amber=>lammps conversion: -0.00322294 Difference in potential energy from amber=>desmond conversion: -0.00374259 Difference in potential energy from amber=>charmm conversion: -0.00757304 ======================================================================= INFO 2017-03-18 23:36:53 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5347550.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5347550.inpcrd') INFO 2017-03-18 23:36:53 Beginning InterMol conversion INFO 2017-03-18 23:36:53 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:36:53 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5371840.inpcrd INFO 2017-03-18 23:36:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5371840/mobley_5371840_converted.input INFO 2017-03-18 23:36:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5371840/mobley_5371840_converted.cms INFO 2017-03-18 23:37:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5371840/mobley_5371840_converted.rst7 WARNING 2017-03-18 23:37:09 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:37:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5371840/mobley_5371840_converted.inp INFO 2017-03-18 23:37:09 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5371840/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5371840/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5371840/mobley_5371840_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_5371840/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5371840/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -30.50074698 -30.50074698 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -3.60857448 -3.60857448 coulomb total -3.66392880 -3.67207820 -0.00814940 -3.67207814 -0.00814934 -3.67215124 -0.00822244 -3.66392880 0.00000000 -3.60857448 0.05535432 coulomb-14 26.82697120 26.82866878 0.00169758 0.00000000 -26.82697120 26.82857986 0.00160866 26.82697120 0.00000000 0.00000000 -26.82697120 improper 0.00000000 0.00012085 0.00012085 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00125520 0.00100010 -0.00025510 0.00112092 -0.00013428 0.00111027 -0.00014493 0.00125520 0.00000000 0.00100416 -0.00025104 vdw (SR) 0.00000000 -7.60711167 -7.60711167 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 39.72256128 39.72256128 vdw total 39.72289600 39.72262645 -0.00026955 39.72262655 -0.00026945 39.72269291 -0.00020309 39.72289600 0.00000000 39.72256128 -0.00033472 vdw-14 47.32982640 47.32973812 -0.00008828 0.00000000 -47.32982640 47.32981552 -0.00001088 47.32982640 0.00000000 0.00000000 -47.32982640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 7.04041680 7.04058945 0.00017265 7.04058960 0.00017280 7.04128770 0.00087090 7.04041680 0.00000000 7.04058416 0.00016736 bond 1.59745120 1.59749340 0.00004220 1.59749342 0.00004222 1.59774557 0.00029437 1.59745120 0.00000000 1.59749304 0.00004184 bonded 8.63912320 8.63920379 0.00008059 8.63920394 0.00008074 8.64014353 0.00102033 8.63912320 0.00000000 8.63920688 0.00008368 dihedral 0.00125520 0.00112094 -0.00013426 0.00112092 -0.00013428 0.00111027 -0.00014493 0.00125520 0.00000000 0.00112968 -0.00012552 nonbonded 36.05896720 36.05054825 -0.00841895 36.05054816 -0.00841904 36.05054167 -0.00842553 36.05896720 0.00000000 36.11398680 0.05501960 potential 44.69809040 44.68975204 -0.00833836 44.68975169 -0.00833871 44.69053912 -0.00755128 44.69809040 0.00000000 44.75319368 0.05510328 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 44.69809040 Difference in potential energy from amber=>gromacs conversion: -0.00833836 Difference in potential energy from amber=>lammps conversion: -0.00833871 Difference in potential energy from amber=>desmond conversion: -0.00755128 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.05510328 ======================================================================= INFO 2017-03-18 23:37:09 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5371840.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5371840.inpcrd') INFO 2017-03-18 23:37:09 Beginning InterMol conversion INFO 2017-03-18 23:37:09 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:37:09 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:37:09 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5390332.inpcrd INFO 2017-03-18 23:37:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5390332/mobley_5390332_converted.input INFO 2017-03-18 23:37:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5390332/mobley_5390332_converted.cms WARNING 2017-03-18 23:37:25 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:37:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5390332/mobley_5390332_converted.inp INFO 2017-03-18 23:37:25 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5390332/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5390332/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5390332/mobley_5390332_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5390332/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -46.53529131 -46.53529131 0.00000000 0.00000000 0.00000000 0.00000000 -63.26710080 -63.26710080 coulomb total -63.26249840 -63.26392894 -0.00143054 -63.26392933 -0.00143093 -63.26387966 -0.00138126 -63.26710080 -0.00460240 coulomb-14 -16.72428480 -16.72863763 -0.00435283 0.00000000 16.72428480 -16.72863210 -0.00434730 0.00000000 16.72428480 improper 0.00000000 0.00003243 0.00003243 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 3.26937760 3.26948209 0.00010449 3.26951454 0.00013694 3.26949414 0.00011654 3.26950312 0.00012552 vdw (SR) 0.00000000 -1.76368033 -1.76368033 0.00000000 0.00000000 0.00000000 0.00000000 10.08030200 10.08030200 vdw total 10.08051120 10.08019452 -0.00031668 10.08019447 -0.00031673 10.08027765 -0.00023355 10.08030200 -0.00020920 vdw-14 11.84406720 11.84387485 -0.00019235 0.00000000 -11.84406720 11.84395837 -0.00010883 0.00000000 -11.84406720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.84763040 2.84744462 -0.00018578 2.84744463 -0.00018577 2.84761782 -0.00001258 2.84746304 -0.00016736 bond 1.88823920 1.88825165 0.00001245 1.88825167 0.00001247 1.88759838 -0.00064082 1.88823920 0.00000000 bonded 8.00524720 8.00521080 -0.00003640 8.00521084 -0.00003636 8.00471034 -0.00053686 8.00524720 0.00000000 dihedral 3.26937760 3.26951452 0.00013692 3.26951454 0.00013694 3.26949414 0.00011654 3.26954496 0.00016736 nonbonded -53.18198720 -53.18373442 -0.00174722 -53.18373193 -0.00174473 -53.18360201 -0.00161481 -53.18679880 -0.00481160 potential -45.17674000 -45.17852361 -0.00178361 -45.17852238 -0.00178238 -45.17893702 -0.00219702 -45.18155160 -0.00481160 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -45.17674000 Difference in potential energy from amber=>gromacs conversion: -0.00178361 Difference in potential energy from amber=>lammps conversion: -0.00178238 Difference in potential energy from amber=>desmond conversion: -0.00219702 Difference in potential energy from amber=>charmm conversion: -0.00481160 ======================================================================= INFO 2017-03-18 23:37:25 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5390332.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5390332.inpcrd') INFO 2017-03-18 23:37:25 Beginning InterMol conversion INFO 2017-03-18 23:37:25 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:37:26 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:37:26 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5393242.inpcrd INFO 2017-03-18 23:37:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5393242/mobley_5393242_converted.input INFO 2017-03-18 23:37:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5393242/mobley_5393242_converted.cms WARNING 2017-03-18 23:37:41 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:37:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5393242/mobley_5393242_converted.inp INFO 2017-03-18 23:37:41 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5393242/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5393242/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5393242/mobley_5393242_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5393242/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 804.46311902 804.46311902 0.00000000 0.00000000 0.00000000 0.00000000 -1183.99271320 -1183.99271320 coulomb total -1183.93309120 -1183.97996834 -0.04687714 -1183.97995200 -0.04686080 -1183.98002313 -0.04693193 -1183.99271320 -0.05962200 coulomb-14 -1988.38114800 -1988.44308736 -0.06193936 0.00000000 1988.38114800 -1988.44382432 -0.06267632 0.00000000 1988.38114800 improper 0.00000000 0.00004878 0.00004878 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 41.68268160 41.68259905 -0.00008255 41.68264771 -0.00003389 41.68262219 -0.00005941 41.68259792 -0.00008368 vdw (SR) 0.00000000 -21.48080675 -21.48080675 0.00000000 0.00000000 0.00000000 0.00000000 21.66885232 21.66885232 vdw total 21.66893600 21.66872124 -0.00021476 21.66872094 -0.00021506 21.66884588 -0.00009012 21.66885232 -0.00008368 vdw-14 43.14959200 43.14952799 -0.00006401 0.00000000 -43.14959200 43.14960497 0.00001297 0.00000000 -43.14959200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 8.69100480 8.69112123 0.00011643 8.69112112 0.00011632 8.69098606 -0.00001874 8.69113032 0.00012552 bond 8.05503680 8.05509791 0.00006111 8.05509789 0.00006109 8.05467505 -0.00036175 8.05507864 0.00004184 bonded 58.42872320 58.42886697 0.00014377 58.42886671 0.00014351 58.42828329 -0.00043991 58.42884872 0.00012552 dihedral 41.68268160 41.68264783 -0.00003377 41.68264771 -0.00003389 41.68262219 -0.00005941 41.68263976 -0.00004184 nonbonded -1162.26415520 -1162.31124710 -0.04709190 -1162.31122520 -0.04707000 -1162.31117725 -0.04702205 -1162.32386088 -0.05970568 potential -1103.83543200 -1103.88238013 -0.04694813 -1103.88237648 -0.04694448 -1103.88328441 -0.04785241 -1103.89497032 -0.05953832 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -1103.83543200 Difference in potential energy from amber=>gromacs conversion: -0.04694813 Difference in potential energy from amber=>lammps conversion: -0.04694448 Difference in potential energy from amber=>desmond conversion: -0.04785241 Difference in potential energy from amber=>charmm conversion: -0.05953832 ======================================================================= INFO 2017-03-18 23:37:41 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5393242.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5393242.inpcrd') INFO 2017-03-18 23:37:42 Beginning InterMol conversion INFO 2017-03-18 23:37:42 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:37:42 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:37:42 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5445548.inpcrd INFO 2017-03-18 23:37:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5445548/mobley_5445548_converted.input INFO 2017-03-18 23:37:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5445548/mobley_5445548_converted.cms WARNING 2017-03-18 23:37:57 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:37:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5445548/mobley_5445548_converted.inp INFO 2017-03-18 23:37:58 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5445548/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5445548/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5445548/mobley_5445548_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5445548/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -5.79924352 -5.79924352 0.00000000 0.00000000 0.00000000 0.00000000 -7.87508296 -7.87508296 coulomb total -7.86843040 -7.87470033 -0.00626993 -7.87470012 -0.00626972 -7.87485617 -0.00642577 -7.87508296 -0.00665256 coulomb-14 -2.07610080 -2.07545681 0.00064399 0.00000000 2.07610080 -2.07548461 0.00061619 0.00000000 2.07610080 improper 0.00000000 0.00001306 0.00001306 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.21003680 0.21010702 0.00007022 0.21012007 0.00008327 0.21009865 0.00006185 0.21016232 0.00012552 vdw (SR) 0.00000000 4.51860357 4.51860357 0.00000000 0.00000000 0.00000000 0.00000000 28.82081456 28.82081456 vdw total 28.82064720 28.82072080 0.00007360 28.82072084 0.00007364 28.82077590 0.00012870 28.82081456 0.00016736 vdw-14 24.30192720 24.30211723 0.00019003 0.00000000 -24.30192720 24.30221000 0.00028280 0.00000000 -24.30192720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.12379840 2.12390099 0.00010259 2.12390099 0.00010259 2.12372381 -0.00007459 2.12384024 0.00004184 bond 1.55142720 1.55150970 0.00008250 1.55150971 0.00008251 1.55154175 0.00011455 1.55151088 0.00008368 bonded 3.88526240 3.88553077 0.00026837 3.88553077 0.00026837 3.88536421 0.00010181 3.88551344 0.00025104 dihedral 0.21003680 0.21012008 0.00008328 0.21012007 0.00008327 0.21009865 0.00006185 0.21016232 0.00012552 nonbonded 20.95221680 20.94602047 -0.00619633 20.94602071 -0.00619609 20.94591973 -0.00629707 20.94573160 -0.00648520 potential 24.83747920 24.83155124 -0.00592796 24.83155131 -0.00592789 24.83121115 -0.00626805 24.83128688 -0.00619232 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 24.83747920 Difference in potential energy from amber=>gromacs conversion: -0.00592796 Difference in potential energy from amber=>lammps conversion: -0.00592789 Difference in potential energy from amber=>desmond conversion: -0.00626805 Difference in potential energy from amber=>charmm conversion: -0.00619232 ======================================================================= INFO 2017-03-18 23:37:58 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5445548.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5445548.inpcrd') INFO 2017-03-18 23:37:58 Beginning InterMol conversion INFO 2017-03-18 23:37:58 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:37:58 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:37:58 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5449201.inpcrd INFO 2017-03-18 23:37:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5449201/mobley_5449201_converted.input INFO 2017-03-18 23:37:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5449201/mobley_5449201_converted.cms WARNING 2017-03-18 23:38:14 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:38:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5449201/mobley_5449201_converted.inp INFO 2017-03-18 23:38:14 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5449201/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5449201/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5449201/mobley_5449201_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5449201/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 4.45328425 4.45328425 0.00000000 0.00000000 0.00000000 0.00000000 3.09795912 3.09795912 coulomb total 3.11624320 3.10577083 -0.01047237 3.10577082 -0.01047238 3.10575623 -0.01048697 3.09795912 -0.01828408 coulomb-14 -1.34431920 -1.34751342 -0.00319422 0.00000000 1.34431920 -1.34750333 -0.00318413 0.00000000 1.34431920 proper 3.40828640 3.40840303 0.00011663 3.40840305 0.00011665 3.40841642 0.00013002 3.40841192 0.00012552 vdw (SR) 0.00000000 -1.13947290 -1.13947290 0.00000000 0.00000000 0.00000000 0.00000000 4.20370664 4.20370664 vdw total 4.20366480 4.20363292 -0.00003188 4.20363300 -0.00003180 4.20363730 -0.00002750 4.20370664 0.00004184 vdw-14 5.34296800 5.34310582 0.00013782 0.00000000 -5.34296800 5.34312176 0.00015376 0.00000000 -5.34296800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.85855680 0.85850835 -0.00004845 0.85850835 -0.00004845 0.85882710 0.00027030 0.85847312 -0.00008368 bond 0.90248880 0.90247390 -0.00001490 0.90247390 -0.00001490 0.90280485 0.00031605 0.90248880 0.00000000 bonded 5.16933200 5.16938528 0.00005328 5.16938530 0.00005330 5.17004837 0.00071637 5.16937384 0.00004184 dihedral 3.40828640 3.40840303 0.00011663 3.40840305 0.00011665 3.40841642 0.00013002 3.40841192 0.00012552 nonbonded 7.31990800 7.30940375 -0.01050425 7.30940365 -0.01050435 7.30939354 -0.01051446 7.30166576 -0.01824224 potential 12.48924000 12.47878902 -0.01045098 12.47878920 -0.01045080 12.47940944 -0.00983056 12.47103960 -0.01820040 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 12.48924000 Difference in potential energy from amber=>gromacs conversion: -0.01045098 Difference in potential energy from amber=>lammps conversion: -0.01045080 Difference in potential energy from amber=>desmond conversion: -0.00983056 Difference in potential energy from amber=>charmm conversion: -0.01820040 ======================================================================= INFO 2017-03-18 23:38:14 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5449201.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5449201.inpcrd') INFO 2017-03-18 23:38:14 Beginning InterMol conversion INFO 2017-03-18 23:38:14 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:38:14 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5456566.inpcrd INFO 2017-03-18 23:38:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5456566/mobley_5456566_converted.input INFO 2017-03-18 23:38:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5456566/mobley_5456566_converted.cms INFO 2017-03-18 23:38:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5456566/mobley_5456566_converted.rst7 WARNING 2017-03-18 23:38:30 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:38:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5456566/mobley_5456566_converted.inp INFO 2017-03-18 23:38:30 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5456566/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5456566/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5456566/mobley_5456566_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_5456566/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5456566/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -2.53811136 -2.53811136 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.55291560 0.55291560 coulomb total 0.55186960 0.55110957 -0.00076003 0.55110958 -0.00076002 0.55110659 -0.00076301 0.55186960 0.00000000 0.55291560 0.00104600 coulomb-14 3.08904720 3.08922093 0.00017373 0.00000000 -3.08904720 3.08921499 0.00016779 3.08904720 0.00000000 0.00000000 -3.08904720 improper 0.00000000 0.00015145 0.00015145 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00016736 0.00016736 proper 33.47367360 33.47348379 -0.00018981 33.47363511 -0.00003849 33.47362674 -0.00004686 33.47367360 0.00000000 33.47346440 -0.00020920 vdw (SR) 0.00000000 -25.98878261 -25.98878261 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 40.66496544 40.66496544 vdw total 40.66471440 40.66480115 0.00008675 40.66480101 0.00008661 40.66505259 0.00033819 40.66471440 0.00000000 40.66496544 0.00025104 vdw-14 66.65363040 66.65358376 -0.00004664 0.00000000 -66.65363040 66.65384797 0.00021757 66.65363040 0.00000000 0.00000000 -66.65363040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.99325760 1.99332699 0.00006939 1.99332697 0.00006937 1.99337001 0.00011241 1.99325760 0.00000000 1.99342496 0.00016736 bond 5.48145840 5.48154402 0.00008562 5.48154417 0.00008577 5.48099034 -0.00046806 5.48145840 0.00000000 5.48154208 0.00008368 bonded 40.94838960 40.94850626 0.00011666 40.94850625 0.00011665 40.94798709 -0.00040251 40.94838960 0.00000000 40.94859880 0.00020920 dihedral 33.47367360 33.47363525 -0.00003835 33.47363511 -0.00003849 33.47362674 -0.00004686 33.47367360 0.00000000 33.47363176 -0.00004184 nonbonded 41.21658400 41.21591072 -0.00067328 41.21591079 -0.00067321 41.21615919 -0.00042481 41.21658400 0.00000000 41.21788104 0.00129704 potential 82.16497360 82.16441698 -0.00055662 82.16441713 -0.00055647 82.16367196 -0.00130164 82.16497360 0.00000000 82.16647984 0.00150624 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 82.16497360 Difference in potential energy from amber=>gromacs conversion: -0.00055662 Difference in potential energy from amber=>lammps conversion: -0.00055647 Difference in potential energy from amber=>desmond conversion: -0.00130164 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00150624 ======================================================================= INFO 2017-03-18 23:38:30 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5456566.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5456566.inpcrd') INFO 2017-03-18 23:38:30 Beginning InterMol conversion INFO 2017-03-18 23:38:30 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:38:30 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:38:30 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5467162.inpcrd INFO 2017-03-18 23:38:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5467162/mobley_5467162_converted.input INFO 2017-03-18 23:38:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5467162/mobley_5467162_converted.cms WARNING 2017-03-18 23:38:46 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:38:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5467162/mobley_5467162_converted.inp INFO 2017-03-18 23:38:46 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5467162/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5467162/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5467162/mobley_5467162_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5467162/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 19.06234955 19.06234955 0.00000000 0.00000000 0.00000000 0.00000000 -93.45143912 -93.45143912 coulomb total -93.41198400 -93.44640115 -0.03441715 -93.44640158 -0.03441758 -93.44694421 -0.03496021 -93.45143912 -0.03945512 coulomb-14 -112.52909840 -112.50875070 0.02034770 0.00000000 112.52909840 -112.50874952 0.02034888 0.00000000 112.52909840 improper 0.00000000 0.00013357 0.00013357 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.12761200 0.12766006 0.00004806 0.12779356 0.00018156 0.12778542 0.00017342 0.12765384 0.00004184 vdw (SR) 0.00000000 5.80717084 5.80717084 0.00000000 0.00000000 0.00000000 0.00000000 34.90539656 34.90539656 vdw total 34.90543840 34.90522598 -0.00021242 34.90522627 -0.00021213 34.90511397 -0.00032443 34.90539656 -0.00004184 vdw-14 29.09804640 29.09805514 0.00000874 0.00000000 -29.09804640 29.09803619 -0.00001021 0.00000000 -29.09804640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.16807680 5.16819246 0.00011566 5.16819228 0.00011548 5.16842570 0.00034890 5.16811864 0.00004184 bond 2.10246000 2.10233603 -0.00012397 2.10233603 -0.00012397 2.10203496 -0.00042504 2.10233448 -0.00012552 bonded 7.39814880 7.39832211 0.00017331 7.39832187 0.00017307 7.39824609 0.00009729 7.39823248 0.00008368 dihedral 0.12761200 0.12779363 0.00018163 0.12779356 0.00018156 0.12778542 0.00017342 0.12777936 0.00016736 nonbonded -58.50654560 -58.54117517 -0.03462957 -58.54117238 -0.03462678 -58.54183023 -0.03528463 -58.54604256 -0.03949696 potential -51.10839680 -51.14285305 -0.03445625 -51.14285204 -0.03445524 -51.14368633 -0.03528953 -51.14781008 -0.03941328 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -51.10839680 Difference in potential energy from amber=>gromacs conversion: -0.03445625 Difference in potential energy from amber=>lammps conversion: -0.03445524 Difference in potential energy from amber=>desmond conversion: -0.03528953 Difference in potential energy from amber=>charmm conversion: -0.03941328 ======================================================================= INFO 2017-03-18 23:38:46 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5467162.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5467162.inpcrd') INFO 2017-03-18 23:38:46 Beginning InterMol conversion INFO 2017-03-18 23:38:46 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:38:46 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:38:46 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5471704.inpcrd INFO 2017-03-18 23:38:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5471704/mobley_5471704_converted.input INFO 2017-03-18 23:38:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5471704/mobley_5471704_converted.cms WARNING 2017-03-18 23:39:02 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:39:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5471704/mobley_5471704_converted.inp INFO 2017-03-18 23:39:02 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5471704/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5471704/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5471704/mobley_5471704_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5471704/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 21.26770323 21.26770323 0.00000000 0.00000000 0.00000000 0.00000000 -125.56794864 -125.56794864 coulomb total -125.50535600 -125.51035836 -0.00500236 -125.51035588 -0.00499988 -125.51020647 -0.00485047 -125.56794864 -0.06259264 coulomb-14 -146.77597520 -146.77806160 -0.00208640 0.00000000 146.77597520 -146.77786511 -0.00188991 0.00000000 146.77597520 improper 0.00000000 0.00000114 0.00000114 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 24.86258320 24.86258708 0.00000388 24.86259199 0.00000879 24.86264362 0.00006042 24.86258320 0.00000000 vdw (SR) 0.00000000 1.61159559 1.61159559 0.00000000 0.00000000 0.00000000 0.00000000 16.22199560 16.22199560 vdw total 16.22178640 16.22178455 -0.00000185 16.22178473 -0.00000167 16.22180862 0.00002222 16.22199560 0.00020920 vdw-14 14.61010960 14.61018896 0.00007936 0.00000000 -14.61010960 14.61013014 0.00002054 0.00000000 -14.61010960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.61871760 4.61873126 0.00001366 4.61873141 0.00001381 4.61951022 0.00079262 4.61875944 0.00004184 bond 2.35517360 2.35498356 -0.00019004 2.35498356 -0.00019004 2.35516007 -0.00001353 2.35496440 -0.00020920 bonded 31.83647440 31.83630304 -0.00017136 31.83630696 -0.00016744 31.83731391 0.00083951 31.83630704 -0.00016736 dihedral 24.86258320 24.86258821 0.00000501 24.86259199 0.00000879 24.86264362 0.00006042 24.86258320 0.00000000 nonbonded -109.28356960 -109.28857381 -0.00500421 -109.28857366 -0.00500406 -109.28839785 -0.00482825 -109.34595304 -0.06238344 potential -77.44709520 -77.45227078 -0.00517558 -77.45226662 -0.00517142 -77.45116581 -0.00407061 -77.50964600 -0.06255080 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -77.44709520 Difference in potential energy from amber=>gromacs conversion: -0.00517558 Difference in potential energy from amber=>lammps conversion: -0.00517142 Difference in potential energy from amber=>desmond conversion: -0.00407061 Difference in potential energy from amber=>charmm conversion: -0.06255080 ======================================================================= INFO 2017-03-18 23:39:02 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5471704.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5471704.inpcrd') INFO 2017-03-18 23:39:02 Beginning InterMol conversion INFO 2017-03-18 23:39:02 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:39:03 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:39:03 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_547634.inpcrd INFO 2017-03-18 23:39:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_547634/mobley_547634_converted.input INFO 2017-03-18 23:39:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_547634/mobley_547634_converted.cms WARNING 2017-03-18 23:39:18 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:39:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_547634/mobley_547634_converted.inp INFO 2017-03-18 23:39:18 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_547634/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_547634/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_547634/mobley_547634_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_547634/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -3.53628716 -3.53628716 0.00000000 0.00000000 0.00000000 0.00000000 -22.28118072 -22.28118072 coulomb total -22.30657760 -22.31308433 -0.00650673 -22.31308414 -0.00650654 -22.31324068 -0.00666308 -22.28118072 0.02539688 coulomb-14 -18.77862880 -18.77679717 0.00183163 0.00000000 18.77862880 -18.77682278 0.00180602 0.00000000 18.77862880 improper 0.00000000 0.00004902 0.00004902 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00055641 0.00013801 0.00060535 0.00018695 0.00059503 0.00017663 0.00054392 0.00012552 vdw (SR) 0.00000000 21.69996580 21.69996580 0.00000000 0.00000000 0.00000000 0.00000000 58.84699768 58.84699768 vdw total 58.84712320 58.84671017 -0.00041303 58.84670898 -0.00041422 58.84648581 -0.00063739 58.84699768 -0.00012552 vdw-14 37.14680720 37.14674437 -0.00006283 0.00000000 -37.14680720 37.14696983 0.00016263 0.00000000 -37.14680720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.85602240 1.85592259 -0.00009981 1.85592257 -0.00009983 1.85574757 -0.00027483 1.85593872 -0.00008368 bond 5.82998560 5.82987080 -0.00011480 5.82987096 -0.00011464 5.82979117 -0.00019443 5.82986008 -0.00012552 bonded 7.68642640 7.68639881 -0.00002759 7.68639888 -0.00002752 7.68613377 -0.00029263 7.68638456 -0.00004184 dihedral 0.00041840 0.00060542 0.00018702 0.00060535 0.00018695 0.00059503 0.00017663 0.00058576 0.00016736 nonbonded 36.54054560 36.53362584 -0.00691976 36.53362652 -0.00691908 36.53324513 -0.00730047 36.56581696 0.02527136 potential 44.22697200 44.22002464 -0.00694736 44.22002656 -0.00694544 44.21926967 -0.00770233 44.25224336 0.02527136 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 44.22697200 Difference in potential energy from amber=>gromacs conversion: -0.00694736 Difference in potential energy from amber=>lammps conversion: -0.00694544 Difference in potential energy from amber=>desmond conversion: -0.00770233 Difference in potential energy from amber=>charmm conversion: 0.02527136 ======================================================================= INFO 2017-03-18 23:39:18 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_547634.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_547634.inpcrd') INFO 2017-03-18 23:39:19 Beginning InterMol conversion INFO 2017-03-18 23:39:19 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:39:19 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:39:19 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5494918.inpcrd INFO 2017-03-18 23:39:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5494918/mobley_5494918_converted.input INFO 2017-03-18 23:39:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5494918/mobley_5494918_converted.cms WARNING 2017-03-18 23:39:34 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:39:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5494918/mobley_5494918_converted.inp INFO 2017-03-18 23:39:34 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5494918/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5494918/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5494918/mobley_5494918_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5494918/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 61.73714522 61.73714522 0.00000000 0.00000000 0.00000000 0.00000000 -53.06144616 -53.06144616 coulomb total -53.04642560 -53.04833263 -0.00190703 -53.04833350 -0.00190790 -53.04832472 -0.00189912 -53.06144616 -0.01502056 coulomb-14 -114.78134560 -114.78547785 -0.00413225 0.00000000 114.78134560 -114.78544299 -0.00409739 0.00000000 114.78134560 improper 0.00000000 0.00000794 0.00000794 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00000000 0.00005466 0.00005466 0.00006254 0.00006254 0.00006534 0.00006534 0.00004184 0.00004184 vdw (SR) 0.00000000 0.65344984 0.65344984 0.00000000 0.00000000 0.00000000 0.00000000 7.51567736 7.51567736 vdw total 7.51571920 7.51586806 0.00014886 7.51586815 0.00014895 7.51575286 0.00003366 7.51567736 -0.00004184 vdw-14 6.86217840 6.86241822 0.00023982 0.00000000 -6.86217840 6.86232551 0.00014711 0.00000000 -6.86217840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 14.06242400 14.06221975 -0.00020425 14.06221982 -0.00020418 14.06231894 -0.00010506 14.06225664 -0.00016736 bond 2.35182640 2.35169900 -0.00012740 2.35169900 -0.00012740 2.35239163 0.00056523 2.35170088 -0.00012552 bonded 16.41425040 16.41398135 -0.00026905 16.41398136 -0.00026904 16.41477591 0.00052551 16.41399936 -0.00025104 dihedral 0.00000000 0.00006260 0.00006260 0.00006254 0.00006254 0.00006534 0.00006534 0.00004184 0.00004184 nonbonded -45.53070640 -45.53246456 -0.00175816 -45.53246368 -0.00175728 -45.53257185 -0.00186545 -45.54576880 -0.01506240 potential -29.11645600 -29.11848321 -0.00202721 -29.11848273 -0.00202673 -29.11782103 -0.00136503 -29.13172760 -0.01527160 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -29.11645600 Difference in potential energy from amber=>gromacs conversion: -0.00202721 Difference in potential energy from amber=>lammps conversion: -0.00202673 Difference in potential energy from amber=>desmond conversion: -0.00136503 Difference in potential energy from amber=>charmm conversion: -0.01527160 ======================================================================= INFO 2017-03-18 23:39:34 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5494918.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5494918.inpcrd') INFO 2017-03-18 23:39:35 Beginning InterMol conversion INFO 2017-03-18 23:39:35 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:39:35 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:39:35 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5499659.inpcrd INFO 2017-03-18 23:39:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5499659/mobley_5499659_converted.input INFO 2017-03-18 23:39:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5499659/mobley_5499659_converted.cms WARNING 2017-03-18 23:39:50 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:39:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5499659/mobley_5499659_converted.inp INFO 2017-03-18 23:39:50 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5499659/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5499659/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5499659/mobley_5499659_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5499659/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 2.73495079 2.73495079 0.00000000 0.00000000 0.00000000 0.00000000 -0.31346528 -0.31346528 coulomb total -0.30668720 -0.29873512 0.00795208 -0.29873511 0.00795209 -0.29883368 0.00785352 -0.31346528 -0.00677808 coulomb-14 -3.03842080 -3.03368591 0.00473489 0.00000000 3.03842080 -3.03373284 0.00468796 0.00000000 3.03842080 improper 0.00000000 0.00000632 0.00000632 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00041840 0.00031634 -0.00010206 0.00032256 -0.00009584 0.00032221 -0.00009619 0.00033472 -0.00008368 vdw (SR) 0.00000000 -0.75442024 -0.75442024 0.00000000 0.00000000 0.00000000 0.00000000 -0.88968576 -0.88968576 vdw total -0.88951840 -0.88968174 -0.00016334 -0.88968174 -0.00016334 -0.88966312 -0.00014472 -0.88968576 -0.00016736 vdw-14 -0.13514320 -0.13526151 -0.00011831 0.00000000 0.13514320 -0.13524255 -0.00009935 0.00000000 0.13514320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 10.92065840 10.92046603 -0.00019237 10.92046594 -0.00019246 10.92090162 0.00024322 10.92049104 -0.00016736 bond 8.60021200 8.60024557 0.00003357 8.60024547 0.00003347 8.59904571 -0.00116629 8.60025384 0.00004184 bonded 19.52128880 19.52103426 -0.00025454 19.52103396 -0.00025484 19.52026953 -0.00101927 19.52107960 -0.00020920 dihedral 0.00041840 0.00032266 -0.00009574 0.00032256 -0.00009584 0.00032221 -0.00009619 0.00033472 -0.00008368 nonbonded -1.19620560 -1.18841686 0.00778874 -1.18841687 0.00778873 -1.18849680 0.00770880 -1.20315104 -0.00694544 potential 18.32508320 18.33261740 0.00753420 18.33261733 0.00753413 18.33174434 0.00666114 18.31792856 -0.00715464 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 18.32508320 Difference in potential energy from amber=>gromacs conversion: 0.00753420 Difference in potential energy from amber=>lammps conversion: 0.00753413 Difference in potential energy from amber=>desmond conversion: 0.00666114 Difference in potential energy from amber=>charmm conversion: -0.00715464 ======================================================================= INFO 2017-03-18 23:39:50 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5499659.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5499659.inpcrd') INFO 2017-03-18 23:39:51 Beginning InterMol conversion INFO 2017-03-18 23:39:51 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:39:51 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:39:51 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_550662.inpcrd INFO 2017-03-18 23:39:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_550662/mobley_550662_converted.input INFO 2017-03-18 23:39:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_550662/mobley_550662_converted.cms WARNING 2017-03-18 23:40:06 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:40:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_550662/mobley_550662_converted.inp INFO 2017-03-18 23:40:06 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_550662/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_550662/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_550662/mobley_550662_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_550662/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -30.55739148 -30.55739148 0.00000000 0.00000000 0.00000000 0.00000000 -207.28046448 -207.28046448 coulomb total -207.26615520 -207.26501090 0.00114430 -207.26500878 0.00114642 -207.26496577 0.00118943 -207.28046448 -0.01430928 coulomb-14 -176.70036160 -176.70761943 -0.00725783 0.00000000 176.70036160 -176.70755766 -0.00719606 0.00000000 176.70036160 proper 64.02398640 64.02405656 0.00007016 64.02403661 0.00005021 64.02402406 0.00003766 64.02402824 0.00004184 vdw (SR) 0.00000000 7.30816078 7.30816078 0.00000000 0.00000000 0.00000000 0.00000000 24.92530136 24.92530136 vdw total 24.92492480 24.92500686 0.00008206 24.92500722 0.00008242 24.92505940 0.00013460 24.92530136 0.00037656 vdw-14 17.61673200 17.61684608 0.00011408 0.00000000 -17.61673200 17.61690785 0.00017585 0.00000000 -17.61673200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.48901360 4.48888322 -0.00013038 4.48888306 -0.00013054 4.48900653 -0.00000707 4.48897176 -0.00004184 bond 1.41753920 1.41750532 -0.00003388 1.41750531 -0.00003389 1.41730038 -0.00023882 1.41749736 -0.00004184 bonded 69.93053920 69.93044510 -0.00009410 69.93042498 -0.00011422 69.93033097 -0.00020823 69.93049736 -0.00004184 dihedral 64.02398640 64.02405656 0.00007016 64.02403661 0.00005021 64.02402406 0.00003766 64.02402824 0.00004184 nonbonded -182.34123040 -182.34000404 0.00122636 -182.34000030 0.00123010 -182.33990637 0.00132403 -182.35516312 -0.01393272 potential -112.41069120 -112.40955895 0.00113225 -112.40957826 0.00111294 -112.40963558 0.00105562 -112.42466576 -0.01397456 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -112.41069120 Difference in potential energy from amber=>gromacs conversion: 0.00113225 Difference in potential energy from amber=>lammps conversion: 0.00111294 Difference in potential energy from amber=>desmond conversion: 0.00105562 Difference in potential energy from amber=>charmm conversion: -0.01397456 ======================================================================= INFO 2017-03-18 23:40:06 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_550662.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_550662.inpcrd') INFO 2017-03-18 23:40:07 Beginning InterMol conversion INFO 2017-03-18 23:40:07 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:40:07 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5510474.inpcrd INFO 2017-03-18 23:40:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5510474/mobley_5510474_converted.input INFO 2017-03-18 23:40:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5510474/mobley_5510474_converted.cms INFO 2017-03-18 23:40:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5510474/mobley_5510474_converted.rst7 WARNING 2017-03-18 23:40:23 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:40:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5510474/mobley_5510474_converted.inp INFO 2017-03-18 23:40:23 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5510474/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5510474/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5510474/mobley_5510474_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_5510474/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5510474/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -6.83196891 -6.83196891 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 25.76574144 25.76574144 coulomb total 25.76674560 25.76629062 -0.00045498 25.76629038 -0.00045522 25.76629046 -0.00045514 25.76674560 0.00000000 25.76574144 -0.00100416 coulomb-14 32.59628880 32.59825953 0.00197073 0.00000000 -32.59628880 32.59824867 0.00195987 32.59628880 0.00000000 0.00000000 -32.59628880 improper 0.00000000 0.00013859 0.00013859 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00125520 0.00128341 0.00002821 0.00142193 0.00016673 0.00142150 0.00016630 0.00125520 0.00000000 0.00129704 0.00004184 vdw (SR) 0.00000000 -11.73847349 -11.73847349 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 48.54527840 48.54527840 vdw total 48.54527840 48.54520811 -0.00007029 48.54520727 -0.00007113 48.54515058 -0.00012782 48.54486000 -0.00041840 48.54527840 0.00000000 vdw-14 60.28390880 60.28368160 -0.00022720 0.00000000 -60.28390880 60.28362261 -0.00028619 60.28349040 -0.00041840 0.00000000 -60.28390880 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 7.62743200 7.62726706 -0.00016494 7.62726715 -0.00016485 7.62800826 0.00057626 7.62743200 0.00000000 7.62730648 -0.00012552 bond 2.19994720 2.19977150 -0.00017570 2.19977151 -0.00017569 2.20028265 0.00033545 2.19994720 0.00000000 2.19977984 -0.00016736 bonded 9.82863440 9.82846057 -0.00017383 9.82846060 -0.00017380 9.82971241 0.00107801 9.82863440 0.00000000 9.82850888 -0.00012552 dihedral 0.00125520 0.00142201 0.00016681 0.00142193 0.00016673 0.00142150 0.00016630 0.00125520 0.00000000 0.00142256 0.00016736 nonbonded 74.31202400 74.31149873 -0.00052527 74.31149682 -0.00052718 74.31144104 -0.00058296 74.31160560 -0.00041840 74.31101984 -0.00100416 potential 84.14065840 84.13995930 -0.00069910 84.13995967 -0.00069873 84.14090735 0.00024895 84.14024000 -0.00041840 84.13952872 -0.00112968 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 84.14065840 Difference in potential energy from amber=>gromacs conversion: -0.00069910 Difference in potential energy from amber=>lammps conversion: -0.00069873 Difference in potential energy from amber=>desmond conversion: 0.00024895 Difference in potential energy from amber=>amber conversion: -0.00041840 Difference in potential energy from amber=>charmm conversion: -0.00112968 ======================================================================= INFO 2017-03-18 23:40:23 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5510474.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5510474.inpcrd') INFO 2017-03-18 23:40:23 Beginning InterMol conversion INFO 2017-03-18 23:40:23 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:40:23 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:40:23 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5518547.inpcrd INFO 2017-03-18 23:40:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5518547/mobley_5518547_converted.input INFO 2017-03-18 23:40:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5518547/mobley_5518547_converted.cms WARNING 2017-03-18 23:40:39 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:40:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5518547/mobley_5518547_converted.inp INFO 2017-03-18 23:40:39 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5518547/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5518547/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5518547/mobley_5518547_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5518547/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 45.05995181 45.05995181 0.00000000 0.00000000 0.00000000 0.00000000 -124.64525112 -124.64525112 coulomb total -124.63131840 -124.66094129 -0.02962289 -124.66094112 -0.02962272 -124.66129258 -0.02997418 -124.64525112 -0.01393272 coulomb-14 -169.73023600 -169.72089311 0.00934289 0.00000000 169.73023600 -169.72079815 0.00943785 0.00000000 169.73023600 improper 0.00000000 0.11590930 0.11590930 0.00000000 0.00000000 0.00000000 0.00000000 0.11589680 0.11589680 proper 0.22258880 0.10679145 -0.11579735 0.22269929 0.00011049 0.22272898 0.00014018 0.10677568 -0.11581312 vdw (SR) 0.00000000 -1.98232650 -1.98232650 0.00000000 0.00000000 0.00000000 0.00000000 16.12195616 16.12195616 vdw total 16.12178880 16.12197650 0.00018770 16.12197666 0.00018786 16.12206042 0.00027162 16.12195616 0.00016736 vdw-14 18.10416800 18.10430300 0.00013500 0.00000000 -18.10416800 18.10438603 0.00021803 0.00000000 -18.10416800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.68819600 3.68825224 0.00005624 3.68825223 0.00005623 3.68821443 0.00001843 3.68832152 0.00012552 bond 5.95215840 5.95216045 0.00000205 5.95216049 0.00000209 5.95250521 0.00034681 5.95215840 0.00000000 bonded 9.86294320 9.86311344 0.00017024 9.86311202 0.00016882 9.86344863 0.00050543 9.86315240 0.00020920 dihedral 0.22258880 0.22270075 0.00011195 0.22269929 0.00011049 0.22272898 0.00014018 0.22267248 0.00008368 nonbonded -108.50952960 -108.53896479 -0.02943519 -108.53896404 -0.02943444 -108.53923216 -0.02970256 -108.52329496 -0.01376536 potential -98.64658640 -98.67585136 -0.02926496 -98.67585348 -0.02926708 -98.67582001 -0.02923361 -98.66010072 -0.01351432 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -98.64658640 Difference in potential energy from amber=>gromacs conversion: -0.02926496 Difference in potential energy from amber=>lammps conversion: -0.02926708 Difference in potential energy from amber=>desmond conversion: -0.02923361 Difference in potential energy from amber=>charmm conversion: -0.01351432 ======================================================================= INFO 2017-03-18 23:40:39 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5518547.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5518547.inpcrd') INFO 2017-03-18 23:40:39 Beginning InterMol conversion INFO 2017-03-18 23:40:39 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:40:39 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5520946.inpcrd INFO 2017-03-18 23:40:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5520946/mobley_5520946_converted.input INFO 2017-03-18 23:40:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5520946/mobley_5520946_converted.cms INFO 2017-03-18 23:40:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5520946/mobley_5520946_converted.rst7 WARNING 2017-03-18 23:40:55 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:40:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5520946/mobley_5520946_converted.inp INFO 2017-03-18 23:40:55 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5520946/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5520946/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5520946/mobley_5520946_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_5520946/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5520946/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 17.44063354 17.44063354 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -13.65385640 -13.65385640 coulomb total -13.59967360 -13.60023676 -0.00056316 -13.60023677 -0.00056317 -13.60023589 -0.00056229 -13.59967360 0.00000000 -13.65385640 -0.05418280 coulomb-14 -31.03984080 -31.04087029 -0.00102949 0.00000000 31.03984080 -31.04083584 -0.00099504 -31.03984080 0.00000000 0.00000000 31.03984080 improper 0.00000000 0.00001531 0.00001531 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00000000 0.00012911 0.00012911 0.00014439 0.00014439 0.00014464 0.00014464 0.00000000 0.00000000 0.00012552 0.00012552 vdw (SR) 0.00000000 -1.17532167 -1.17532167 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 14.32978160 14.32978160 vdw total 14.32978160 14.32978879 0.00000719 14.32978871 0.00000711 14.32985007 0.00006847 14.32978160 0.00000000 14.32978160 0.00000000 vdw-14 15.50506720 15.50511046 0.00004326 0.00000000 -15.50506720 15.50516942 0.00010222 15.50506720 0.00000000 0.00000000 -15.50506720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.12675120 1.12676265 0.00001145 1.12676266 0.00001146 1.12690282 0.00015162 1.12675120 0.00000000 1.12675120 0.00000000 bond 0.77111120 0.77119264 0.00008144 0.77119262 0.00008142 0.77114744 0.00003624 0.77111120 0.00000000 0.77119488 0.00008368 bonded 1.89786240 1.89809971 0.00023731 1.89809968 0.00023728 1.89819490 0.00033250 1.89786240 0.00000000 1.89807160 0.00020920 dihedral 0.00000000 0.00014442 0.00014442 0.00014439 0.00014439 0.00014464 0.00014464 0.00000000 0.00000000 0.00012552 0.00012552 nonbonded 0.73010800 0.72955203 -0.00055597 0.72955220 -0.00055580 0.72961418 -0.00049382 0.73010800 0.00000000 0.67592520 -0.05418280 potential 2.62797040 2.62765174 -0.00031866 2.62765187 -0.00031853 2.62777239 -0.00019801 2.62797040 0.00000000 2.57403864 -0.05393176 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 2.62797040 Difference in potential energy from amber=>gromacs conversion: -0.00031866 Difference in potential energy from amber=>lammps conversion: -0.00031853 Difference in potential energy from amber=>desmond conversion: -0.00019801 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.05393176 ======================================================================= INFO 2017-03-18 23:40:55 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5520946.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5520946.inpcrd') INFO 2017-03-18 23:40:55 Beginning InterMol conversion INFO 2017-03-18 23:40:55 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:40:55 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5538249.inpcrd INFO 2017-03-18 23:40:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5538249/mobley_5538249_converted.input INFO 2017-03-18 23:40:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5538249/mobley_5538249_converted.cms INFO 2017-03-18 23:41:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5538249/mobley_5538249_converted.rst7 WARNING 2017-03-18 23:41:11 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:41:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5538249/mobley_5538249_converted.inp INFO 2017-03-18 23:41:11 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5538249/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5538249/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5538249/mobley_5538249_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_5538249/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5538249/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 26.68410257 26.68410257 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -17.69070512 -17.69070512 coulomb total -17.68367600 -17.68403093 -0.00035493 -17.68403080 -0.00035480 -17.68401553 -0.00033953 -17.68367600 0.00000000 -17.69070512 -0.00702912 coulomb-14 -44.36671760 -44.36813350 -0.00141590 0.00000000 44.36671760 -44.36812008 -0.00140248 -44.36671760 0.00000000 0.00000000 44.36671760 improper 0.00000000 0.00021439 0.00021439 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00020920 0.00020920 proper 33.47409200 33.47381404 -0.00027796 33.47402840 -0.00006360 33.47402351 -0.00006849 33.47409200 0.00000000 33.47379912 -0.00029288 vdw (SR) 0.00000000 -12.41637548 -12.41637548 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 25.09199192 25.09199192 vdw total 25.09186640 25.09203266 0.00016626 25.09203250 0.00016610 25.09201794 0.00015154 25.09186640 0.00000000 25.09199192 0.00012552 vdw-14 37.50830480 37.50840815 0.00010335 0.00000000 -37.50830480 37.50839082 0.00008602 37.50830480 0.00000000 0.00000000 -37.50830480 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.36437840 2.36452601 0.00014761 2.36452601 0.00014761 2.36466006 0.00028166 2.36437840 0.00000000 2.36454576 0.00016736 bond 3.88358880 3.88370520 0.00011640 3.88370520 0.00011640 3.88334787 -0.00024093 3.88358880 0.00000000 3.88371432 0.00012552 bonded 39.72205920 39.72225965 0.00020045 39.72225961 0.00020041 39.72203144 -0.00002776 39.72205920 0.00000000 39.72226840 0.00020920 dihedral 33.47409200 33.47402843 -0.00006357 33.47402840 -0.00006360 33.47402351 -0.00006849 33.47409200 0.00000000 33.47400832 -0.00008368 nonbonded 7.40819040 7.40800173 -0.00018867 7.40800212 -0.00018828 7.40800241 -0.00018799 7.40819040 0.00000000 7.40128680 -0.00690360 potential 47.13024960 47.13026138 0.00001178 47.13026215 0.00001255 47.12985170 -0.00039790 47.13024960 0.00000000 47.12355520 -0.00669440 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 47.13024960 Difference in potential energy from amber=>gromacs conversion: 0.00001178 Difference in potential energy from amber=>lammps conversion: 0.00001255 Difference in potential energy from amber=>desmond conversion: -0.00039790 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.00669440 ======================================================================= INFO 2017-03-18 23:41:11 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5538249.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5538249.inpcrd') INFO 2017-03-18 23:41:11 Beginning InterMol conversion INFO 2017-03-18 23:41:11 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:41:11 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5561855.inpcrd INFO 2017-03-18 23:41:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5561855/mobley_5561855_converted.input INFO 2017-03-18 23:41:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5561855/mobley_5561855_converted.cms INFO 2017-03-18 23:41:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5561855/mobley_5561855_converted.rst7 WARNING 2017-03-18 23:41:27 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:41:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5561855/mobley_5561855_converted.inp INFO 2017-03-18 23:41:27 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5561855/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5561855/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5561855/mobley_5561855_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_5561855/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5561855/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 14.52269167 14.52269167 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -23.75863480 -23.75863480 coulomb total -23.75214960 -23.75300200 -0.00085240 -23.75300188 -0.00085228 -23.75300991 -0.00086031 -23.75214960 0.00000000 -23.75863480 -0.00648520 coulomb-14 -38.27439520 -38.27569367 -0.00129847 0.00000000 38.27439520 -38.27569358 -0.00129838 -38.27439520 0.00000000 0.00000000 38.27439520 improper 0.00000000 0.00006044 0.00006044 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 33.47241840 33.47253480 0.00011640 33.47259538 0.00017698 33.47260103 0.00018263 33.47241840 0.00000000 33.47254392 0.00012552 vdw (SR) 0.00000000 -20.24653138 -20.24653138 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 21.16166784 21.16166784 vdw total 21.16183520 21.16170088 -0.00013432 21.16170089 -0.00013431 21.16168780 -0.00014740 21.16183520 0.00000000 21.16166784 -0.00016736 vdw-14 41.40821120 41.40823226 0.00002106 0.00000000 -41.40821120 41.40822513 0.00001393 41.40821120 0.00000000 0.00000000 -41.40821120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.45556560 3.45558221 0.00001661 3.45558221 0.00001661 3.45584732 0.00028172 3.45556560 0.00000000 3.45560744 0.00004184 bond 2.93172880 2.93184876 0.00011996 2.93184876 0.00011996 2.93133652 -0.00039228 2.93172880 0.00000000 2.93185432 0.00012552 bonded 39.85971280 39.86002622 0.00031342 39.86002635 0.00031355 39.85978487 0.00007207 39.85971280 0.00000000 39.86004752 0.00033472 dihedral 33.47241840 33.47259525 0.00017685 33.47259538 0.00017698 33.47260103 0.00018263 33.47241840 0.00000000 33.47258576 0.00016736 nonbonded -2.59031440 -2.59130112 -0.00098672 -2.59130082 -0.00098642 -2.59132212 -0.00100772 -2.59031440 0.00000000 -2.59696696 -0.00665256 potential 37.26939840 37.26872510 -0.00067330 37.26872519 -0.00067321 37.26821002 -0.00118838 37.26939840 0.00000000 37.26312240 -0.00627600 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 37.26939840 Difference in potential energy from amber=>gromacs conversion: -0.00067330 Difference in potential energy from amber=>lammps conversion: -0.00067321 Difference in potential energy from amber=>desmond conversion: -0.00118838 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.00627600 ======================================================================= INFO 2017-03-18 23:41:27 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5561855.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5561855.inpcrd') INFO 2017-03-18 23:41:27 Beginning InterMol conversion INFO 2017-03-18 23:41:27 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:41:27 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:41:27 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5571660.inpcrd INFO 2017-03-18 23:41:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5571660/mobley_5571660_converted.input INFO 2017-03-18 23:41:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5571660/mobley_5571660_converted.cms WARNING 2017-03-18 23:41:43 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:41:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5571660/mobley_5571660_converted.inp INFO 2017-03-18 23:41:43 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5571660/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5571660/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5571660/mobley_5571660_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5571660/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -94.71059887 -94.71059887 0.00000000 0.00000000 0.00000000 0.00000000 -105.20157552 -105.20157552 coulomb total -105.11923440 -105.13038887 -0.01115447 -105.13038894 -0.01115454 -105.13042991 -0.01119551 -105.20157552 -0.08234112 coulomb-14 -10.42150720 -10.41978999 0.00171721 0.00000000 10.42150720 -10.41980050 0.00170670 0.00000000 10.42150720 improper 0.00000000 0.11687569 0.11687569 0.00000000 0.00000000 0.00000000 0.00000000 0.11685912 0.11685912 proper 0.22342560 0.10654959 -0.11687601 0.22342391 -0.00000169 0.22343025 0.00000465 0.10656648 -0.11685912 vdw (SR) 0.00000000 2.60650574 2.60650574 0.00000000 0.00000000 0.00000000 0.00000000 28.45860568 28.45860568 vdw total 28.45873120 28.45861821 -0.00011299 28.45861823 -0.00011297 28.45858738 -0.00014382 28.45860568 -0.00012552 vdw-14 25.85209920 25.85211248 0.00001328 0.00000000 -25.85209920 25.85210033 0.00000113 0.00000000 -25.85209920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.52457760 4.52446900 -0.00010860 4.52446882 -0.00010878 4.52475902 0.00018142 4.52453576 -0.00004184 bond 7.38810720 7.38802981 -0.00007739 7.38802980 -0.00007740 7.38892961 0.00082241 7.38802352 -0.00008368 bonded 12.13611040 12.13592409 -0.00018631 12.13592252 -0.00018788 12.13711887 0.00100847 12.13598488 -0.00012552 dihedral 0.22342560 0.22342528 -0.00000032 0.22342391 -0.00000169 0.22343025 0.00000465 0.22342560 -0.00000000 nonbonded -76.66050320 -76.67177065 -0.01126745 -76.67177071 -0.01126751 -76.67184253 -0.01133933 -76.74296984 -0.08246664 potential -64.52439280 -64.53584656 -0.01145376 -64.53584859 -0.01145579 -64.53479339 -0.01040059 -64.60698496 -0.08259216 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -64.52439280 Difference in potential energy from amber=>gromacs conversion: -0.01145376 Difference in potential energy from amber=>lammps conversion: -0.01145579 Difference in potential energy from amber=>desmond conversion: -0.01040059 Difference in potential energy from amber=>charmm conversion: -0.08259216 ======================================================================= INFO 2017-03-18 23:41:43 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5571660.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5571660.inpcrd') INFO 2017-03-18 23:41:43 Beginning InterMol conversion INFO 2017-03-18 23:41:43 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:41:44 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:41:44 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5600967.inpcrd INFO 2017-03-18 23:41:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5600967/mobley_5600967_converted.input INFO 2017-03-18 23:41:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5600967/mobley_5600967_converted.cms WARNING 2017-03-18 23:41:59 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:41:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5600967/mobley_5600967_converted.inp INFO 2017-03-18 23:41:59 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5600967/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5600967/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5600967/mobley_5600967_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5600967/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -89.84222853 -89.84222853 0.00000000 0.00000000 0.00000000 0.00000000 -44.71365488 -44.71365488 coulomb total -44.68344640 -44.69874266 -0.01529626 -44.69874310 -0.01529670 -44.69891590 -0.01546950 -44.71365488 -0.03020848 coulomb-14 45.16167760 45.14348587 -0.01819173 0.00000000 -45.16167760 45.14343243 -0.01824517 0.00000000 -45.16167760 improper 0.00000000 0.01554337 0.01554337 0.00000000 0.00000000 0.00000000 0.00000000 0.01556448 0.01556448 proper 33.49543040 33.47988486 -0.01554554 33.49542914 -0.00000126 33.49542504 -0.00000536 33.47986592 -0.01556448 vdw (SR) 0.00000000 8.45531180 8.45531180 0.00000000 0.00000000 0.00000000 0.00000000 42.28860848 42.28860848 vdw total 42.28852480 42.28848901 -0.00003579 42.28849133 -0.00003347 42.28945541 0.00093061 42.28860848 0.00008368 vdw-14 33.83307920 33.83317721 0.00009801 0.00000000 -33.83307920 33.83352894 0.00044974 0.00000000 -33.83307920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 8.61109040 8.61120640 0.00011600 8.61120630 0.00011590 8.61016666 -0.00092374 8.61121592 0.00012552 bond 8.22825440 8.22828296 0.00002856 8.22828285 0.00002845 8.22867669 0.00042229 8.22829624 0.00004184 bonded 50.33477520 50.33491759 0.00014239 50.33491829 0.00014309 50.33426839 -0.00050681 50.33494256 0.00016736 dihedral 33.49543040 33.49542823 -0.00000217 33.49542914 -0.00000126 33.49542504 -0.00000536 33.49543040 0.00000000 nonbonded -2.39492160 -2.41025365 -0.01533205 -2.41025270 -0.01533110 -2.40946050 -0.01453890 -2.42504640 -0.03012480 potential 47.93985360 47.92466394 -0.01518966 47.92466568 -0.01518792 47.92467196 -0.01518164 47.90989616 -0.02995744 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 47.93985360 Difference in potential energy from amber=>gromacs conversion: -0.01518966 Difference in potential energy from amber=>lammps conversion: -0.01518792 Difference in potential energy from amber=>desmond conversion: -0.01518164 Difference in potential energy from amber=>charmm conversion: -0.02995744 ======================================================================= INFO 2017-03-18 23:41:59 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5600967.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5600967.inpcrd') INFO 2017-03-18 23:42:00 Beginning InterMol conversion INFO 2017-03-18 23:42:00 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:42:00 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:42:00 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5616693.inpcrd INFO 2017-03-18 23:42:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5616693/mobley_5616693_converted.input INFO 2017-03-18 23:42:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5616693/mobley_5616693_converted.cms WARNING 2017-03-18 23:42:15 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:42:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5616693/mobley_5616693_converted.inp INFO 2017-03-18 23:42:15 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5616693/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5616693/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5616693/mobley_5616693_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5616693/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 49.87307991 49.87307991 0.00000000 0.00000000 0.00000000 0.00000000 -21.21363312 -21.21363312 coulomb total -21.21455360 -21.21832634 -0.00377274 -21.21832589 -0.00377229 -21.21830079 -0.00374719 -21.21363312 0.00092048 coulomb-14 -71.08950720 -71.09140625 -0.00189905 0.00000000 71.08950720 -71.09129712 -0.00178992 0.00000000 71.08950720 improper 0.00000000 0.06203948 0.06203948 0.00000000 0.00000000 0.00000000 0.00000000 0.06204872 0.06204872 proper 25.44081200 25.37873573 -0.06207627 25.44077518 -0.00003682 25.44066104 -0.00015096 25.37905616 -0.06175584 vdw (SR) 0.00000000 19.15534528 19.15534528 0.00000000 0.00000000 0.00000000 0.00000000 51.43964408 51.43964408 vdw total 51.43976960 51.43926486 -0.00050474 51.43926752 -0.00050208 51.43856846 -0.00120114 51.43964408 -0.00012552 vdw-14 32.28416240 32.28391958 -0.00024282 0.00000000 -32.28416240 32.28367471 -0.00048769 0.00000000 -32.28416240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.78986720 3.78978789 -0.00007931 3.78978787 -0.00007933 3.78989057 0.00002337 3.78965800 -0.00020920 bond 2.04513920 2.04533862 0.00019942 2.04533861 0.00019941 2.04488063 -0.00025857 2.04534840 0.00020920 bonded 31.27581840 31.27590172 0.00008332 31.27590166 0.00008326 31.27543224 -0.00038616 31.27611128 0.00029288 dihedral 25.44081200 25.44077521 -0.00003679 25.44077518 -0.00003682 25.44066104 -0.00015096 25.44110488 0.00029288 nonbonded 30.22521600 30.22093853 -0.00427747 30.22093995 -0.00427605 30.22026767 -0.00494833 30.22601096 0.00079496 potential 61.50103440 61.49684024 -0.00419416 61.49684203 -0.00419237 61.49557721 -0.00545719 61.50216408 0.00112968 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 61.50103440 Difference in potential energy from amber=>gromacs conversion: -0.00419416 Difference in potential energy from amber=>lammps conversion: -0.00419237 Difference in potential energy from amber=>desmond conversion: -0.00545719 Difference in potential energy from amber=>charmm conversion: 0.00112968 ======================================================================= INFO 2017-03-18 23:42:15 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5616693.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5616693.inpcrd') INFO 2017-03-18 23:42:16 Beginning InterMol conversion INFO 2017-03-18 23:42:16 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:42:16 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:42:16 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5627459.inpcrd INFO 2017-03-18 23:42:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5627459/mobley_5627459_converted.input INFO 2017-03-18 23:42:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5627459/mobley_5627459_converted.cms WARNING 2017-03-18 23:42:32 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:42:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5627459/mobley_5627459_converted.inp INFO 2017-03-18 23:42:32 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5627459/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5627459/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5627459/mobley_5627459_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5627459/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -48.55041563 -48.55041563 0.00000000 0.00000000 0.00000000 0.00000000 27.92790712 27.92790712 coulomb total 27.93363920 27.93743504 0.00379584 27.93743492 0.00379572 27.93747760 0.00383840 27.92790712 -0.00573208 coulomb-14 76.47054960 76.48785067 0.01730107 0.00000000 -76.47054960 76.48778266 0.01723306 0.00000000 -76.47054960 improper 0.00000000 0.01553137 0.01553137 0.00000000 0.00000000 0.00000000 0.00000000 0.01552264 0.01552264 proper 1.62088160 1.60550287 -0.01537873 1.62103482 0.00015322 1.62104053 0.00015893 1.60552632 -0.01535528 vdw (SR) 0.00000000 -0.64393168 -0.64393168 0.00000000 0.00000000 0.00000000 0.00000000 5.15903936 5.15903936 vdw total 5.15887200 5.15896727 0.00009527 5.15896740 0.00009540 5.15881075 -0.00006125 5.15903936 0.00016736 vdw-14 5.80278960 5.80289895 0.00010935 0.00000000 -5.80278960 5.80276596 -0.00002364 0.00000000 -5.80278960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.71753200 1.71769072 0.00015872 1.71769074 0.00015874 1.71767577 0.00014377 1.71769936 0.00016736 bond 1.08993200 1.08979048 -0.00014152 1.08979050 -0.00014150 1.08990652 -0.00002548 1.08980648 -0.00012552 bonded 4.42834560 4.42851544 0.00016984 4.42851606 0.00017046 4.42862281 0.00027721 4.42855480 0.00020920 dihedral 1.62088160 1.62103424 0.00015264 1.62103482 0.00015322 1.62104053 0.00015893 1.62104896 0.00016736 nonbonded 33.09251120 33.09640231 0.00389111 33.09640190 0.00389070 33.09628835 0.00377715 33.08694648 -0.00556472 potential 37.52085680 37.52491775 0.00406095 37.52491821 0.00406141 37.52488415 0.00402735 37.51550128 -0.00535552 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 37.52085680 Difference in potential energy from amber=>gromacs conversion: 0.00406095 Difference in potential energy from amber=>lammps conversion: 0.00406141 Difference in potential energy from amber=>desmond conversion: 0.00402735 Difference in potential energy from amber=>charmm conversion: -0.00535552 ======================================================================= INFO 2017-03-18 23:42:32 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5627459.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5627459.inpcrd') INFO 2017-03-18 23:42:32 Beginning InterMol conversion INFO 2017-03-18 23:42:32 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:42:32 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:42:32 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5665561.inpcrd INFO 2017-03-18 23:42:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5665561/mobley_5665561_converted.input INFO 2017-03-18 23:42:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5665561/mobley_5665561_converted.cms WARNING 2017-03-18 23:42:48 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:42:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5665561/mobley_5665561_converted.inp INFO 2017-03-18 23:42:48 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5665561/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5665561/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5665561/mobley_5665561_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5665561/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 4.97079175 4.97079175 0.00000000 0.00000000 0.00000000 0.00000000 -19.31204696 -19.31204696 coulomb total -19.31627280 -19.31702361 -0.00075081 -19.31702341 -0.00075061 -19.31724340 -0.00097060 -19.31204696 0.00422584 coulomb-14 -24.28686480 -24.28781535 -0.00095055 0.00000000 24.28686480 -24.28782955 -0.00096475 0.00000000 24.28686480 improper 0.00000000 0.00008130 0.00008130 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00083680 0.00070593 -0.00013087 0.00078716 -0.00004964 0.00077709 -0.00005971 0.00071128 -0.00012552 vdw (SR) 0.00000000 5.01473818 5.01473818 0.00000000 0.00000000 0.00000000 0.00000000 41.85351432 41.85351432 vdw total 41.85338880 41.85340900 0.00002020 41.85340972 0.00002092 41.85324069 -0.00014811 41.85351432 0.00012552 vdw-14 36.83844640 36.83867083 0.00022443 0.00000000 -36.83844640 36.83881832 0.00037192 0.00000000 -36.83844640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.69324080 2.69314263 -0.00009817 2.69314264 -0.00009816 2.69298628 -0.00025452 2.69315712 -0.00008368 bond 5.69777120 5.69756553 -0.00020567 5.69756535 -0.00020585 5.69747539 -0.00029581 5.69756200 -0.00020920 bonded 8.39184880 8.39149539 -0.00035341 8.39149515 -0.00035365 8.39123876 -0.00061004 8.39151408 -0.00033472 dihedral 0.00083680 0.00078723 -0.00004957 0.00078716 -0.00004964 0.00077709 -0.00005971 0.00079496 -0.00004184 nonbonded 22.53711600 22.53638540 -0.00073060 22.53638589 -0.00073011 22.53599728 -0.00111872 22.54146736 0.00435136 potential 30.92896480 30.92788079 -0.00108401 30.92788114 -0.00108366 30.92712865 -0.00183615 30.93298144 0.00401664 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 30.92896480 Difference in potential energy from amber=>gromacs conversion: -0.00108401 Difference in potential energy from amber=>lammps conversion: -0.00108366 Difference in potential energy from amber=>desmond conversion: -0.00183615 Difference in potential energy from amber=>charmm conversion: 0.00401664 ======================================================================= INFO 2017-03-18 23:42:48 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5665561.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5665561.inpcrd') INFO 2017-03-18 23:42:48 Beginning InterMol conversion INFO 2017-03-18 23:42:48 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:42:48 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:42:48 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5690766.inpcrd INFO 2017-03-18 23:42:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5690766/mobley_5690766_converted.input INFO 2017-03-18 23:42:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5690766/mobley_5690766_converted.cms WARNING 2017-03-18 23:43:04 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:43:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5690766/mobley_5690766_converted.inp INFO 2017-03-18 23:43:04 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5690766/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5690766/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5690766/mobley_5690766_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5690766/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 9.54504336 9.54504336 0.00000000 0.00000000 0.00000000 0.00000000 21.27639312 21.27639312 coulomb total 21.26308800 21.26404890 0.00096090 21.26404865 0.00096065 21.26394978 0.00086178 21.27639312 0.01330512 coulomb-14 11.71854720 11.71900555 0.00045835 0.00000000 -11.71854720 11.71896983 0.00042263 0.00000000 -11.71854720 improper 0.00000000 0.00215900 0.00215900 0.00000000 0.00000000 0.00000000 0.00000000 0.00217568 0.00217568 proper 24.26468960 24.26269251 -0.00199709 24.26484859 0.00015899 24.26484391 0.00015431 24.26268128 -0.00200832 vdw (SR) 0.00000000 -2.49254439 -2.49254439 0.00000000 0.00000000 0.00000000 0.00000000 1.91606280 1.91606280 vdw total 1.91627200 1.91600854 -0.00026346 1.91600853 -0.00026347 1.91607749 -0.00019451 1.91606280 -0.00020920 vdw-14 4.40868080 4.40855293 -0.00012787 0.00000000 -4.40868080 4.40862612 -0.00005468 0.00000000 -4.40868080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.58320160 2.58332258 0.00012098 2.58332256 0.00012096 2.58322057 0.00001897 2.58328528 0.00008368 bond 1.26858880 1.26871551 0.00012671 1.26871549 0.00012669 1.26855563 -0.00003317 1.26871432 0.00012552 bonded 28.11648000 28.11688959 0.00040959 28.11688664 0.00040664 28.11662010 0.00014010 28.11685656 0.00037656 dihedral 24.26468960 24.26485151 0.00016191 24.26484859 0.00015899 24.26484391 0.00015431 24.26485696 0.00016736 nonbonded 23.17936000 23.18005744 0.00069744 23.18005705 0.00069705 23.18002727 0.00066727 23.19245592 0.01309592 potential 51.29584000 51.29694703 0.00110703 51.29694458 0.00110458 51.29660944 0.00076944 51.30931248 0.01347248 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 51.29584000 Difference in potential energy from amber=>gromacs conversion: 0.00110703 Difference in potential energy from amber=>lammps conversion: 0.00110458 Difference in potential energy from amber=>desmond conversion: 0.00076944 Difference in potential energy from amber=>charmm conversion: 0.01347248 ======================================================================= INFO 2017-03-18 23:43:04 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5690766.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5690766.inpcrd') INFO 2017-03-18 23:43:04 Beginning InterMol conversion INFO 2017-03-18 23:43:04 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:43:04 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:43:04 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5692472.inpcrd INFO 2017-03-18 23:43:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5692472/mobley_5692472_converted.input INFO 2017-03-18 23:43:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5692472/mobley_5692472_converted.cms WARNING 2017-03-18 23:43:20 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:43:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5692472/mobley_5692472_converted.inp INFO 2017-03-18 23:43:20 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5692472/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5692472/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5692472/mobley_5692472_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5692472/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 3.16940826 3.16940826 0.00000000 0.00000000 0.00000000 0.00000000 41.15273616 41.15273616 coulomb total 41.14796640 41.14939728 0.00143088 41.14939691 0.00143051 41.14941628 0.00144988 41.15273616 0.00476976 coulomb-14 37.97858640 37.97998902 0.00140262 0.00000000 -37.97858640 37.98001193 0.00142553 0.00000000 -37.97858640 proper 0.00209200 0.00199590 -0.00009610 0.00199590 -0.00009610 0.00199459 -0.00009741 0.00200832 -0.00008368 vdw (SR) 0.00000000 -0.14505182 -0.14505182 0.00000000 0.00000000 0.00000000 0.00000000 1.81840824 1.81840824 vdw total 1.81836640 1.81837126 0.00000486 1.81837130 0.00000490 1.81842839 0.00006199 1.81840824 0.00004184 vdw-14 1.96355120 1.96342308 -0.00012812 0.00000000 -1.96355120 1.96347345 -0.00007775 0.00000000 -1.96355120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.27070480 0.27070637 0.00000157 0.27070637 0.00000157 0.27072896 0.00002416 0.27066296 -0.00004184 bond 0.65437760 0.65445546 0.00007786 0.65445546 0.00007786 0.65441558 0.00003798 0.65446128 0.00008368 bonded 0.92717440 0.92715774 -0.00001666 0.92715774 -0.00001666 0.92713913 -0.00003527 0.92713256 -0.00004184 dihedral 0.00209200 0.00199590 -0.00009610 0.00199590 -0.00009610 0.00199459 -0.00009741 0.00200832 -0.00008368 nonbonded 42.96633280 42.96776854 0.00143574 42.96776791 0.00143511 42.96784467 0.00151187 42.97114440 0.00481160 potential 43.89350720 43.89492628 0.00141908 43.89492558 0.00141838 43.89497327 0.00146607 43.89827696 0.00476976 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 43.89350720 Difference in potential energy from amber=>gromacs conversion: 0.00141908 Difference in potential energy from amber=>lammps conversion: 0.00141838 Difference in potential energy from amber=>desmond conversion: 0.00146607 Difference in potential energy from amber=>charmm conversion: 0.00476976 ======================================================================= INFO 2017-03-18 23:43:20 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5692472.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5692472.inpcrd') INFO 2017-03-18 23:43:20 Beginning InterMol conversion INFO 2017-03-18 23:43:20 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:43:20 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:43:20 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5708811.inpcrd INFO 2017-03-18 23:43:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5708811/mobley_5708811_converted.input INFO 2017-03-18 23:43:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5708811/mobley_5708811_converted.cms WARNING 2017-03-18 23:43:36 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:43:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5708811/mobley_5708811_converted.inp INFO 2017-03-18 23:43:36 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5708811/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5708811/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5708811/mobley_5708811_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5708811/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 165.30074911 165.30074911 0.00000000 0.00000000 0.00000000 0.00000000 -166.15061480 -166.15061480 coulomb total -166.12823040 -166.13332785 -0.00509745 -166.13332651 -0.00509611 -166.13339764 -0.00516724 -166.15061480 -0.02238440 coulomb-14 -331.42091600 -331.43407696 -0.01316096 0.00000000 331.42091600 -331.43411108 -0.01319508 0.00000000 331.42091600 improper 0.00000000 0.00004460 0.00004460 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 56.05890560 56.05882383 -0.00008177 56.05888886 -0.00001674 56.05889514 -0.00001046 56.05886376 -0.00004184 vdw (SR) 0.00000000 -7.20944636 -7.20944636 0.00000000 0.00000000 0.00000000 0.00000000 17.80622536 17.80622536 vdw total 17.80626720 17.80614140 -0.00012580 17.80614126 -0.00012594 17.80629758 0.00003038 17.80622536 -0.00004184 vdw-14 25.01571760 25.01558777 -0.00012983 0.00000000 -25.01571760 25.01577982 0.00006222 0.00000000 -25.01571760 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.65012160 3.65031610 0.00019450 3.65031611 0.00019451 3.65069877 0.00057717 3.65037264 0.00025104 bond 8.46465040 8.46465036 -0.00000004 8.46465040 0.00000000 8.46530503 0.00065463 8.46465040 0.00000000 bonded 68.17367760 68.17383489 0.00015729 68.17385538 0.00017778 68.17489894 0.00122134 68.17392864 0.00025104 dihedral 56.05890560 56.05886842 -0.00003718 56.05888886 -0.00001674 56.05889514 -0.00001046 56.05890560 0.00000000 nonbonded -148.32196320 -148.32718645 -0.00522325 -148.32718483 -0.00522163 -148.32710006 -0.00513686 -148.34438944 -0.02242624 potential -80.14828560 -80.15335156 -0.00506596 -80.15332732 -0.00504172 -80.15233948 -0.00405388 -80.17041896 -0.02213336 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -80.14828560 Difference in potential energy from amber=>gromacs conversion: -0.00506596 Difference in potential energy from amber=>lammps conversion: -0.00504172 Difference in potential energy from amber=>desmond conversion: -0.00405388 Difference in potential energy from amber=>charmm conversion: -0.02213336 ======================================================================= INFO 2017-03-18 23:43:36 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5708811.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5708811.inpcrd') INFO 2017-03-18 23:43:36 Beginning InterMol conversion INFO 2017-03-18 23:43:36 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:43:36 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:43:36 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5732611.inpcrd INFO 2017-03-18 23:43:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5732611/mobley_5732611_converted.input INFO 2017-03-18 23:43:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5732611/mobley_5732611_converted.cms WARNING 2017-03-18 23:43:52 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:43:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5732611/mobley_5732611_converted.inp INFO 2017-03-18 23:43:52 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5732611/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5732611/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5732611/mobley_5732611_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5732611/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 17.92865740 17.92865740 0.00000000 0.00000000 0.00000000 0.00000000 -64.69660624 -64.69660624 coulomb total -64.69091600 -64.69682056 -0.00590456 -64.69681962 -0.00590362 -64.69681234 -0.00589634 -64.69660624 -0.00569024 coulomb-14 -82.62646880 -82.62547795 0.00099085 0.00000000 82.62646880 -82.62544749 0.00102131 0.00000000 82.62646880 improper 0.00000000 0.00004719 0.00004719 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00046418 0.00004578 0.00051130 0.00009290 0.00050725 0.00008885 0.00046024 0.00004184 vdw (SR) 0.00000000 -0.70977949 -0.70977949 0.00000000 0.00000000 0.00000000 0.00000000 -1.01520576 -1.01520576 vdw total -1.01503840 -1.01523172 -0.00019332 -1.01523174 -0.00019334 -1.01524941 -0.00021101 -1.01520576 -0.00016736 vdw-14 -0.30543200 -0.30545223 -0.00002023 0.00000000 0.30543200 -0.30547073 -0.00003873 0.00000000 0.30543200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 21.95679520 21.95687312 0.00007792 21.95687302 0.00007782 21.95715741 0.00036221 21.95696256 0.00016736 bond 10.06837760 10.06829427 -0.00008333 10.06829434 -0.00008326 10.06704290 -0.00133470 10.06829392 -0.00008368 bonded 32.02559120 32.02567876 0.00008756 32.02567866 0.00008746 32.02470756 -0.00088364 32.02575856 0.00016736 dihedral 0.00041840 0.00051137 0.00009297 0.00051130 0.00009290 0.00050725 0.00008885 0.00050208 0.00008368 nonbonded -65.70595440 -65.71205228 -0.00609788 -65.71205049 -0.00609609 -65.71206175 -0.00610735 -65.71181200 -0.00585760 potential -33.68036320 -33.68637352 -0.00601032 -33.68637268 -0.00600948 -33.68739303 -0.00702983 -33.68609528 -0.00573208 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -33.68036320 Difference in potential energy from amber=>gromacs conversion: -0.00601032 Difference in potential energy from amber=>lammps conversion: -0.00600948 Difference in potential energy from amber=>desmond conversion: -0.00702983 Difference in potential energy from amber=>charmm conversion: -0.00573208 ======================================================================= INFO 2017-03-18 23:43:52 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5732611.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5732611.inpcrd') INFO 2017-03-18 23:43:52 Beginning InterMol conversion INFO 2017-03-18 23:43:52 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:43:52 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:43:52 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5747188.inpcrd INFO 2017-03-18 23:43:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5747188/mobley_5747188_converted.input INFO 2017-03-18 23:43:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5747188/mobley_5747188_converted.cms WARNING 2017-03-18 23:44:08 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:44:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5747188/mobley_5747188_converted.inp INFO 2017-03-18 23:44:08 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5747188/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5747188/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5747188/mobley_5747188_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5747188/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 20.27983428 20.27983428 0.00000000 0.00000000 0.00000000 0.00000000 4.51277872 4.51277872 coulomb total 4.50951520 4.51462761 0.00511241 4.51462763 0.00511243 4.51455244 0.00503724 4.51277872 0.00326352 coulomb-14 -15.76531200 -15.76520667 0.00010533 0.00000000 15.76531200 -15.76517389 0.00013811 0.00000000 15.76531200 improper 0.00000000 0.00015656 0.00015656 0.00000000 0.00000000 0.00000000 0.00000000 0.00016736 0.00016736 proper 20.08529200 20.08497326 -0.00031874 20.08512966 -0.00016234 20.08513104 -0.00016096 20.08495728 -0.00033472 vdw (SR) 0.00000000 -2.93928621 -2.93928621 0.00000000 0.00000000 0.00000000 0.00000000 17.72053704 17.72053704 vdw total 17.72049520 17.72054407 0.00004887 17.72054415 0.00004895 17.72041190 -0.00008330 17.72053704 0.00004184 vdw-14 20.65975520 20.65983028 0.00007508 0.00000000 -20.65975520 20.65980403 0.00004883 0.00000000 -20.65975520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.81083520 1.81096406 0.00012886 1.81096407 0.00012887 1.81100951 0.00017431 1.81096072 0.00012552 bond 11.53403280 11.53390376 -0.00012904 11.53390393 -0.00012887 11.53157503 -0.00245777 11.53390728 -0.00012552 bonded 33.43016000 33.42999763 -0.00016237 33.42999766 -0.00016234 33.42771559 -0.00244441 33.42999264 -0.00016736 dihedral 20.08529200 20.08512982 -0.00016218 20.08512966 -0.00016234 20.08513104 -0.00016096 20.08512464 -0.00016736 nonbonded 22.23001040 22.23517169 0.00516129 22.23517178 0.00516138 22.23496434 0.00495394 22.23331576 0.00330536 potential 55.66017040 55.66516932 0.00499892 55.66517028 0.00499988 55.66260800 0.00243760 55.66330840 0.00313800 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 55.66017040 Difference in potential energy from amber=>gromacs conversion: 0.00499892 Difference in potential energy from amber=>lammps conversion: 0.00499988 Difference in potential energy from amber=>desmond conversion: 0.00243760 Difference in potential energy from amber=>charmm conversion: 0.00313800 ======================================================================= INFO 2017-03-18 23:44:08 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5747188.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5747188.inpcrd') INFO 2017-03-18 23:44:08 Beginning InterMol conversion INFO 2017-03-18 23:44:08 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:44:09 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:44:09 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5747981.inpcrd INFO 2017-03-18 23:44:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5747981/mobley_5747981_converted.input INFO 2017-03-18 23:44:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5747981/mobley_5747981_converted.cms WARNING 2017-03-18 23:44:24 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:44:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5747981/mobley_5747981_converted.inp INFO 2017-03-18 23:44:24 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5747981/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5747981/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5747981/mobley_5747981_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5747981/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -143.94672031 -143.94672031 0.00000000 0.00000000 0.00000000 0.00000000 -11.26755384 -11.26755384 coulomb total -11.21144640 -11.21398721 -0.00254081 -11.21398692 -0.00254052 -11.21377772 -0.00233132 -11.26755384 -0.05610744 coulomb-14 132.72945040 132.73273310 0.00328270 0.00000000 -132.72945040 132.73286287 0.00341247 0.00000000 -132.72945040 proper 76.65673760 76.65686101 0.00012341 76.65684220 0.00010460 76.65677944 0.00004184 76.65682128 0.00008368 vdw (SR) 0.00000000 -1.39497178 -1.39497178 0.00000000 0.00000000 0.00000000 0.00000000 21.49822880 21.49822880 vdw total 21.49822880 21.49794403 -0.00028477 21.49794429 -0.00028451 21.49791556 -0.00031324 21.49822880 0.00000000 vdw-14 22.89317440 22.89291581 -0.00025859 0.00000000 -22.89317440 22.89298122 -0.00019318 0.00000000 -22.89317440 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.67436480 4.67429168 -0.00007312 4.67429158 -0.00007322 4.67445425 0.00008945 4.67440664 0.00004184 bond 2.24680800 2.24687470 0.00006670 2.24687469 0.00006669 2.24730170 0.00049370 2.24689168 0.00008368 bonded 83.57791040 83.57802740 0.00011700 83.57800847 0.00009807 83.57853539 0.00062499 83.57811960 0.00020920 dihedral 76.65673760 76.65686101 0.00012341 76.65684220 0.00010460 76.65677944 0.00004184 76.65682128 0.00008368 nonbonded 10.28678240 10.28395682 -0.00282558 10.28395736 -0.00282504 10.28413784 -0.00264456 10.23067496 -0.05610744 potential 93.86469280 93.86198422 -0.00270858 93.86196483 -0.00272797 93.86259829 -0.00209451 93.80879456 -0.05589824 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 93.86469280 Difference in potential energy from amber=>gromacs conversion: -0.00270858 Difference in potential energy from amber=>lammps conversion: -0.00272797 Difference in potential energy from amber=>desmond conversion: -0.00209451 Difference in potential energy from amber=>charmm conversion: -0.05589824 ======================================================================= INFO 2017-03-18 23:44:24 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5747981.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5747981.inpcrd') INFO 2017-03-18 23:44:24 Beginning InterMol conversion INFO 2017-03-18 23:44:24 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:44:25 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:44:25 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5759258.inpcrd INFO 2017-03-18 23:44:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5759258/mobley_5759258_converted.input INFO 2017-03-18 23:44:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5759258/mobley_5759258_converted.cms WARNING 2017-03-18 23:44:40 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:44:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5759258/mobley_5759258_converted.inp INFO 2017-03-18 23:44:40 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5759258/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5759258/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5759258/mobley_5759258_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5759258/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 10.97451793 10.97451793 0.00000000 0.00000000 0.00000000 0.00000000 -6.73611448 -6.73611448 coulomb total -6.72703520 -6.73385005 -0.00681485 -6.73385010 -0.00681490 -6.73388851 -0.00685331 -6.73611448 -0.00907928 coulomb-14 -17.70585120 -17.70836798 -0.00251678 0.00000000 17.70585120 -17.70837988 -0.00252868 0.00000000 17.70585120 proper 6.63456880 6.63471299 0.00014419 6.63471315 0.00014435 6.63473859 0.00016979 6.63473616 0.00016736 vdw (SR) 0.00000000 -1.64906292 -1.64906292 0.00000000 0.00000000 0.00000000 0.00000000 3.76195992 3.76195992 vdw total 3.76225280 3.76187088 -0.00038192 3.76187093 -0.00038187 3.76178282 -0.00046998 3.76195992 -0.00029288 vdw-14 5.41116720 5.41093380 -0.00023340 0.00000000 -5.41116720 5.41085382 -0.00031338 0.00000000 -5.41116720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.44850080 1.44852803 0.00002723 1.44852804 0.00002724 1.44861178 0.00011098 1.44850080 0.00000000 bond 0.89119200 0.89136059 0.00016859 0.89136057 0.00016857 0.89176717 0.00057517 0.89135936 0.00016736 bonded 8.97426160 8.97460161 0.00034001 8.97460176 0.00034016 8.97511755 0.00085595 8.97459632 0.00033472 dihedral 6.63456880 6.63471299 0.00014419 6.63471315 0.00014435 6.63473859 0.00016979 6.63473616 0.00016736 nonbonded -2.96478240 -2.97197917 -0.00719677 -2.97197905 -0.00719665 -2.97210568 -0.00732328 -2.97415456 -0.00937216 potential 6.00947920 6.00262244 -0.00685676 6.00262246 -0.00685674 6.00297199 -0.00650721 6.00044176 -0.00903744 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 6.00947920 Difference in potential energy from amber=>gromacs conversion: -0.00685676 Difference in potential energy from amber=>lammps conversion: -0.00685674 Difference in potential energy from amber=>desmond conversion: -0.00650721 Difference in potential energy from amber=>charmm conversion: -0.00903744 ======================================================================= INFO 2017-03-18 23:44:40 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5759258.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5759258.inpcrd') INFO 2017-03-18 23:44:41 Beginning InterMol conversion INFO 2017-03-18 23:44:41 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:44:41 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:44:41 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5760563.inpcrd INFO 2017-03-18 23:44:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5760563/mobley_5760563_converted.input INFO 2017-03-18 23:44:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5760563/mobley_5760563_converted.cms WARNING 2017-03-18 23:44:56 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:44:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5760563/mobley_5760563_converted.inp INFO 2017-03-18 23:44:56 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5760563/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5760563/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5760563/mobley_5760563_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5760563/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -213.94985033 -213.94985033 0.00000000 0.00000000 0.00000000 0.00000000 -183.45538776 -183.45538776 coulomb total -183.41233440 -183.42037655 -0.00804215 -183.42037605 -0.00804165 -183.42052542 -0.00819102 -183.45538776 -0.04305336 coulomb-14 30.50387040 30.52947378 0.02560338 0.00000000 -30.50387040 30.52922921 0.02535881 0.00000000 -30.50387040 proper 33.51509520 33.51500930 -0.00008590 33.51500985 -0.00008535 33.51511658 0.00002138 33.51501152 -0.00008368 vdw (SR) 0.00000000 -2.03627930 -2.03627930 0.00000000 0.00000000 0.00000000 0.00000000 -1.02269512 -1.02269512 vdw total -1.02256960 -1.02274592 -0.00017632 -1.02274591 -0.00017631 -1.02271918 -0.00014958 -1.02269512 -0.00012552 vdw-14 1.01378320 1.01353337 -0.00024983 0.00000000 -1.01378320 1.01356360 -0.00021960 0.00000000 -1.01378320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.19448400 3.19447773 -0.00000627 3.19447772 -0.00000628 3.19425827 -0.00022573 3.19460952 0.00012552 bond 11.99343600 11.99324648 -0.00018952 11.99324646 -0.00018954 11.99317073 -0.00026527 11.99322680 -0.00020920 bonded 48.70301520 48.70273351 -0.00028169 48.70273404 -0.00028116 48.70254559 -0.00046961 48.70284784 -0.00016736 dihedral 33.51509520 33.51500930 -0.00008590 33.51500985 -0.00008535 33.51511658 0.00002138 33.51501152 -0.00008368 nonbonded -184.43490400 -184.44312248 -0.00821848 -184.44312138 -0.00821738 -184.44324459 -0.00834059 -184.47808288 -0.04317888 potential -135.73188880 -135.74038897 -0.00850017 -135.74038650 -0.00849770 -135.74075428 -0.00886548 -135.77523504 -0.04334624 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -135.73188880 Difference in potential energy from amber=>gromacs conversion: -0.00850017 Difference in potential energy from amber=>lammps conversion: -0.00849770 Difference in potential energy from amber=>desmond conversion: -0.00886548 Difference in potential energy from amber=>charmm conversion: -0.04334624 ======================================================================= INFO 2017-03-18 23:44:56 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5760563.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5760563.inpcrd') INFO 2017-03-18 23:44:57 Beginning InterMol conversion INFO 2017-03-18 23:44:57 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:44:57 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:44:57 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5816127.inpcrd INFO 2017-03-18 23:44:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5816127/mobley_5816127_converted.input INFO 2017-03-18 23:44:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5816127/mobley_5816127_converted.cms WARNING 2017-03-18 23:45:12 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:45:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5816127/mobley_5816127_converted.inp INFO 2017-03-18 23:45:12 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5816127/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5816127/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5816127/mobley_5816127_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5816127/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -57.63249549 -57.63249549 0.00000000 0.00000000 0.00000000 0.00000000 63.29659800 63.29659800 coulomb total 63.29262320 63.29453011 0.00190691 63.29453110 0.00190790 63.29462357 0.00200037 63.29659800 0.00397480 coulomb-14 120.92303920 120.92702560 0.00398640 0.00000000 -120.92303920 120.92706212 0.00402292 0.00000000 -120.92303920 proper 5.65091040 5.65085867 -0.00005173 5.65085852 -0.00005188 5.65087601 -0.00003439 5.65086856 -0.00004184 vdw (SR) 0.00000000 -0.91703356 -0.91703356 0.00000000 0.00000000 0.00000000 0.00000000 3.85338032 3.85338032 vdw total 3.85346400 3.85329689 -0.00016711 3.85329693 -0.00016707 3.85324588 -0.00021812 3.85338032 -0.00008368 vdw-14 4.77059680 4.77033045 -0.00026635 0.00000000 -4.77059680 4.77027246 -0.00032434 0.00000000 -4.77059680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.88031360 0.88048589 0.00017229 0.88048590 0.00017230 0.88056879 0.00025519 0.88048096 0.00016736 bond 1.24097440 1.24111291 0.00013851 1.24111293 0.00013853 1.24109390 0.00011950 1.24109992 0.00012552 bonded 7.77219840 7.77245747 0.00025907 7.77245735 0.00025895 7.77253869 0.00034029 7.77244944 0.00025104 dihedral 5.65091040 5.65085867 -0.00005173 5.65085852 -0.00005188 5.65087601 -0.00003439 5.65086856 -0.00004184 nonbonded 67.14608720 67.14782700 0.00173980 67.14782774 0.00174054 67.14786945 0.00178225 67.14997832 0.00389112 potential 74.91828560 74.92028447 0.00199887 74.92028555 0.00199995 74.92038932 0.00210372 74.92238592 0.00410032 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 74.91828560 Difference in potential energy from amber=>gromacs conversion: 0.00199887 Difference in potential energy from amber=>lammps conversion: 0.00199995 Difference in potential energy from amber=>desmond conversion: 0.00210372 Difference in potential energy from amber=>charmm conversion: 0.00410032 ======================================================================= INFO 2017-03-18 23:45:12 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5816127.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5816127.inpcrd') INFO 2017-03-18 23:45:13 Beginning InterMol conversion INFO 2017-03-18 23:45:13 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:45:13 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:45:13 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5852491.inpcrd INFO 2017-03-18 23:45:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5852491/mobley_5852491_converted.input INFO 2017-03-18 23:45:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5852491/mobley_5852491_converted.cms WARNING 2017-03-18 23:45:28 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:45:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5852491/mobley_5852491_converted.inp INFO 2017-03-18 23:45:28 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5852491/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5852491/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5852491/mobley_5852491_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5852491/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 13.12309741 13.12309741 0.00000000 0.00000000 0.00000000 0.00000000 -2.24061568 -2.24061568 coulomb total -2.24931840 -2.24274042 0.00657798 -2.24274040 0.00657800 -2.24275370 0.00656470 -2.24061568 0.00870272 coulomb-14 -15.36615840 -15.36583783 0.00032057 0.00000000 15.36615840 -15.36583259 0.00032581 0.00000000 15.36615840 proper 36.95099600 36.95112440 0.00012840 36.95112445 0.00012845 36.95108960 0.00009360 36.95112152 0.00012552 vdw (SR) 0.00000000 -1.41012115 -1.41012115 0.00000000 0.00000000 0.00000000 0.00000000 3.96228984 3.96228984 vdw total 3.96224800 3.96217702 -0.00007098 3.96217708 -0.00007092 3.96208593 -0.00016207 3.96228984 0.00004184 vdw-14 5.37225600 5.37229817 0.00004217 0.00000000 -5.37225600 5.37222018 -0.00003582 0.00000000 -5.37225600 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 19.07527440 19.07513476 -0.00013964 19.07513465 -0.00013975 19.07528791 0.00001351 19.07502336 -0.00025104 bond 1.06692000 1.06710085 0.00018085 1.06710087 0.00018087 1.06721567 0.00029567 1.06708736 0.00016736 bonded 57.09319040 57.09336001 0.00016961 57.09335998 0.00016958 57.09359318 0.00040278 57.09323224 0.00004184 dihedral 36.95099600 36.95112440 0.00012840 36.95112445 0.00012845 36.95108960 0.00009360 36.95112152 0.00012552 nonbonded 1.71292960 1.71943660 0.00650700 1.71943668 0.00650708 1.71933223 0.00640263 1.72167416 0.00874456 potential 58.80612000 58.81279661 0.00667661 58.81279766 0.00667766 58.81288344 0.00676344 58.81490640 0.00878640 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 58.80612000 Difference in potential energy from amber=>gromacs conversion: 0.00667661 Difference in potential energy from amber=>lammps conversion: 0.00667766 Difference in potential energy from amber=>desmond conversion: 0.00676344 Difference in potential energy from amber=>charmm conversion: 0.00878640 ======================================================================= INFO 2017-03-18 23:45:28 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5852491.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5852491.inpcrd') INFO 2017-03-18 23:45:29 Beginning InterMol conversion INFO 2017-03-18 23:45:29 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:45:29 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5857.inpcrd INFO 2017-03-18 23:45:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5857/mobley_5857_converted.input INFO 2017-03-18 23:45:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5857/mobley_5857_converted.cms INFO 2017-03-18 23:45:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5857/mobley_5857_converted.rst7 WARNING 2017-03-18 23:45:44 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:45:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5857/mobley_5857_converted.inp INFO 2017-03-18 23:45:45 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5857/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5857/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5857/mobley_5857_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_5857/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5857/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -34.12489372 -34.12489372 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -61.34154032 -61.34154032 coulomb total -61.34706320 -61.34360408 0.00345912 -61.34360303 0.00346017 -61.34378123 0.00328197 -61.34706320 0.00000000 -61.34154032 0.00552288 coulomb-14 -27.21859360 -27.21871036 -0.00011676 0.00000000 27.21859360 -27.21879560 -0.00020200 -27.21859360 0.00000000 0.00000000 27.21859360 improper 0.00000000 0.00012803 0.00012803 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00125520 0.00126966 0.00001446 0.00139769 0.00014249 0.00138509 0.00012989 0.00125520 0.00000000 0.00125520 0.00000000 vdw (SR) 0.00000000 -3.44552666 -3.44552666 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 31.08209920 31.08209920 vdw total 31.08209920 31.08215247 0.00005327 31.08215234 0.00005314 31.08256509 0.00046589 31.08209920 0.00000000 31.08209920 0.00000000 vdw-14 34.52762320 34.52767913 0.00005593 0.00000000 -34.52762320 34.52810026 0.00047706 34.52762320 0.00000000 0.00000000 -34.52762320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.45431040 3.45413939 -0.00017101 3.45413940 -0.00017100 3.45401139 -0.00029901 3.45431040 0.00000000 3.45410120 -0.00020920 bond 2.94511760 2.94492690 -0.00019070 2.94492689 -0.00019071 2.94513980 0.00002220 2.94511760 0.00000000 2.94490840 -0.00020920 bonded 6.40068320 6.40046398 -0.00021922 6.40046398 -0.00021922 6.40053628 -0.00014692 6.40068320 0.00000000 6.40039032 -0.00029288 dihedral 0.00125520 0.00139769 0.00014249 0.00139769 0.00014249 0.00138509 0.00012989 0.00125520 0.00000000 0.00138072 0.00012552 nonbonded -30.26496400 -30.26145160 0.00351240 -30.26145070 0.00351330 -30.26121614 0.00374786 -30.26496400 0.00000000 -30.25944112 0.00552288 potential -23.86428080 -23.86098762 0.00329318 -23.86098674 0.00329406 -23.86075172 0.00352908 -23.86428080 0.00000000 -23.85900896 0.00527184 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -23.86428080 Difference in potential energy from amber=>gromacs conversion: 0.00329318 Difference in potential energy from amber=>lammps conversion: 0.00329406 Difference in potential energy from amber=>desmond conversion: 0.00352908 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00527184 ======================================================================= INFO 2017-03-18 23:45:45 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5857.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5857.inpcrd') INFO 2017-03-18 23:45:45 Beginning InterMol conversion INFO 2017-03-18 23:45:45 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:45:45 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:45:45 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5880265.inpcrd INFO 2017-03-18 23:45:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5880265/mobley_5880265_converted.input INFO 2017-03-18 23:45:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5880265/mobley_5880265_converted.cms WARNING 2017-03-18 23:46:01 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:46:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5880265/mobley_5880265_converted.inp INFO 2017-03-18 23:46:01 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5880265/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5880265/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5880265/mobley_5880265_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5880265/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -57.65645166 -57.65645166 0.00000000 0.00000000 0.00000000 0.00000000 55.54674216 55.54674216 coulomb total 55.54218160 55.54396220 0.00178060 55.54395980 0.00177820 55.54406356 0.00188196 55.54674216 0.00456056 coulomb-14 113.19644640 113.20041386 0.00396746 0.00000000 -113.19644640 113.20057517 0.00412877 0.00000000 -113.19644640 proper 10.57673360 10.57693328 0.00019968 10.57693318 0.00019958 10.57693527 0.00020167 10.57694280 0.00020920 vdw (SR) 0.00000000 -3.31198797 -3.31198797 0.00000000 0.00000000 0.00000000 0.00000000 4.92105344 4.92105344 vdw total 4.92080240 4.92091452 0.00011212 4.92091453 0.00011213 4.92095901 0.00015661 4.92105344 0.00025104 vdw-14 8.23285680 8.23290249 0.00004569 0.00000000 -8.23285680 8.23294211 0.00008531 0.00000000 -8.23285680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.70205120 1.70207201 0.00002081 1.70207199 0.00002079 1.70225030 0.00019910 1.70205120 0.00000000 bond 1.97610320 1.97597723 -0.00012597 1.97597722 -0.00012598 1.97575496 -0.00034824 1.97597768 -0.00012552 bonded 14.25488800 14.25498251 0.00009451 14.25498239 0.00009439 14.25494053 0.00005253 14.25497168 0.00008368 dihedral 10.57673360 10.57693328 0.00019968 10.57693318 0.00019958 10.57693527 0.00020167 10.57694280 0.00020920 nonbonded 60.46298400 60.46487673 0.00189273 60.46487517 0.00189117 60.46502257 0.00203857 60.46779560 0.00481160 potential 74.71787200 74.71985924 0.00198724 74.71985940 0.00198740 74.71990166 0.00202966 74.72272544 0.00485344 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 74.71787200 Difference in potential energy from amber=>gromacs conversion: 0.00198724 Difference in potential energy from amber=>lammps conversion: 0.00198740 Difference in potential energy from amber=>desmond conversion: 0.00202966 Difference in potential energy from amber=>charmm conversion: 0.00485344 ======================================================================= INFO 2017-03-18 23:46:01 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5880265.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5880265.inpcrd') INFO 2017-03-18 23:46:01 Beginning InterMol conversion INFO 2017-03-18 23:46:01 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:46:01 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:46:01 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_588781.inpcrd INFO 2017-03-18 23:46:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_588781/mobley_588781_converted.input INFO 2017-03-18 23:46:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_588781/mobley_588781_converted.cms WARNING 2017-03-18 23:46:17 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:46:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_588781/mobley_588781_converted.inp INFO 2017-03-18 23:46:17 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_588781/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_588781/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_588781/mobley_588781_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_588781/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 9.35967854 9.35967854 0.00000000 0.00000000 0.00000000 0.00000000 -0.51655664 -0.51655664 coulomb total -0.51463200 -0.52127338 -0.00664138 -0.52127339 -0.00664139 -0.52131686 -0.00668486 -0.51655664 -0.00192464 coulomb-14 -9.88009760 -9.88095192 -0.00085432 0.00000000 9.88009760 -9.88096009 -0.00086249 0.00000000 9.88009760 improper 0.00000000 0.00002152 0.00002152 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 5.11535840 5.11517853 -0.00017987 5.11520024 -0.00015816 5.11520242 -0.00015598 5.11519104 -0.00016736 vdw (SR) 0.00000000 -6.20729402 -6.20729402 0.00000000 0.00000000 0.00000000 0.00000000 19.46066264 19.46066264 vdw total 19.46062080 19.46055608 -0.00006472 19.46055595 -0.00006485 19.46066360 0.00004280 19.46066264 0.00004184 vdw-14 25.66800320 25.66785009 -0.00015311 0.00000000 -25.66800320 25.66796287 -0.00004033 0.00000000 -25.66800320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.30791840 1.30801617 0.00009777 1.30801618 0.00009778 1.30818482 0.00026642 1.30796024 0.00004184 bond 1.87234000 1.87214850 -0.00019150 1.87214850 -0.00019150 1.87180810 -0.00053190 1.87213080 -0.00020920 bonded 8.29561680 8.29536473 -0.00025207 8.29536492 -0.00025188 8.29519533 -0.00042147 8.29532392 -0.00029288 dihedral 5.11535840 5.11520006 -0.00015834 5.11520024 -0.00015816 5.11520242 -0.00015598 5.11523288 -0.00012552 nonbonded 18.94598880 18.93928270 -0.00670610 18.93928268 -0.00670612 18.93934674 -0.00664206 18.94410600 -0.00188280 potential 27.24160560 27.23464742 -0.00695818 27.23464761 -0.00695799 27.23440607 -0.00719953 27.23942992 -0.00217568 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 27.24160560 Difference in potential energy from amber=>gromacs conversion: -0.00695818 Difference in potential energy from amber=>lammps conversion: -0.00695799 Difference in potential energy from amber=>desmond conversion: -0.00719953 Difference in potential energy from amber=>charmm conversion: -0.00217568 ======================================================================= INFO 2017-03-18 23:46:17 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_588781.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_588781.inpcrd') INFO 2017-03-18 23:46:17 Beginning InterMol conversion INFO 2017-03-18 23:46:17 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:46:17 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:46:17 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5890803.inpcrd INFO 2017-03-18 23:46:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5890803/mobley_5890803_converted.input INFO 2017-03-18 23:46:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5890803/mobley_5890803_converted.cms WARNING 2017-03-18 23:46:33 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:46:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5890803/mobley_5890803_converted.inp INFO 2017-03-18 23:46:33 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5890803/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5890803/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5890803/mobley_5890803_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5890803/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -51.28348141 -51.28348141 0.00000000 0.00000000 0.00000000 0.00000000 -69.85208920 -69.85208920 coulomb total -69.86024800 -69.86318455 -0.00293655 -69.86318517 -0.00293717 -69.86321362 -0.00296562 -69.85208920 0.00815880 coulomb-14 -18.58281760 -18.57970313 0.00311447 0.00000000 18.58281760 -18.57979717 0.00302043 0.00000000 18.58281760 improper 0.00000000 0.00000862 0.00000862 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 13.20428560 13.20448271 0.00019711 13.20449145 0.00020585 13.20446087 0.00017527 13.20449480 0.00020920 vdw (SR) 0.00000000 -2.95325618 -2.95325618 0.00000000 0.00000000 0.00000000 0.00000000 8.86367848 8.86367848 vdw total 8.86380400 8.86355747 -0.00024653 8.86355756 -0.00024644 8.86361295 -0.00019105 8.86367848 -0.00012552 vdw-14 11.81687120 11.81681365 -0.00005755 0.00000000 -11.81687120 11.81686735 -0.00000385 0.00000000 -11.81687120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.21749600 3.21741048 -0.00008552 3.21741048 -0.00008552 3.21705474 -0.00044126 3.21745416 -0.00004184 bond 2.33467200 2.33456417 -0.00010783 2.33456418 -0.00010782 2.33509480 0.00042280 2.33454648 -0.00012552 bonded 18.75645360 18.75646598 0.00001238 18.75646611 0.00001251 18.75661041 0.00015681 18.75649544 0.00004184 dihedral 13.20428560 13.20449132 0.00020572 13.20449145 0.00020585 13.20446087 0.00017527 13.20449480 0.00020920 nonbonded -60.99644400 -60.99962707 -0.00318307 -60.99962802 -0.00318402 -60.99960067 -0.00315667 -60.98841072 0.00803328 potential -42.23999040 -42.24316110 -0.00317070 -42.24316187 -0.00317147 -42.24305602 -0.00306562 -42.23187344 0.00811696 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -42.23999040 Difference in potential energy from amber=>gromacs conversion: -0.00317070 Difference in potential energy from amber=>lammps conversion: -0.00317147 Difference in potential energy from amber=>desmond conversion: -0.00306562 Difference in potential energy from amber=>charmm conversion: 0.00811696 ======================================================================= INFO 2017-03-18 23:46:33 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5890803.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5890803.inpcrd') INFO 2017-03-18 23:46:33 Beginning InterMol conversion INFO 2017-03-18 23:46:33 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:46:33 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:46:33 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_590519.inpcrd INFO 2017-03-18 23:46:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_590519/mobley_590519_converted.input INFO 2017-03-18 23:46:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_590519/mobley_590519_converted.cms WARNING 2017-03-18 23:46:49 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:46:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_590519/mobley_590519_converted.inp INFO 2017-03-18 23:46:49 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_590519/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_590519/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_590519/mobley_590519_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_590519/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -4.20806543 -4.20806543 0.00000000 0.00000000 0.00000000 0.00000000 -21.29028400 -21.29028400 coulomb total -21.30911200 -21.31265869 -0.00354669 -21.31265836 -0.00354636 -21.31266656 -0.00355456 -21.29028400 0.01882800 coulomb-14 -17.10461040 -17.10459326 0.00001714 0.00000000 17.10461040 -17.10460036 0.00001004 0.00000000 17.10461040 proper 2.54638240 2.54626107 -0.00012133 2.54626106 -0.00012134 2.54628853 -0.00009387 2.54625688 -0.00012552 vdw (SR) 0.00000000 -1.66464531 -1.66464531 0.00000000 0.00000000 0.00000000 0.00000000 -1.70962424 -1.70962424 vdw total -1.71000080 -1.70968379 0.00031701 -1.70968382 0.00031698 -1.70969590 0.00030490 -1.70962424 0.00037656 vdw-14 -0.04518720 -0.04503849 0.00014871 0.00000000 0.04518720 -0.04505230 0.00013490 0.00000000 0.04518720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.86648240 1.86662810 0.00014570 1.86662809 0.00014569 1.86641091 -0.00007149 1.86656608 0.00008368 bond 1.21670720 1.21661958 -0.00008762 1.21661959 -0.00008761 1.21626194 -0.00044526 1.21662352 -0.00008368 bonded 5.62957200 5.62950875 -0.00006325 5.62950874 -0.00006326 5.62896138 -0.00061062 5.62944648 -0.00012552 dihedral 2.54638240 2.54626107 -0.00012133 2.54626106 -0.00012134 2.54628853 -0.00009387 2.54625688 -0.00012552 nonbonded -23.01911280 -23.02234248 -0.00322968 -23.02234243 -0.00322963 -23.02236246 -0.00324966 -22.99990824 0.01920456 potential -17.38954080 -17.39283373 -0.00329293 -17.39283361 -0.00329281 -17.39345460 -0.00391380 -17.37041992 0.01912088 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -17.38954080 Difference in potential energy from amber=>gromacs conversion: -0.00329293 Difference in potential energy from amber=>lammps conversion: -0.00329281 Difference in potential energy from amber=>desmond conversion: -0.00391380 Difference in potential energy from amber=>charmm conversion: 0.01912088 ======================================================================= INFO 2017-03-18 23:46:49 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_590519.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_590519.inpcrd') INFO 2017-03-18 23:46:49 Beginning InterMol conversion INFO 2017-03-18 23:46:49 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:46:50 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:46:50 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5917842.inpcrd INFO 2017-03-18 23:46:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5917842/mobley_5917842_converted.input INFO 2017-03-18 23:46:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5917842/mobley_5917842_converted.cms WARNING 2017-03-18 23:47:05 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:47:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5917842/mobley_5917842_converted.inp INFO 2017-03-18 23:47:05 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5917842/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5917842/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5917842/mobley_5917842_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5917842/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -108.36240054 -108.36240054 0.00000000 0.00000000 0.00000000 0.00000000 -46.87590424 -46.87590424 coulomb total -46.88757760 -46.88925186 -0.00167426 -46.88925120 -0.00167360 -46.88930057 -0.00172297 -46.87590424 0.01167336 coulomb-14 61.47090960 61.47314868 0.00223908 0.00000000 -61.47090960 61.47333381 0.00242421 0.00000000 -61.47090960 improper 0.00000000 0.00006504 0.00006504 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00292880 0.00296767 0.00003887 0.00303268 0.00010388 0.00303116 0.00010236 0.00297064 0.00004184 vdw (SR) 0.00000000 13.87650166 13.87650166 0.00000000 0.00000000 0.00000000 0.00000000 43.75685776 43.75685776 vdw total 43.75669040 43.75672068 0.00003028 43.75671969 0.00002929 43.75622355 -0.00046685 43.75685776 0.00016736 vdw-14 29.88003600 29.88021903 0.00018303 0.00000000 -29.88003600 29.87990856 -0.00012744 0.00000000 -29.88003600 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.68701280 0.68680860 -0.00020420 0.68680858 -0.00020422 0.68678104 -0.00023176 0.68684544 -0.00016736 bond 1.86188000 1.86168261 -0.00019739 1.86168260 -0.00019740 1.86165731 -0.00022269 1.86167080 -0.00020920 bonded 2.55182160 2.55152392 -0.00029768 2.55152386 -0.00029774 2.55146951 -0.00035209 2.55157056 -0.00025104 dihedral 0.00292880 0.00303271 0.00010391 0.00303268 0.00010388 0.00303116 0.00010236 0.00305432 0.00012552 nonbonded -3.13088720 -3.13253118 -0.00164398 -3.13253021 -0.00164301 -3.13307702 -0.00218982 -3.11904648 0.01184072 potential -0.57906560 -0.58100726 -0.00194166 -0.58100631 -0.00194071 -0.58167574 -0.00261014 -0.56747592 0.01158968 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -0.57906560 Difference in potential energy from amber=>gromacs conversion: -0.00194166 Difference in potential energy from amber=>lammps conversion: -0.00194071 Difference in potential energy from amber=>desmond conversion: -0.00261014 Difference in potential energy from amber=>charmm conversion: 0.01158968 ======================================================================= INFO 2017-03-18 23:47:05 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5917842.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5917842.inpcrd') INFO 2017-03-18 23:47:05 Beginning InterMol conversion INFO 2017-03-18 23:47:05 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:47:06 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:47:06 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5935995.inpcrd INFO 2017-03-18 23:47:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5935995/mobley_5935995_converted.input INFO 2017-03-18 23:47:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5935995/mobley_5935995_converted.cms WARNING 2017-03-18 23:47:21 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:47:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5935995/mobley_5935995_converted.inp INFO 2017-03-18 23:47:21 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5935995/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5935995/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5935995/mobley_5935995_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5935995/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 12.50188280 12.50188280 0.00000000 0.00000000 0.00000000 0.00000000 -14.00313672 -14.00313672 coulomb total -14.00970560 -14.00085853 0.00884707 -14.00085853 0.00884707 -14.00088908 0.00881652 -14.00313672 0.00656888 coulomb-14 -26.49559840 -26.50274133 -0.00714293 0.00000000 26.49559840 -26.50274250 -0.00714410 0.00000000 26.49559840 proper 5.75843920 5.75843437 -0.00000483 5.75843418 -0.00000502 5.75843476 -0.00000444 5.75843920 0.00000000 vdw (SR) 0.00000000 7.16446119 7.16446119 0.00000000 0.00000000 0.00000000 0.00000000 18.76921480 18.76921480 vdw total 18.76942400 18.76901447 -0.00040953 18.76901480 -0.00040920 18.76901326 -0.00041074 18.76921480 -0.00020920 vdw-14 11.60474240 11.60455327 -0.00018913 0.00000000 -11.60474240 11.60461483 -0.00012757 0.00000000 -11.60474240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.95466880 5.95457623 -0.00009257 5.95457633 -0.00009247 5.95478553 0.00011673 5.95454328 -0.00012552 bond 0.79956240 0.79974469 0.00018229 0.79974470 0.00018230 0.79965118 0.00008878 0.79972976 0.00016736 bonded 12.51267040 12.51275529 0.00008489 12.51275521 0.00008481 12.51287147 0.00020107 12.51271224 0.00004184 dihedral 5.75843920 5.75843437 -0.00000483 5.75843418 -0.00000502 5.75843476 -0.00000444 5.75843920 0.00000000 nonbonded 4.75971840 4.76815594 0.00843754 4.76815627 0.00843787 4.76812418 0.00840578 4.76607808 0.00635968 potential 17.27238880 17.28091123 0.00852243 17.28091161 0.00852281 17.28094793 0.00855913 17.27883216 0.00644336 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 17.27238880 Difference in potential energy from amber=>gromacs conversion: 0.00852243 Difference in potential energy from amber=>lammps conversion: 0.00852281 Difference in potential energy from amber=>desmond conversion: 0.00855913 Difference in potential energy from amber=>charmm conversion: 0.00644336 ======================================================================= INFO 2017-03-18 23:47:21 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5935995.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5935995.inpcrd') INFO 2017-03-18 23:47:22 Beginning InterMol conversion INFO 2017-03-18 23:47:22 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:47:22 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5948990.inpcrd INFO 2017-03-18 23:47:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5948990/mobley_5948990_converted.input INFO 2017-03-18 23:47:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5948990/mobley_5948990_converted.cms INFO 2017-03-18 23:47:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5948990/mobley_5948990_converted.rst7 WARNING 2017-03-18 23:47:37 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:47:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5948990/mobley_5948990_converted.inp INFO 2017-03-18 23:47:37 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5948990/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5948990/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5948990/mobley_5948990_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_5948990/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5948990/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 169.78130431 169.78130431 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -145.96959288 -145.96959288 coulomb total -146.00695600 -146.01934960 -0.01239360 -146.01934901 -0.01239301 -146.01959377 -0.01263777 -146.00695600 0.00000000 -145.96959288 0.03736312 coulomb-14 -315.79116560 -315.80065391 -0.00948831 0.00000000 315.79116560 -315.80051224 -0.00934664 -315.79116560 0.00000000 0.00000000 315.79116560 improper 0.00000000 0.11765154 0.11765154 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.11765408 0.11765408 proper 20.30829920 20.19081492 -0.11748428 20.30846489 0.00016569 20.30853961 0.00024041 20.30829920 0.00000000 20.19081248 -0.11748672 vdw (SR) 0.00000000 -5.43758277 -5.43758277 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 13.77623840 13.77623840 vdw total 13.77623840 13.77628763 0.00004923 13.77628777 0.00004937 13.77630857 0.00007017 13.77623840 0.00000000 13.77623840 0.00000000 vdw-14 19.21376480 19.21387040 0.00010560 0.00000000 -19.21376480 19.21388204 0.00011724 19.21376480 0.00000000 0.00000000 -19.21376480 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.93168080 4.93166702 -0.00001378 4.93166699 -0.00001381 4.93184879 0.00016799 4.93168080 0.00000000 4.93172264 0.00004184 bond 16.64855440 16.64851642 -0.00003798 16.64851633 -0.00003807 16.65029285 0.00173845 16.64855440 0.00000000 16.64851256 -0.00004184 bonded 41.88853440 41.88864990 0.00011550 41.88864820 0.00011380 41.89068125 0.00214685 41.88853440 0.00000000 41.88870176 0.00016736 dihedral 20.30829920 20.30846646 0.00016726 20.30846489 0.00016569 20.30853961 0.00024041 20.30829920 0.00000000 20.30846656 0.00016736 nonbonded -132.23071760 -132.24306197 -0.01234437 -132.24306040 -0.01234280 -132.24328521 -0.01256761 -132.23071760 0.00000000 -132.19335448 0.03736312 potential -90.34218320 -90.35441207 -0.01222887 -90.35441303 -0.01222983 -90.35266119 -0.01047799 -90.34218320 0.00000000 -90.30465272 0.03753048 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -90.34218320 Difference in potential energy from amber=>gromacs conversion: -0.01222887 Difference in potential energy from amber=>lammps conversion: -0.01222983 Difference in potential energy from amber=>desmond conversion: -0.01047799 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.03753048 ======================================================================= INFO 2017-03-18 23:47:37 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5948990.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5948990.inpcrd') INFO 2017-03-18 23:47:38 Beginning InterMol conversion INFO 2017-03-18 23:47:38 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:47:38 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5952846.inpcrd INFO 2017-03-18 23:47:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5952846/mobley_5952846_converted.input INFO 2017-03-18 23:47:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5952846/mobley_5952846_converted.cms INFO 2017-03-18 23:47:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5952846/mobley_5952846_converted.rst7 WARNING 2017-03-18 23:47:54 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:47:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5952846/mobley_5952846_converted.inp INFO 2017-03-18 23:47:54 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5952846/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5952846/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5952846/mobley_5952846_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_5952846/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5952846/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.24511656 1.24511656 coulomb total 1.24139280 1.24400571 0.00261291 1.24400571 0.00261291 1.24400643 0.00261363 1.24139280 0.00000000 1.24511656 0.00372376 coulomb-14 1.24139280 1.24400571 0.00261291 0.00000000 -1.24139280 1.24400643 0.00261363 1.24139280 0.00000000 0.00000000 -1.24139280 improper 0.00000000 0.00000083 0.00000083 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00000000 0.00000583 0.00000583 0.00000666 0.00000666 0.00000499 0.00000499 0.00000000 0.00000000 0.00000000 0.00000000 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 3.33485720 3.33485720 vdw total 3.33464800 3.33480385 0.00015585 3.33480385 0.00015585 3.33486125 0.00021325 3.33464800 0.00000000 3.33485720 0.00020920 vdw-14 3.33464800 3.33480385 0.00015585 0.00000000 -3.33464800 3.33486125 0.00021325 3.33464800 0.00000000 0.00000000 -3.33464800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.08786400 0.08803911 0.00017511 0.08803911 0.00017511 0.08806911 0.00020511 0.08786400 0.00000000 0.08803136 0.00016736 bond 2.13300320 2.13316017 0.00015697 2.13316018 0.00015698 2.13315184 0.00014864 2.13300320 0.00000000 2.13317056 0.00016736 bonded 2.22086720 2.22120595 0.00033875 2.22120596 0.00033876 2.22122594 0.00035874 2.22086720 0.00000000 2.22120192 0.00033472 dihedral 0.00000000 0.00000667 0.00000667 0.00000666 0.00000666 0.00000499 0.00000499 0.00000000 0.00000000 0.00000000 0.00000000 nonbonded 4.57604080 4.57880956 0.00276876 4.57880935 0.00276855 4.57886768 0.00282688 4.57604080 0.00000000 4.57997376 0.00393296 potential 6.79690800 6.80001551 0.00310751 6.80001546 0.00310746 6.80004834 0.00314034 6.79690800 0.00000000 6.80117568 0.00426768 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 6.79690800 Difference in potential energy from amber=>gromacs conversion: 0.00310751 Difference in potential energy from amber=>lammps conversion: 0.00310746 Difference in potential energy from amber=>desmond conversion: 0.00314034 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00426768 ======================================================================= INFO 2017-03-18 23:47:54 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5952846.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5952846.inpcrd') INFO 2017-03-18 23:47:54 Beginning InterMol conversion INFO 2017-03-18 23:47:54 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:47:54 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:47:54 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5973402.inpcrd INFO 2017-03-18 23:47:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5973402/mobley_5973402_converted.input INFO 2017-03-18 23:47:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5973402/mobley_5973402_converted.cms WARNING 2017-03-18 23:48:10 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:48:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5973402/mobley_5973402_converted.inp INFO 2017-03-18 23:48:10 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5973402/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5973402/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5973402/mobley_5973402_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5973402/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 30.04660679 30.04660679 0.00000000 0.00000000 0.00000000 0.00000000 -10.96873256 -10.96873256 coulomb total -10.95413040 -10.96077362 -0.00664322 -10.96077334 -0.00664294 -10.96082447 -0.00669407 -10.96873256 -0.01460216 coulomb-14 -41.00571040 -41.00738042 -0.00167002 0.00000000 41.00571040 -41.00736906 -0.00165866 0.00000000 41.00571040 proper 7.08476720 7.08477737 0.00001017 7.08477975 0.00001255 7.08480398 0.00003678 7.08480904 0.00004184 vdw (SR) 0.00000000 3.91468446 3.91468446 0.00000000 0.00000000 0.00000000 0.00000000 11.39294832 11.39294832 vdw total 11.39303200 11.39280643 -0.00022557 11.39280648 -0.00022552 11.39264288 -0.00038912 11.39294832 -0.00008368 vdw-14 7.47806320 7.47812197 0.00005877 0.00000000 -7.47806320 7.47806194 -0.00000126 0.00000000 -7.47806320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.55765520 3.55758683 -0.00006837 3.55758683 -0.00006837 3.55781804 0.00016284 3.55752968 -0.00012552 bond 0.47697600 0.47698145 0.00000545 0.47698144 0.00000544 0.47692238 -0.00005362 0.47697600 0.00000000 bonded 11.11939840 11.11934564 -0.00005276 11.11934802 -0.00005038 11.11954440 0.00014600 11.11931472 -0.00008368 dihedral 7.08476720 7.08477737 0.00001017 7.08477975 0.00001255 7.08480398 0.00003678 7.08480904 0.00004184 nonbonded 0.43890160 0.43203281 -0.00686879 0.43203315 -0.00686845 0.43181841 -0.00708319 0.42421576 -0.01468584 potential 11.55830000 11.55137845 -0.00692155 11.55138092 -0.00691908 11.55131962 -0.00698038 11.54353048 -0.01476952 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 11.55830000 Difference in potential energy from amber=>gromacs conversion: -0.00692155 Difference in potential energy from amber=>lammps conversion: -0.00691908 Difference in potential energy from amber=>desmond conversion: -0.00698038 Difference in potential energy from amber=>charmm conversion: -0.01476952 ======================================================================= INFO 2017-03-18 23:48:10 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5973402.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5973402.inpcrd') INFO 2017-03-18 23:48:10 Beginning InterMol conversion INFO 2017-03-18 23:48:10 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:48:10 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:48:10 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5977084.inpcrd INFO 2017-03-18 23:48:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5977084/mobley_5977084_converted.input INFO 2017-03-18 23:48:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5977084/mobley_5977084_converted.cms WARNING 2017-03-18 23:48:26 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:48:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5977084/mobley_5977084_converted.inp INFO 2017-03-18 23:48:26 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5977084/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5977084/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5977084/mobley_5977084_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5977084/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -30.58600116 -30.58600116 0.00000000 0.00000000 0.00000000 0.00000000 -38.98216064 -38.98216064 coulomb total -38.96977600 -38.96457807 0.00519793 -38.96457780 0.00519820 -38.96465144 0.00512456 -38.98216064 -0.01238464 coulomb-14 -8.38264400 -8.37857690 0.00406710 0.00000000 8.38264400 -8.37860443 0.00403957 0.00000000 8.38264400 improper 0.00000000 0.00011507 0.00011507 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00083680 0.00085926 0.00002246 0.00097433 0.00013753 0.00097360 0.00013680 0.00087864 0.00004184 vdw (SR) 0.00000000 -1.44777875 -1.44777875 0.00000000 0.00000000 0.00000000 0.00000000 19.59442512 19.59442512 vdw total 19.59450880 19.59445927 -0.00004953 19.59445943 -0.00004937 19.59485086 0.00034206 19.59442512 -0.00008368 vdw-14 21.04217280 21.04223802 0.00006522 0.00000000 -21.04217280 21.04263576 0.00046296 0.00000000 -21.04217280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.59996160 1.59981157 -0.00015003 1.59981156 -0.00015004 1.59983105 -0.00013055 1.59983608 -0.00012552 bond 1.49703520 1.49688926 -0.00014594 1.49688926 -0.00014594 1.49686406 -0.00017114 1.49690968 -0.00012552 bonded 3.09783360 3.09767517 -0.00015843 3.09767515 -0.00015845 3.09766871 -0.00016489 3.09774992 -0.00008368 dihedral 0.00083680 0.00097433 0.00013753 0.00097433 0.00013753 0.00097360 0.00013680 0.00100416 0.00016736 nonbonded -19.37526720 -19.37011879 0.00514841 -19.37011837 0.00514883 -19.36980057 0.00546663 -19.38773552 -0.01246832 potential -16.27743360 -16.27244363 0.00498997 -16.27244334 0.00499026 -16.27217368 0.00525992 -16.29002744 -0.01259384 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -16.27743360 Difference in potential energy from amber=>gromacs conversion: 0.00498997 Difference in potential energy from amber=>lammps conversion: 0.00499026 Difference in potential energy from amber=>desmond conversion: 0.00525992 Difference in potential energy from amber=>charmm conversion: -0.01259384 ======================================================================= INFO 2017-03-18 23:48:26 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5977084.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5977084.inpcrd') INFO 2017-03-18 23:48:26 Beginning InterMol conversion INFO 2017-03-18 23:48:26 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:48:26 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:48:26 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6006813.inpcrd INFO 2017-03-18 23:48:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6006813/mobley_6006813_converted.input INFO 2017-03-18 23:48:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6006813/mobley_6006813_converted.cms WARNING 2017-03-18 23:48:42 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:48:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6006813/mobley_6006813_converted.inp INFO 2017-03-18 23:48:42 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6006813/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6006813/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6006813/mobley_6006813_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6006813/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -6.02310781 -6.02310781 0.00000000 0.00000000 0.00000000 0.00000000 -12.10460488 -12.10460488 coulomb total -12.11519040 -12.11954214 -0.00435174 -12.11954218 -0.00435178 -12.11948933 -0.00429893 -12.10460488 0.01058552 coulomb-14 -6.09357760 -6.09643433 -0.00285673 0.00000000 6.09357760 -6.09640946 -0.00283186 0.00000000 6.09357760 proper 1.72924720 1.72935293 0.00010573 1.72935293 0.00010573 1.72934511 0.00009791 1.72937272 0.00012552 vdw (SR) 0.00000000 -2.66158930 -2.66158930 0.00000000 0.00000000 0.00000000 0.00000000 2.67487304 2.67487304 vdw total 2.67483120 2.67477724 -0.00005396 2.67477727 -0.00005393 2.67473795 -0.00009325 2.67487304 0.00004184 vdw-14 5.33627360 5.33636653 0.00009293 0.00000000 -5.33627360 5.33632640 0.00005280 0.00000000 -5.33627360 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.81415840 2.81431529 0.00015689 2.81431530 0.00015690 2.81473132 0.00057292 2.81436760 0.00020920 bond 11.44826080 11.44843630 0.00017550 11.44843611 0.00017531 11.45039171 0.00213091 11.44842816 0.00016736 bonded 15.99166640 15.99210451 0.00043811 15.99210434 0.00043794 15.99446814 0.00280174 15.99216848 0.00050208 dihedral 1.72924720 1.72935293 0.00010573 1.72935293 0.00010573 1.72934511 0.00009791 1.72937272 0.00012552 nonbonded -9.44035920 -9.44476491 -0.00440571 -9.44476453 -0.00440533 -9.44475139 -0.00439219 -9.42973184 0.01062736 potential 6.55130720 6.54733960 -0.00396760 6.54733993 -0.00396727 6.54966929 -0.00163791 6.56243664 0.01112944 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 6.55130720 Difference in potential energy from amber=>gromacs conversion: -0.00396760 Difference in potential energy from amber=>lammps conversion: -0.00396727 Difference in potential energy from amber=>desmond conversion: -0.00163791 Difference in potential energy from amber=>charmm conversion: 0.01112944 ======================================================================= INFO 2017-03-18 23:48:42 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6006813.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6006813.inpcrd') INFO 2017-03-18 23:48:42 Beginning InterMol conversion INFO 2017-03-18 23:48:42 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:48:42 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:48:42 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6055410.inpcrd INFO 2017-03-18 23:48:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6055410/mobley_6055410_converted.input INFO 2017-03-18 23:48:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6055410/mobley_6055410_converted.cms WARNING 2017-03-18 23:48:58 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:48:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6055410/mobley_6055410_converted.inp INFO 2017-03-18 23:48:58 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6055410/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6055410/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6055410/mobley_6055410_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6055410/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 208.44651711 208.44651711 0.00000000 0.00000000 0.00000000 0.00000000 -269.90398240 -269.90398240 coulomb total -269.83076240 -269.84676354 -0.01600114 -269.84676202 -0.01599962 -269.84708293 -0.01632053 -269.90398240 -0.07322000 coulomb-14 -478.27680560 -478.29328064 -0.01647504 0.00000000 478.27680560 -478.29326127 -0.01645567 0.00000000 478.27680560 improper 0.00000000 0.00018002 0.00018002 0.00000000 0.00000000 0.00000000 0.00000000 0.00016736 0.00016736 proper 49.36366880 49.36336789 -0.00030091 49.36354746 -0.00012134 49.36347801 -0.00019079 49.36337592 -0.00029288 vdw (SR) 0.00000000 -1.46974746 -1.46974746 0.00000000 0.00000000 0.00000000 0.00000000 44.00388112 44.00388112 vdw total 44.00354640 44.00378442 0.00023802 44.00378489 0.00023849 44.00402360 0.00047720 44.00388112 0.00033472 vdw-14 45.47338560 45.47353188 0.00014628 0.00000000 -45.47338560 45.47365296 0.00026736 0.00000000 -45.47338560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.53712960 4.53713410 0.00000450 4.53713420 0.00000460 4.53744696 0.00031736 4.53721328 0.00008368 bond 12.09510720 12.09496794 -0.00013926 12.09496787 -0.00013933 12.09296830 -0.00213890 12.09498168 -0.00012552 bonded 65.99590560 65.99564996 -0.00025564 65.99564954 -0.00025606 65.99389326 -0.00201234 65.99573824 -0.00016736 dihedral 49.36366880 49.36354792 -0.00012088 49.36354746 -0.00012134 49.36347801 -0.00019079 49.36354328 -0.00012552 nonbonded -225.82721600 -225.84297911 -0.01576311 -225.84297713 -0.01576113 -225.84305933 -0.01584333 -225.90010128 -0.07288528 potential -159.83131040 -159.84732915 -0.01601875 -159.84732675 -0.01601635 -159.84932629 -0.01801589 -159.90436304 -0.07305264 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -159.83131040 Difference in potential energy from amber=>gromacs conversion: -0.01601875 Difference in potential energy from amber=>lammps conversion: -0.01601635 Difference in potential energy from amber=>desmond conversion: -0.01801589 Difference in potential energy from amber=>charmm conversion: -0.07305264 ======================================================================= INFO 2017-03-18 23:48:58 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6055410.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6055410.inpcrd') INFO 2017-03-18 23:48:58 Beginning InterMol conversion INFO 2017-03-18 23:48:58 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:48:58 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:48:58 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6060301.inpcrd INFO 2017-03-18 23:48:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6060301/mobley_6060301_converted.input INFO 2017-03-18 23:48:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6060301/mobley_6060301_converted.cms WARNING 2017-03-18 23:49:14 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:49:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6060301/mobley_6060301_converted.inp INFO 2017-03-18 23:49:14 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6060301/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6060301/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6060301/mobley_6060301_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6060301/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 10.48360415 10.48360415 0.00000000 0.00000000 0.00000000 0.00000000 0.78311928 0.78311928 coulomb total 0.84223920 0.83367179 -0.00856741 0.83367179 -0.00856741 0.83363020 -0.00860900 0.78311928 -0.05911992 coulomb-14 -9.64788560 -9.64993236 -0.00204676 0.00000000 9.64788560 -9.64994869 -0.00206309 0.00000000 9.64788560 proper 10.13155600 10.13152526 -0.00003074 10.13152546 -0.00003054 10.13157182 0.00001582 10.13151416 -0.00004184 vdw (SR) 0.00000000 -2.46053544 -2.46053544 0.00000000 0.00000000 0.00000000 0.00000000 3.61744456 3.61744456 vdw total 3.61748640 3.61734775 -0.00013865 3.61734778 -0.00013862 3.61735701 -0.00012939 3.61744456 -0.00004184 vdw-14 6.07809680 6.07788319 -0.00021361 0.00000000 -6.07809680 6.07789053 -0.00020627 0.00000000 -6.07809680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 23.80361280 23.80376111 0.00014831 23.80376091 0.00014811 23.80347285 -0.00013995 23.80390568 0.00029288 bond 2.43634320 2.43645794 0.00011474 2.43645793 0.00011473 2.43572842 -0.00061478 2.43646872 0.00012552 bonded 36.37151200 36.37174431 0.00023231 36.37174430 0.00023230 36.37077308 -0.00073892 36.37188856 0.00037656 dihedral 10.13155600 10.13152526 -0.00003074 10.13152546 -0.00003054 10.13157182 0.00001582 10.13151416 -0.00004184 nonbonded 4.45972560 4.45101953 -0.00870607 4.45101953 -0.00870607 4.45098722 -0.00873838 4.40056384 -0.05916176 potential 40.83123760 40.82276385 -0.00847375 40.82276374 -0.00847386 40.82170657 -0.00953103 40.77245240 -0.05878520 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 40.83123760 Difference in potential energy from amber=>gromacs conversion: -0.00847375 Difference in potential energy from amber=>lammps conversion: -0.00847386 Difference in potential energy from amber=>desmond conversion: -0.00953103 Difference in potential energy from amber=>charmm conversion: -0.05878520 ======================================================================= INFO 2017-03-18 23:49:14 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6060301.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6060301.inpcrd') INFO 2017-03-18 23:49:14 Beginning InterMol conversion INFO 2017-03-18 23:49:14 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:49:15 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:49:15 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6081058.inpcrd INFO 2017-03-18 23:49:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6081058/mobley_6081058_converted.input INFO 2017-03-18 23:49:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6081058/mobley_6081058_converted.cms WARNING 2017-03-18 23:49:30 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:49:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6081058/mobley_6081058_converted.inp INFO 2017-03-18 23:49:30 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6081058/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6081058/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6081058/mobley_6081058_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6081058/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -0.01927702 -0.01927702 0.00000000 0.00000000 0.00000000 0.00000000 -2.99996984 -2.99996984 coulomb total -2.97984480 -2.98617301 -0.00632821 -2.98617297 -0.00632817 -2.98633772 -0.00649292 -2.99996984 -0.02012504 coulomb-14 -2.96520080 -2.96689599 -0.00169519 0.00000000 2.96520080 -2.96694401 -0.00174321 0.00000000 2.96520080 improper 0.00000000 0.00421243 0.00421243 0.00000000 0.00000000 0.00000000 0.00000000 0.00422584 0.00422584 proper 3.48736400 3.48318393 -0.00418007 3.48739693 0.00003293 3.48740919 0.00004519 3.48318000 -0.00418400 vdw (SR) 0.00000000 -2.92290578 -2.92290578 0.00000000 0.00000000 0.00000000 0.00000000 5.04561112 5.04561112 vdw total 5.04548560 5.04551375 0.00002815 5.04551363 0.00002803 5.04553595 0.00005035 5.04561112 0.00012552 vdw-14 7.96842800 7.96841953 -0.00000847 0.00000000 -7.96842800 7.96843612 0.00000812 0.00000000 -7.96842800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.19615760 3.19614249 -0.00001511 3.19614250 -0.00001510 3.19630919 0.00015159 3.19611576 -0.00004184 bond 1.21043120 1.21036016 -0.00007104 1.21036016 -0.00007104 1.21044290 0.00001170 1.21034752 -0.00008368 bonded 7.89395280 7.89389900 -0.00005380 7.89389958 -0.00005322 7.89416129 0.00020849 7.89386912 -0.00008368 dihedral 3.48736400 3.48739636 0.00003236 3.48739693 0.00003293 3.48740919 0.00004519 3.48740584 0.00004184 nonbonded 2.06564080 2.05934074 -0.00630006 2.05934083 -0.00629997 2.05919822 -0.00644258 2.04564128 -0.01999952 potential 9.95959360 9.95323974 -0.00635386 9.95324020 -0.00635340 9.95327676 -0.00631684 9.93951040 -0.02008320 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 9.95959360 Difference in potential energy from amber=>gromacs conversion: -0.00635386 Difference in potential energy from amber=>lammps conversion: -0.00635340 Difference in potential energy from amber=>desmond conversion: -0.00631684 Difference in potential energy from amber=>charmm conversion: -0.02008320 ======================================================================= INFO 2017-03-18 23:49:30 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6081058.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6081058.inpcrd') INFO 2017-03-18 23:49:31 Beginning InterMol conversion INFO 2017-03-18 23:49:31 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:49:31 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6082662.inpcrd INFO 2017-03-18 23:49:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6082662/mobley_6082662_converted.input INFO 2017-03-18 23:49:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6082662/mobley_6082662_converted.cms INFO 2017-03-18 23:49:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6082662/mobley_6082662_converted.rst7 WARNING 2017-03-18 23:49:46 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:49:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6082662/mobley_6082662_converted.inp INFO 2017-03-18 23:49:46 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6082662/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6082662/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6082662/mobley_6082662_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_6082662/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6082662/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 93.14156747 93.14156747 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -169.11493696 -169.11493696 coulomb total -169.04949920 -169.06324040 -0.01374120 -169.06323946 -0.01374026 -169.06332523 -0.01382603 -169.04908080 0.00041840 -169.11493696 -0.06543776 coulomb-14 -262.19830960 -262.20480787 -0.00649827 0.00000000 262.19830960 -262.20466928 -0.00635968 -262.19789120 0.00041840 0.00000000 262.19830960 improper 0.00000000 0.11425603 0.11425603 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.11426504 0.11426504 proper 0.21966000 0.10529798 -0.11436202 0.21955249 -0.00010751 0.21952911 -0.00013089 0.21966000 0.00000000 0.10531128 -0.11434872 vdw (SR) 0.00000000 1.54982698 1.54982698 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 26.04201096 26.04201096 vdw total 26.04205280 26.04193436 -0.00011844 26.04193439 -0.00011841 26.04181134 -0.00024146 26.04205280 0.00000000 26.04201096 -0.00004184 vdw-14 24.49229920 24.49210738 -0.00019182 0.00000000 -24.49229920 24.49209490 -0.00020430 24.49229920 0.00000000 0.00000000 -24.49229920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.61495200 4.61499869 0.00004669 4.61499886 0.00004686 4.61518396 0.00023196 4.61495200 0.00000000 4.61507752 0.00012552 bond 16.51508480 16.51523820 0.00015340 16.51523835 0.00015355 16.51486564 -0.00021916 16.51508480 0.00000000 16.51525216 0.00016736 bonded 21.34969680 21.34979089 0.00009409 21.34978971 0.00009291 21.34957871 -0.00011809 21.34969680 0.00000000 21.34990600 0.00020920 dihedral 0.21966000 0.21955401 -0.00010599 0.21955249 -0.00010751 0.21952911 -0.00013089 0.21966000 0.00000000 0.21957632 -0.00008368 nonbonded -143.00744640 -143.02130604 -0.01385964 -143.02130381 -0.01385741 -143.02151389 -0.01406749 -143.00702800 0.00041840 -143.07292600 -0.06547960 potential -121.65774960 -121.67151515 -0.01376555 -121.67151496 -0.01376536 -121.67199989 -0.01425029 -121.65733120 0.00041840 -121.72310368 -0.06535408 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -121.65774960 Difference in potential energy from amber=>gromacs conversion: -0.01376555 Difference in potential energy from amber=>lammps conversion: -0.01376536 Difference in potential energy from amber=>desmond conversion: -0.01425029 Difference in potential energy from amber=>amber conversion: 0.00041840 Difference in potential energy from amber=>charmm conversion: -0.06535408 ======================================================================= INFO 2017-03-18 23:49:46 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6082662.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6082662.inpcrd') INFO 2017-03-18 23:49:47 Beginning InterMol conversion INFO 2017-03-18 23:49:47 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:49:47 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6091882.inpcrd INFO 2017-03-18 23:49:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6091882/mobley_6091882_converted.input INFO 2017-03-18 23:49:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6091882/mobley_6091882_converted.cms INFO 2017-03-18 23:50:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6091882/mobley_6091882_converted.rst7 WARNING 2017-03-18 23:50:02 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:50:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6091882/mobley_6091882_converted.inp INFO 2017-03-18 23:50:02 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6091882/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6091882/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6091882/mobley_6091882_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_6091882/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6091882/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 20.23767328 20.23767328 coulomb total 20.20662800 20.21337695 0.00674895 20.21337679 0.00674879 20.21336173 0.00673373 20.20662800 0.00000000 20.23767328 0.03104528 coulomb-14 20.20662800 20.21337695 0.00674895 0.00000000 -20.20662800 20.21336173 0.00673373 20.20662800 0.00000000 0.00000000 -20.20662800 improper 0.00000000 0.00000709 0.00000709 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00000000 0.00008356 0.00008356 0.00009076 0.00009076 0.00008529 0.00008529 0.00000000 0.00000000 0.00008368 0.00008368 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.10602256 0.10602256 vdw total 0.10585520 0.10600908 0.00015388 0.10600908 0.00015388 0.10600653 0.00015133 0.10585520 0.00000000 0.10602256 0.00016736 vdw-14 0.10585520 0.10600908 0.00015388 0.00000000 -0.10585520 0.10600653 0.00015133 0.10585520 0.00000000 0.00000000 -0.10585520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.07740400 0.07741156 0.00000756 0.07741156 0.00000756 0.07747043 0.00006643 0.07740400 0.00000000 0.07740400 0.00000000 bond 0.30585040 0.30575165 -0.00009875 0.30575165 -0.00009875 0.30605413 0.00020373 0.30585040 0.00000000 0.30576672 -0.00008368 bonded 0.38325440 0.38325385 -0.00000055 0.38325397 -0.00000043 0.38360985 0.00035545 0.38325440 0.00000000 0.38325440 0.00000000 dihedral 0.00000000 0.00009064 0.00009064 0.00009076 0.00009076 0.00008529 0.00008529 0.00000000 0.00000000 0.00008368 0.00008368 nonbonded 20.31248320 20.31938603 0.00690283 20.31938596 0.00690276 20.31936826 0.00688506 20.31248320 0.00000000 20.34369584 0.03121264 potential 20.69573760 20.70263989 0.00690229 20.70263994 0.00690234 20.70297533 0.00723773 20.69573760 0.00000000 20.72695024 0.03121264 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 20.69573760 Difference in potential energy from amber=>gromacs conversion: 0.00690229 Difference in potential energy from amber=>lammps conversion: 0.00690234 Difference in potential energy from amber=>desmond conversion: 0.00723773 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.03121264 ======================================================================= INFO 2017-03-18 23:50:02 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6091882.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6091882.inpcrd') INFO 2017-03-18 23:50:03 Beginning InterMol conversion INFO 2017-03-18 23:50:03 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:50:03 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6102880.inpcrd INFO 2017-03-18 23:50:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6102880/mobley_6102880_converted.input INFO 2017-03-18 23:50:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6102880/mobley_6102880_converted.cms INFO 2017-03-18 23:50:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6102880/mobley_6102880_converted.rst7 WARNING 2017-03-18 23:50:19 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:50:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6102880/mobley_6102880_converted.inp INFO 2017-03-18 23:50:19 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6102880/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6102880/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6102880/mobley_6102880_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_6102880/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6102880/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 17.69855328 17.69855328 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -36.43715896 -36.43715896 coulomb total -36.44180320 -36.43600886 0.00579434 -36.43600836 0.00579484 -36.43599941 0.00580379 -36.44180320 0.00000000 -36.43715896 0.00464424 coulomb-14 -54.13342880 -54.13456213 -0.00113333 0.00000000 54.13342880 -54.13455639 -0.00112759 -54.13342880 0.00000000 0.00000000 54.13342880 improper 0.00000000 0.00024143 0.00024143 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00025104 0.00025104 proper 15.05528720 15.05522689 -0.00006031 15.05544703 0.00015983 15.05540184 0.00011464 15.05528720 0.00000000 15.05520352 -0.00008368 vdw (SR) 0.00000000 -3.99182605 -3.99182605 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 34.15047744 34.15047744 vdw total 34.15022640 34.15053218 0.00030578 34.15053225 0.00030585 34.15009812 -0.00012828 34.15022640 0.00000000 34.15047744 0.00025104 vdw-14 38.14218080 38.14235823 0.00017743 0.00000000 -38.14218080 38.14186692 -0.00031388 38.14218080 0.00000000 0.00000000 -38.14218080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.71839280 0.71823681 -0.00015599 0.71823682 -0.00015598 0.71816981 -0.00022299 0.71839280 0.00000000 0.71826728 -0.00012552 bond 2.03677120 2.03679853 0.00002733 2.03679852 0.00002732 2.03723369 0.00046249 2.03677120 0.00000000 2.03681304 0.00004184 bonded 17.81045120 17.81050367 0.00005247 17.81048237 0.00003117 17.81080533 0.00035413 17.81045120 0.00000000 17.81053488 0.00008368 dihedral 15.05528720 15.05546833 0.00018113 15.05544703 0.00015983 15.05540184 0.00011464 15.05528720 0.00000000 15.05545456 0.00016736 nonbonded -2.29157680 -2.28547668 0.00610012 -2.28547624 0.00610056 -2.28590129 0.00567551 -2.29157680 0.00000000 -2.28668152 0.00489528 potential 15.51887440 15.52502699 0.00615259 15.52500605 0.00613165 15.52479284 0.00591844 15.51887440 0.00000000 15.52381152 0.00493712 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 15.51887440 Difference in potential energy from amber=>gromacs conversion: 0.00615259 Difference in potential energy from amber=>lammps conversion: 0.00613165 Difference in potential energy from amber=>desmond conversion: 0.00591844 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00493712 ======================================================================= INFO 2017-03-18 23:50:19 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6102880.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6102880.inpcrd') INFO 2017-03-18 23:50:19 Beginning InterMol conversion INFO 2017-03-18 23:50:19 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:50:19 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:50:19 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6115639.inpcrd INFO 2017-03-18 23:50:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6115639/mobley_6115639_converted.input INFO 2017-03-18 23:50:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6115639/mobley_6115639_converted.cms WARNING 2017-03-18 23:50:35 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:50:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6115639/mobley_6115639_converted.inp INFO 2017-03-18 23:50:35 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6115639/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6115639/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6115639/mobley_6115639_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6115639/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -233.24531869 -233.24531869 0.00000000 0.00000000 0.00000000 0.00000000 -267.46851784 -267.46851784 coulomb total -267.40529760 -267.40493866 0.00035894 -267.40493359 0.00036401 -267.40476975 0.00052785 -267.46851784 -0.06322024 coulomb-14 -34.30294240 -34.15961997 0.14332243 0.00000000 34.30294240 -34.15959664 0.14334576 0.00000000 34.30294240 proper 40.74755760 40.74762222 0.00006462 40.74762203 0.00006443 40.74764823 0.00009063 40.74764128 0.00008368 vdw (SR) 0.00000000 -4.12648143 -4.12648143 0.00000000 0.00000000 0.00000000 0.00000000 -0.62186792 -0.62186792 vdw total -0.62174240 -0.62200752 -0.00026512 -0.62200754 -0.00026514 -0.62194350 -0.00020110 -0.62186792 -0.00012552 vdw-14 3.50451840 3.50447391 -0.00004449 0.00000000 -3.50451840 3.50452711 0.00000871 0.00000000 -3.50451840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.07317200 2.07329331 0.00012131 2.07329329 0.00012129 2.07325289 0.00008089 2.07333936 0.00016736 bond 4.05680640 4.05659978 -0.00020662 4.05659979 -0.00020661 4.05697573 0.00016933 4.05659720 -0.00020920 bonded 46.87753600 46.87751531 -0.00002069 46.87751512 -0.00002088 46.87787685 0.00034085 46.87757784 0.00004184 dihedral 40.74755760 40.74762222 0.00006462 40.74762203 0.00006443 40.74764823 0.00009063 40.74764128 0.00008368 nonbonded -268.02704000 -268.02694619 0.00009381 -268.02694377 0.00009623 -268.02671324 0.00032676 -268.09038576 -0.06334576 potential -221.14950400 -221.14943087 0.00007313 -221.14942869 0.00007531 -221.14887556 0.00062844 -221.21284976 -0.06334576 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -221.14950400 Difference in potential energy from amber=>gromacs conversion: 0.00007313 Difference in potential energy from amber=>lammps conversion: 0.00007531 Difference in potential energy from amber=>desmond conversion: 0.00062844 Difference in potential energy from amber=>charmm conversion: -0.06334576 ======================================================================= INFO 2017-03-18 23:50:35 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6115639.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6115639.inpcrd') INFO 2017-03-18 23:50:35 Beginning InterMol conversion INFO 2017-03-18 23:50:35 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:50:35 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:50:35 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6175884.inpcrd INFO 2017-03-18 23:50:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6175884/mobley_6175884_converted.input INFO 2017-03-18 23:50:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6175884/mobley_6175884_converted.cms WARNING 2017-03-18 23:50:51 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:50:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6175884/mobley_6175884_converted.inp INFO 2017-03-18 23:50:51 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6175884/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6175884/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6175884/mobley_6175884_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6175884/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 3.28574586 3.28574586 0.00000000 0.00000000 0.00000000 0.00000000 16.10166376 16.10166376 coulomb total 16.10170560 16.11263224 0.01092664 16.11263212 0.01092652 16.11284494 0.01113934 16.10166376 -0.00004184 coulomb-14 12.82437840 12.82688638 0.00250798 0.00000000 -12.82437840 12.82681872 0.00244032 0.00000000 -12.82437840 improper 0.00000000 0.00002417 0.00002417 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00000000 0.00018312 0.00018312 0.00020732 0.00020732 0.00020475 0.00020475 0.00016736 0.00016736 vdw (SR) 0.00000000 -1.52863058 -1.52863058 0.00000000 0.00000000 0.00000000 0.00000000 19.24920328 19.24920328 vdw total 19.24932880 19.24916335 -0.00016545 19.24916353 -0.00016527 19.24917422 -0.00015458 19.24920328 -0.00012552 vdw-14 20.77774400 20.77779393 0.00004993 0.00000000 -20.77774400 20.77783755 0.00009355 0.00000000 -20.77774400 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.82090080 0.82110189 0.00020109 0.82110188 0.00020108 0.82113454 0.00023374 0.82111000 0.00020920 bond 4.04509120 4.04507489 -0.00001631 4.04507488 -0.00001632 4.04492860 -0.00016260 4.04509120 0.00000000 bonded 4.86599200 4.86638407 0.00039207 4.86638408 0.00039208 4.86626789 0.00027589 4.86641040 0.00041840 dihedral 0.00000000 0.00020729 0.00020729 0.00020732 0.00020732 0.00020475 0.00020475 0.00020920 0.00020920 nonbonded 35.35103440 35.36179559 0.01076119 35.36179523 0.01076083 35.36201916 0.01098476 35.35086704 -0.00016736 potential 40.21702640 40.22817966 0.01115326 40.22817969 0.01115329 40.22822605 0.01119965 40.21727744 0.00025104 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 40.21702640 Difference in potential energy from amber=>gromacs conversion: 0.01115326 Difference in potential energy from amber=>lammps conversion: 0.01115329 Difference in potential energy from amber=>desmond conversion: 0.01119965 Difference in potential energy from amber=>charmm conversion: 0.00025104 ======================================================================= INFO 2017-03-18 23:50:51 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6175884.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6175884.inpcrd') INFO 2017-03-18 23:50:51 Beginning InterMol conversion INFO 2017-03-18 23:50:51 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:50:51 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:50:51 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6190089.inpcrd INFO 2017-03-18 23:50:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6190089/mobley_6190089_converted.input INFO 2017-03-18 23:50:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6190089/mobley_6190089_converted.cms WARNING 2017-03-18 23:51:07 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:51:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6190089/mobley_6190089_converted.inp INFO 2017-03-18 23:51:07 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6190089/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6190089/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6190089/mobley_6190089_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6190089/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 5.01833144 5.01833144 coulomb total 4.98565440 4.99118110 0.00552670 4.99118105 0.00552665 4.99117966 0.00552526 5.01833144 0.03267704 coulomb-14 4.98565440 4.99118110 0.00552670 0.00000000 -4.98565440 4.99117966 0.00552526 0.00000000 -4.98565440 proper 6.80192880 6.80197414 0.00004534 6.80197608 0.00004728 6.80197662 0.00004782 6.80197064 0.00004184 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.91960136 0.91960136 vdw total 0.91964320 0.91958450 -0.00005870 0.91958450 -0.00005870 0.91953214 -0.00011106 0.91960136 -0.00004184 vdw-14 0.91964320 0.91958450 -0.00005870 0.00000000 -0.91964320 0.91953214 -0.00011106 0.00000000 -0.91964320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.22588800 2.22581139 -0.00007661 2.22581139 -0.00007661 2.22575769 -0.00013031 2.22580432 -0.00008368 bond 0.09665040 0.09664572 -0.00000468 0.09664571 -0.00000469 0.09655901 -0.00009139 0.09665040 0.00000000 bonded 9.12446720 9.12443125 -0.00003595 9.12443318 -0.00003402 9.12429332 -0.00017388 9.12442536 -0.00004184 dihedral 6.80192880 6.80197414 0.00004534 6.80197608 0.00004728 6.80197662 0.00004782 6.80197064 0.00004184 nonbonded 5.90529760 5.91076559 0.00546799 5.91076567 0.00546807 5.91071180 0.00541420 5.93793280 0.03263520 potential 15.02976480 15.03519684 0.00543204 15.03519898 0.00543418 15.03495380 0.00518900 15.06235816 0.03259336 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 15.02976480 Difference in potential energy from amber=>gromacs conversion: 0.00543204 Difference in potential energy from amber=>lammps conversion: 0.00543418 Difference in potential energy from amber=>desmond conversion: 0.00518900 Difference in potential energy from amber=>charmm conversion: 0.03259336 ======================================================================= INFO 2017-03-18 23:51:07 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6190089.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6190089.inpcrd') INFO 2017-03-18 23:51:07 Beginning InterMol conversion INFO 2017-03-18 23:51:07 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:51:07 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:51:07 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6195751.inpcrd INFO 2017-03-18 23:51:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6195751/mobley_6195751_converted.input INFO 2017-03-18 23:51:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6195751/mobley_6195751_converted.cms WARNING 2017-03-18 23:51:23 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:51:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6195751/mobley_6195751_converted.inp INFO 2017-03-18 23:51:23 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6195751/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6195751/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6195751/mobley_6195751_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6195751/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -134.05031489 -134.05031489 0.00000000 0.00000000 0.00000000 0.00000000 11.79825240 11.79825240 coulomb total 11.77879680 11.77933924 0.00054244 11.77933905 0.00054225 11.78033149 0.00153469 11.79825240 0.01945560 coulomb-14 145.82453360 145.82965413 0.00512053 0.00000000 -145.82453360 145.82963180 0.00509820 0.00000000 -145.82453360 improper 0.00000000 0.00010008 0.00010008 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 55.23047360 55.23029256 -0.00018104 55.23037318 -0.00010042 55.23043553 -0.00003807 55.23026440 -0.00020920 vdw (SR) 0.00000000 -11.10147022 -11.10147022 0.00000000 0.00000000 0.00000000 0.00000000 20.93953928 20.93953928 vdw total 20.93966480 20.93936153 -0.00030327 20.93936146 -0.00030334 20.93944070 -0.00022410 20.93953928 -0.00012552 vdw-14 32.04107200 32.04083175 -0.00024025 0.00000000 -32.04107200 32.04091631 -0.00015569 0.00000000 -32.04107200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.38155680 1.38135103 -0.00020577 1.38135103 -0.00020577 1.38181362 0.00025682 1.38138944 -0.00016736 bond 3.18904480 3.18920892 0.00016412 3.18920894 0.00016414 3.18898924 -0.00005556 3.18921216 0.00016736 bonded 59.80107520 59.80095259 -0.00012261 59.80093315 -0.00014205 59.80123838 0.00016318 59.80094968 -0.00012552 dihedral 55.23047360 55.23039264 -0.00008096 55.23037318 -0.00010042 55.23043553 -0.00003807 55.23034808 -0.00012552 nonbonded 32.71846160 32.71870076 0.00023916 32.71870051 0.00023891 32.71977220 0.00131060 32.73779168 0.01933008 potential 92.51953680 92.51965335 0.00011655 92.51963303 0.00009623 92.52082296 0.00128616 92.53878320 0.01924640 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 92.51953680 Difference in potential energy from amber=>gromacs conversion: 0.00011655 Difference in potential energy from amber=>lammps conversion: 0.00009623 Difference in potential energy from amber=>desmond conversion: 0.00128616 Difference in potential energy from amber=>charmm conversion: 0.01924640 ======================================================================= INFO 2017-03-18 23:51:23 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6195751.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6195751.inpcrd') INFO 2017-03-18 23:51:23 Beginning InterMol conversion INFO 2017-03-18 23:51:23 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:51:23 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:51:23 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6198745.inpcrd INFO 2017-03-18 23:51:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6198745/mobley_6198745_converted.input INFO 2017-03-18 23:51:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6198745/mobley_6198745_converted.cms WARNING 2017-03-18 23:51:39 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:51:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6198745/mobley_6198745_converted.inp INFO 2017-03-18 23:51:39 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6198745/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6198745/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6198745/mobley_6198745_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6198745/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -220.27991432 -220.27991432 0.00000000 0.00000000 0.00000000 0.00000000 -324.36167120 -324.36167120 coulomb total -324.27046000 -324.29811722 -0.02765722 -324.29811206 -0.02765206 -324.29793800 -0.02747800 -324.36167120 -0.09121120 coulomb-14 -104.00043280 -104.01820290 -0.01777010 0.00000000 104.00043280 -104.01833363 -0.01790083 0.00000000 104.00043280 improper 0.00000000 0.00002531 0.00002531 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 70.87863360 70.87874897 0.00011537 70.87877586 0.00014226 70.87870598 0.00007238 70.87863360 0.00000000 vdw (SR) 0.00000000 -8.62821440 -8.62821440 0.00000000 0.00000000 0.00000000 0.00000000 20.25683600 20.25683600 vdw total 20.25683600 20.25647692 -0.00035908 20.25647701 -0.00035899 20.25603953 -0.00079647 20.25683600 0.00000000 vdw-14 28.88508080 28.88469132 -0.00038948 0.00000000 -28.88508080 28.88445107 -0.00062973 0.00000000 -28.88508080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 6.42746080 6.42756586 0.00010506 6.42756582 0.00010502 6.42771092 0.00025012 6.42767000 0.00020920 bond 4.52457760 4.52475078 0.00017318 4.52475082 0.00017322 4.52555318 0.00097558 4.52474496 0.00016736 bonded 81.83067200 81.83109092 0.00041892 81.83109249 0.00042049 81.83197009 0.00129809 81.83109040 0.00041840 dihedral 70.87863360 70.87877428 0.00014068 70.87877586 0.00014226 70.87870598 0.00007238 70.87867544 0.00004184 nonbonded -304.01362400 -304.04164030 -0.02801630 -304.04163588 -0.02801188 -304.04189847 -0.02827447 -304.10483520 -0.09121120 potential -222.18295200 -222.21054938 -0.02759738 -222.21054130 -0.02758930 -222.21010532 -0.02715332 -222.27378664 -0.09083464 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -222.18295200 Difference in potential energy from amber=>gromacs conversion: -0.02759738 Difference in potential energy from amber=>lammps conversion: -0.02758930 Difference in potential energy from amber=>desmond conversion: -0.02715332 Difference in potential energy from amber=>charmm conversion: -0.09083464 ======================================================================= INFO 2017-03-18 23:51:39 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6198745.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6198745.inpcrd') INFO 2017-03-18 23:51:39 Beginning InterMol conversion INFO 2017-03-18 23:51:39 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:51:39 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:51:40 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6201330.inpcrd INFO 2017-03-18 23:51:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6201330/mobley_6201330_converted.input INFO 2017-03-18 23:51:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6201330/mobley_6201330_converted.cms WARNING 2017-03-18 23:51:55 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:51:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6201330/mobley_6201330_converted.inp INFO 2017-03-18 23:51:55 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6201330/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6201330/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6201330/mobley_6201330_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6201330/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -1.44109051 -1.44109051 0.00000000 0.00000000 0.00000000 0.00000000 -107.60202000 -107.60202000 coulomb total -107.55390400 -107.55772881 -0.00382481 -107.55772818 -0.00382418 -107.55807753 -0.00417353 -107.60202000 -0.04811600 coulomb-14 -106.11293440 -106.11663830 -0.00370390 0.00000000 106.11293440 -106.11661004 -0.00367564 0.00000000 106.11293440 improper 0.00000000 0.00009295 0.00009295 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 9.94160240 9.94152948 -0.00007292 9.94162248 0.00002008 9.94160608 0.00000368 9.94151872 -0.00008368 vdw (SR) 0.00000000 0.01081198 0.01081198 0.00000000 0.00000000 0.00000000 0.00000000 31.37117176 31.37117176 vdw total 31.37121360 31.37099914 -0.00021446 31.37099938 -0.00021422 31.37078324 -0.00043036 31.37117176 -0.00004184 vdw-14 31.36033520 31.36018716 -0.00014804 0.00000000 -31.36033520 31.36002441 -0.00031079 0.00000000 -31.36033520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.60911840 3.60891917 -0.00019923 3.60891916 -0.00019924 3.60859843 -0.00051997 3.60890920 -0.00020920 bond 2.71750800 2.71755441 0.00004641 2.71755440 0.00004640 2.71701195 -0.00049605 2.71754984 0.00004184 bonded 16.26822880 16.26809602 -0.00013278 16.26809604 -0.00013276 16.26721646 -0.00101234 16.26806144 -0.00016736 dihedral 9.94160240 9.94162244 0.00002004 9.94162248 0.00002008 9.94160608 0.00000368 9.94160240 -0.00000000 nonbonded -76.18269040 -76.18672967 -0.00403927 -76.18672796 -0.00403756 -76.18729428 -0.00460388 -76.23084824 -0.04815784 potential -59.91446160 -59.91863365 -0.00417205 -59.91863305 -0.00417145 -59.92018866 -0.00572706 -59.96270312 -0.04824152 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -59.91446160 Difference in potential energy from amber=>gromacs conversion: -0.00417205 Difference in potential energy from amber=>lammps conversion: -0.00417145 Difference in potential energy from amber=>desmond conversion: -0.00572706 Difference in potential energy from amber=>charmm conversion: -0.04824152 ======================================================================= INFO 2017-03-18 23:51:55 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6201330.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6201330.inpcrd') INFO 2017-03-18 23:51:55 Beginning InterMol conversion INFO 2017-03-18 23:51:55 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:51:56 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6232400.inpcrd INFO 2017-03-18 23:51:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6232400/mobley_6232400_converted.input INFO 2017-03-18 23:51:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6232400/mobley_6232400_converted.cms INFO 2017-03-18 23:52:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6232400/mobley_6232400_converted.rst7 WARNING 2017-03-18 23:52:11 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:52:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6232400/mobley_6232400_converted.inp INFO 2017-03-18 23:52:11 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6232400/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6232400/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6232400/mobley_6232400_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_6232400/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6232400/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 106.39437451 106.39437451 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -158.76581296 -158.76581296 coulomb total -158.73761280 -158.74724462 -0.00963182 -158.74724437 -0.00963157 -158.74707324 -0.00946044 -158.73719440 0.00041840 -158.76581296 -0.02820016 coulomb-14 -265.12418080 -265.14161912 -0.01743832 0.00000000 265.12418080 -265.14169586 -0.01751506 -265.12376240 0.00041840 0.00000000 265.12418080 improper 0.00000000 0.00010499 0.00010499 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00167360 0.00154675 -0.00012685 0.00165181 -0.00002179 0.00165368 -0.00001992 0.00167360 0.00000000 0.00154808 -0.00012552 vdw (SR) 0.00000000 -1.01099024 -1.01099024 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 20.82694784 20.82694784 vdw total 20.82711520 20.82695636 -0.00015884 20.82695621 -0.00015899 20.82736375 0.00024855 20.82711520 0.00000000 20.82694784 -0.00016736 vdw-14 21.83796960 21.83794660 -0.00002300 0.00000000 -21.83796960 21.83837101 0.00040141 21.83796960 0.00000000 0.00000000 -21.83796960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.05141520 2.05143273 0.00001753 2.05143273 0.00001753 2.05126156 -0.00015364 2.05141520 0.00000000 2.05145704 0.00004184 bond 3.48861920 3.48879486 0.00017566 3.48879484 0.00017564 3.48841958 -0.00019962 3.48861920 0.00000000 3.48878656 0.00016736 bonded 5.54170800 5.54187934 0.00017134 5.54187938 0.00017138 5.54133482 -0.00037318 5.54170800 0.00000000 5.54191720 0.00020920 dihedral 0.00167360 0.00165174 -0.00002186 0.00165181 -0.00002179 0.00165368 -0.00001992 0.00167360 0.00000000 0.00167360 0.00000000 nonbonded -137.91049760 -137.92028826 -0.00979066 -137.92028816 -0.00979056 -137.91970949 -0.00921189 -137.91007920 0.00041840 -137.93886512 -0.02836752 potential -132.36878960 -132.37840892 -0.00961932 -132.37840862 -0.00961902 -132.37841657 -0.00962697 -132.36837120 0.00041840 -132.39698976 -0.02820016 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -132.36878960 Difference in potential energy from amber=>gromacs conversion: -0.00961932 Difference in potential energy from amber=>lammps conversion: -0.00961902 Difference in potential energy from amber=>desmond conversion: -0.00962697 Difference in potential energy from amber=>amber conversion: 0.00041840 Difference in potential energy from amber=>charmm conversion: -0.02820016 ======================================================================= INFO 2017-03-18 23:52:11 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6232400.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6232400.inpcrd') INFO 2017-03-18 23:52:12 Beginning InterMol conversion INFO 2017-03-18 23:52:12 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:52:12 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:52:12 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6235784.inpcrd INFO 2017-03-18 23:52:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6235784/mobley_6235784_converted.input INFO 2017-03-18 23:52:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6235784/mobley_6235784_converted.cms WARNING 2017-03-18 23:52:27 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:52:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6235784/mobley_6235784_converted.inp INFO 2017-03-18 23:52:27 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6235784/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6235784/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6235784/mobley_6235784_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6235784/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -3.72123044 -3.72123044 0.00000000 0.00000000 0.00000000 0.00000000 -8.52243144 -8.52243144 coulomb total -8.52741040 -8.52772842 -0.00031802 -8.52772838 -0.00031798 -8.52772787 -0.00031747 -8.52243144 0.00497896 coulomb-14 -4.80616080 -4.80649798 -0.00033718 0.00000000 4.80616080 -4.80647765 -0.00031685 0.00000000 4.80616080 proper 6.42034800 6.42028195 -0.00006605 6.42028189 -0.00006611 6.42028624 -0.00006176 6.42030616 -0.00004184 vdw (SR) 0.00000000 0.76848276 0.76848276 0.00000000 0.00000000 0.00000000 0.00000000 5.05272392 5.05272392 vdw total 5.05259840 5.05263072 0.00003232 5.05263062 0.00003222 5.05264249 0.00004409 5.05272392 0.00012552 vdw-14 4.28399760 4.28414796 0.00015036 0.00000000 -4.28399760 4.28413785 0.00014025 0.00000000 -4.28399760 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.09827600 2.09828269 0.00000669 2.09828269 0.00000669 2.09841668 0.00014068 2.09827600 0.00000000 bond 0.51002960 0.51012321 0.00009361 0.51012320 0.00009360 0.50993835 -0.00009125 0.51011328 0.00008368 bonded 9.02865360 9.02868786 0.00003426 9.02868778 0.00003418 9.02864127 -0.00001233 9.02869544 0.00004184 dihedral 6.42034800 6.42028195 -0.00006605 6.42028189 -0.00006611 6.42028624 -0.00006176 6.42030616 -0.00004184 nonbonded -3.47481200 -3.47509770 -0.00028570 -3.47509756 -0.00028556 -3.47508538 -0.00027338 -3.46970752 0.00510448 potential 5.55384160 5.55359016 -0.00025144 5.55359014 -0.00025146 5.55352190 -0.00031970 5.55898792 0.00514632 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 5.55384160 Difference in potential energy from amber=>gromacs conversion: -0.00025144 Difference in potential energy from amber=>lammps conversion: -0.00025146 Difference in potential energy from amber=>desmond conversion: -0.00031970 Difference in potential energy from amber=>charmm conversion: 0.00514632 ======================================================================= INFO 2017-03-18 23:52:27 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6235784.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6235784.inpcrd') INFO 2017-03-18 23:52:28 Beginning InterMol conversion INFO 2017-03-18 23:52:28 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:52:28 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:52:28 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6239320.inpcrd INFO 2017-03-18 23:52:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6239320/mobley_6239320_converted.input INFO 2017-03-18 23:52:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6239320/mobley_6239320_converted.cms WARNING 2017-03-18 23:52:43 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:52:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6239320/mobley_6239320_converted.inp INFO 2017-03-18 23:52:43 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6239320/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6239320/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6239320/mobley_6239320_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6239320/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 996.36517157 996.36517157 0.00000000 0.00000000 0.00000000 0.00000000 -1669.22855680 -1669.22855680 coulomb total -1668.39845120 -1668.46905542 -0.07060422 -1668.46903528 -0.07058408 -1668.46926958 -0.07081838 -1669.22855680 -0.83010560 coulomb-14 -2664.73646320 -2664.83422699 -0.09776379 0.00000000 2664.73646320 -2664.83464913 -0.09818593 0.00000000 2664.73646320 improper 0.00000000 0.00007274 0.00007274 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 100.41641840 100.41635764 -0.00006076 100.41643095 0.00001255 100.41642886 0.00001046 100.41637656 -0.00004184 vdw (SR) 0.00000000 -2.36870798 -2.36870798 0.00000000 0.00000000 0.00000000 0.00000000 12.14071280 12.14071280 vdw total 12.14071280 12.14079145 0.00007865 12.14079146 0.00007866 12.14075310 0.00004030 12.14071280 0.00000000 vdw-14 14.50927520 14.50949943 0.00022423 0.00000000 -14.50927520 14.50947013 0.00019493 0.00000000 -14.50927520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.78866000 1.78878689 0.00012689 1.78878690 0.00012690 1.78871592 0.00005592 1.78878552 0.00012552 bond 30.03275200 30.03276354 0.00001154 30.03276372 0.00001172 30.03204997 -0.00070203 30.03275200 0.00000000 bonded 132.23783040 132.23798081 0.00015041 132.23798157 0.00015117 132.23719475 -0.00063565 132.23799776 0.00016736 dihedral 100.41641840 100.41643037 0.00001197 100.41643095 0.00001255 100.41642886 0.00001046 100.41646024 0.00004184 nonbonded -1656.25773840 -1656.32826397 -0.07052557 -1656.32823880 -0.07050040 -1656.32851649 -0.07077809 -1657.08784400 -0.83010560 potential -1524.01990800 -1524.09028316 -0.07037516 -1524.09028288 -0.07037488 -1524.09127030 -0.07136230 -1524.84984624 -0.82993824 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -1524.01990800 Difference in potential energy from amber=>gromacs conversion: -0.07037516 Difference in potential energy from amber=>lammps conversion: -0.07037488 Difference in potential energy from amber=>desmond conversion: -0.07136230 Difference in potential energy from amber=>charmm conversion: -0.82993824 ======================================================================= INFO 2017-03-18 23:52:43 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6239320.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6239320.inpcrd') INFO 2017-03-18 23:52:44 Beginning InterMol conversion INFO 2017-03-18 23:52:44 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:52:44 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:52:44 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6248915.inpcrd INFO 2017-03-18 23:52:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6248915/mobley_6248915_converted.input INFO 2017-03-18 23:52:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6248915/mobley_6248915_converted.cms WARNING 2017-03-18 23:53:00 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:53:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6248915/mobley_6248915_converted.inp INFO 2017-03-18 23:53:00 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6248915/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6248915/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6248915/mobley_6248915_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6248915/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 12.54668687 12.54668687 0.00000000 0.00000000 0.00000000 0.00000000 0.40145480 0.40145480 coulomb total 0.44978000 0.44999954 0.00021954 0.44999953 0.00021953 0.44988556 0.00010556 0.40145480 -0.04832520 coulomb-14 -12.09636240 -12.09668733 -0.00032493 0.00000000 12.09636240 -12.09669273 -0.00033033 0.00000000 12.09636240 proper 13.58084560 13.58082268 -0.00002292 13.58082259 -0.00002301 13.58081246 -0.00003314 13.58084560 0.00000000 vdw (SR) 0.00000000 -3.86980437 -3.86980437 0.00000000 0.00000000 0.00000000 0.00000000 4.85486256 4.85486256 vdw total 4.85469520 4.85472850 0.00003330 4.85472867 0.00003347 4.85470515 0.00000995 4.85486256 0.00016736 vdw-14 8.72447680 8.72453287 0.00005607 0.00000000 -8.72447680 8.72450036 0.00002356 0.00000000 -8.72447680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 27.40603680 27.40589669 -0.00014011 27.40589664 -0.00014016 27.40538878 -0.00064802 27.40603680 0.00000000 bond 2.64135920 2.64143456 0.00007536 2.64143455 0.00007535 2.64164435 0.00028515 2.64144288 0.00008368 bonded 43.62824160 43.62815393 -0.00008767 43.62815378 -0.00008782 43.62784560 -0.00039600 43.62832528 0.00008368 dihedral 13.58084560 13.58082268 -0.00002292 13.58082259 -0.00002301 13.58081246 -0.00003314 13.58084560 0.00000000 nonbonded 5.30447520 5.30472804 0.00025284 5.30472791 0.00025271 5.30459071 0.00011551 5.25631736 -0.04815784 potential 48.93271680 48.93288197 0.00016517 48.93287998 0.00016318 48.93233857 -0.00037823 48.88460080 -0.04811600 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 48.93271680 Difference in potential energy from amber=>gromacs conversion: 0.00016517 Difference in potential energy from amber=>lammps conversion: 0.00016318 Difference in potential energy from amber=>desmond conversion: -0.00037823 Difference in potential energy from amber=>charmm conversion: -0.04811600 ======================================================================= INFO 2017-03-18 23:53:00 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6248915.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6248915.inpcrd') INFO 2017-03-18 23:53:00 Beginning InterMol conversion INFO 2017-03-18 23:53:00 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:53:00 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:53:00 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6250025.inpcrd INFO 2017-03-18 23:53:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6250025/mobley_6250025_converted.input INFO 2017-03-18 23:53:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6250025/mobley_6250025_converted.cms WARNING 2017-03-18 23:53:16 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:53:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6250025/mobley_6250025_converted.inp INFO 2017-03-18 23:53:16 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6250025/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6250025/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6250025/mobley_6250025_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6250025/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 7.79196858 7.79196858 0.00000000 0.00000000 0.00000000 0.00000000 4.33993768 4.33993768 coulomb total 4.33336880 4.33320203 -0.00016677 4.33320186 -0.00016694 4.33317259 -0.00019621 4.33993768 0.00656888 coulomb-14 -3.45849440 -3.45876655 -0.00027215 0.00000000 3.45849440 -3.45875931 -0.00026491 0.00000000 3.45849440 proper 5.24966480 5.24959581 -0.00006899 5.24959576 -0.00006904 5.24961781 -0.00004699 5.24962296 -0.00004184 vdw (SR) 0.00000000 -2.47189225 -2.47189225 0.00000000 0.00000000 0.00000000 0.00000000 3.54769728 3.54769728 vdw total 3.54761360 3.54761270 -0.00000090 3.54761276 -0.00000084 3.54764265 0.00002905 3.54769728 0.00008368 vdw-14 6.01952080 6.01950495 -0.00001585 0.00000000 -6.01952080 6.01952611 0.00000531 0.00000000 -6.01952080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.41453840 4.41435931 -0.00017909 4.41435932 -0.00017908 4.41477722 0.00023882 4.41437104 -0.00016736 bond 1.27946720 1.27946494 -0.00000226 1.27946494 -0.00000226 1.27949203 0.00002483 1.27946720 0.00000000 bonded 10.94367040 10.94342006 -0.00025034 10.94342003 -0.00025037 10.94388706 0.00021666 10.94346120 -0.00020920 dihedral 5.24966480 5.24959581 -0.00006899 5.24959576 -0.00006904 5.24961781 -0.00004699 5.24962296 -0.00004184 nonbonded 7.88098240 7.88081473 -0.00016767 7.88081462 -0.00016778 7.88081524 -0.00016716 7.88763496 0.00665256 potential 18.82465280 18.82423479 -0.00041801 18.82423482 -0.00041798 18.82461816 -0.00003464 18.83109616 0.00644336 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 18.82465280 Difference in potential energy from amber=>gromacs conversion: -0.00041801 Difference in potential energy from amber=>lammps conversion: -0.00041798 Difference in potential energy from amber=>desmond conversion: -0.00003464 Difference in potential energy from amber=>charmm conversion: 0.00644336 ======================================================================= INFO 2017-03-18 23:53:16 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6250025.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6250025.inpcrd') INFO 2017-03-18 23:53:16 Beginning InterMol conversion INFO 2017-03-18 23:53:16 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:53:16 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6257907.inpcrd INFO 2017-03-18 23:53:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6257907/mobley_6257907_converted.input INFO 2017-03-18 23:53:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6257907/mobley_6257907_converted.cms INFO 2017-03-18 23:53:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6257907/mobley_6257907_converted.rst7 WARNING 2017-03-18 23:53:32 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:53:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6257907/mobley_6257907_converted.inp INFO 2017-03-18 23:53:32 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6257907/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6257907/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6257907/mobley_6257907_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_6257907/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6257907/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 120.69093104 120.69093104 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -141.33359536 -141.33359536 coulomb total -141.31711040 -141.30446861 0.01264179 -141.30446635 0.01264405 -141.30493956 0.01217084 -141.31711040 0.00000000 -141.33359536 -0.01648496 coulomb-14 -261.97739440 -261.99539965 -0.01800525 0.00000000 261.97739440 -261.99539648 -0.01800208 -261.97739440 0.00000000 0.00000000 261.97739440 improper 0.00000000 0.11370353 0.11370353 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.11372112 0.11372112 proper 0.21840480 0.10450204 -0.11390276 0.21820411 -0.00020069 0.21820662 -0.00019818 0.21840480 0.00000000 0.10451632 -0.11388848 vdw (SR) 0.00000000 -1.80427634 -1.80427634 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 14.28672824 14.28672824 vdw total 14.28668640 14.28676287 0.00007647 14.28676297 0.00007657 14.28680381 0.00011741 14.28710480 0.00041840 14.28672824 0.00004184 vdw-14 16.09082720 16.09103921 0.00021201 0.00000000 -16.09082720 16.09107724 0.00025004 16.09124560 0.00041840 0.00000000 -16.09082720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.48234320 3.48243240 0.00008920 3.48243240 0.00008920 3.48251713 0.00017393 3.48234320 0.00000000 3.48251056 0.00016736 bond 5.51074640 5.51064997 -0.00009643 5.51065017 -0.00009623 5.51038407 -0.00036233 5.51074640 0.00000000 5.51066272 -0.00008368 bonded 9.21149440 9.21128794 -0.00020646 9.21128668 -0.00020772 9.21110781 -0.00038659 9.21149440 0.00000000 9.21141072 -0.00008368 dihedral 0.21840480 0.21820557 -0.00019923 0.21820411 -0.00020069 0.21820662 -0.00019818 0.21840480 0.00000000 0.21823744 -0.00016736 nonbonded -127.03042400 -127.01770574 0.01271826 -127.01770464 0.01271936 -127.01813575 0.01228825 -127.03000560 0.00041840 -127.04686712 -0.01644312 potential -117.81892960 -117.80641780 0.01251180 -117.80641944 0.01251016 -117.80707549 0.01185411 -117.81851120 0.00041840 -117.83549824 -0.01656864 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -117.81892960 Difference in potential energy from amber=>gromacs conversion: 0.01251180 Difference in potential energy from amber=>lammps conversion: 0.01251016 Difference in potential energy from amber=>desmond conversion: 0.01185411 Difference in potential energy from amber=>amber conversion: 0.00041840 Difference in potential energy from amber=>charmm conversion: -0.01656864 ======================================================================= INFO 2017-03-18 23:53:32 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6257907.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6257907.inpcrd') INFO 2017-03-18 23:53:32 Beginning InterMol conversion INFO 2017-03-18 23:53:32 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:53:32 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:53:32 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6266306.inpcrd INFO 2017-03-18 23:53:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6266306/mobley_6266306_converted.input INFO 2017-03-18 23:53:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6266306/mobley_6266306_converted.cms WARNING 2017-03-18 23:53:48 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:53:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6266306/mobley_6266306_converted.inp INFO 2017-03-18 23:53:48 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6266306/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6266306/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6266306/mobley_6266306_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6266306/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 18.37396282 18.37396282 0.00000000 0.00000000 0.00000000 0.00000000 17.75572448 17.75572448 coulomb total 17.75647760 17.75723816 0.00076056 17.75723783 0.00076023 17.75717278 0.00069518 17.75572448 -0.00075312 coulomb-14 -0.61672160 -0.61672466 -0.00000306 0.00000000 0.61672160 -0.61676795 -0.00004635 0.00000000 0.61672160 proper 42.37220480 42.37224547 0.00004067 42.37224664 0.00004184 42.37217760 -0.00002720 42.37722560 0.00502080 vdw (SR) 0.00000000 -0.13111320 -0.13111320 0.00000000 0.00000000 0.00000000 0.00000000 0.79207304 0.79207304 vdw total 0.79203120 0.79204549 0.00001429 0.79204551 0.00001431 0.79204981 0.00001861 0.79207304 0.00004184 vdw-14 0.92299040 0.92315870 0.00016830 0.00000000 -0.92299040 0.92316266 0.00017226 0.00000000 -0.92299040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.72587600 2.72582911 -0.00004689 2.72582910 -0.00004690 2.72597052 0.00009452 2.72583416 -0.00004184 bond 2.06480400 2.06495151 0.00014751 2.06495153 0.00014753 2.06475312 -0.00005088 2.06497136 0.00016736 bonded 47.16288480 47.16302609 0.00014129 47.16302727 0.00014247 47.16290125 0.00001645 47.16803112 0.00514632 dihedral 42.37220480 42.37224547 0.00004067 42.37224664 0.00004184 42.37217760 -0.00002720 42.37722560 0.00502080 nonbonded 18.54850880 18.54928366 0.00077486 18.54928326 0.00077446 18.54922259 0.00071379 18.54779752 -0.00071128 potential 65.71139360 65.71230975 0.00091615 65.71230990 0.00091630 65.71210781 0.00071421 65.71578680 0.00439320 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 65.71139360 Difference in potential energy from amber=>gromacs conversion: 0.00091615 Difference in potential energy from amber=>lammps conversion: 0.00091630 Difference in potential energy from amber=>desmond conversion: 0.00071421 Difference in potential energy from amber=>charmm conversion: 0.00439320 ======================================================================= INFO 2017-03-18 23:53:48 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6266306.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6266306.inpcrd') INFO 2017-03-18 23:53:48 Beginning InterMol conversion INFO 2017-03-18 23:53:48 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:53:48 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:53:48 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_627267.inpcrd INFO 2017-03-18 23:53:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_627267/mobley_627267_converted.input INFO 2017-03-18 23:53:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_627267/mobley_627267_converted.cms WARNING 2017-03-18 23:54:04 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:54:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_627267/mobley_627267_converted.inp INFO 2017-03-18 23:54:04 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_627267/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_627267/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_627267/mobley_627267_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_627267/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 5.50199413 5.50199413 0.00000000 0.00000000 0.00000000 0.00000000 1.66874656 1.66874656 coulomb total 1.66565040 1.67020134 0.00455094 1.67020134 0.00455094 1.67015764 0.00450724 1.66874656 0.00309616 coulomb-14 -3.83212560 -3.83179279 0.00033281 0.00000000 3.83212560 -3.83180860 0.00031700 0.00000000 3.83212560 proper 3.53673520 3.53693856 0.00020336 3.53693854 0.00020334 3.53693666 0.00020146 3.53694440 0.00020920 vdw (SR) 0.00000000 1.54166061 1.54166061 0.00000000 0.00000000 0.00000000 0.00000000 6.55310632 6.55310632 vdw total 6.55339920 6.55303602 -0.00036318 6.55303603 -0.00036317 6.55308867 -0.00031053 6.55310632 -0.00029288 vdw-14 5.01159520 5.01137542 -0.00021978 0.00000000 -5.01159520 5.01138077 -0.00021443 0.00000000 -5.01159520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.37104880 3.37124255 0.00019375 3.37124256 0.00019376 3.37159908 0.00055028 3.37129984 0.00025104 bond 0.54308320 0.54296712 -0.00011608 0.54296714 -0.00011606 0.54336800 0.00028480 0.54295768 -0.00012552 bonded 7.45086720 7.45114824 0.00028104 7.45114824 0.00028104 7.45190374 0.00103654 7.45120192 0.00033472 dihedral 3.53673520 3.53693856 0.00020336 3.53693854 0.00020334 3.53693666 0.00020146 3.53694440 0.00020920 nonbonded 8.21904960 8.22323736 0.00418776 8.22323737 0.00418777 8.22324631 0.00419671 8.22185288 0.00280328 potential 15.66991680 15.67438560 0.00446880 15.67438573 0.00446893 15.67511082 0.00519402 15.67309664 0.00317984 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 15.66991680 Difference in potential energy from amber=>gromacs conversion: 0.00446880 Difference in potential energy from amber=>lammps conversion: 0.00446893 Difference in potential energy from amber=>desmond conversion: 0.00519402 Difference in potential energy from amber=>charmm conversion: 0.00317984 ======================================================================= INFO 2017-03-18 23:54:04 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_627267.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_627267.inpcrd') INFO 2017-03-18 23:54:04 Beginning InterMol conversion INFO 2017-03-18 23:54:04 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:54:04 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:54:04 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_628086.inpcrd INFO 2017-03-18 23:54:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_628086/mobley_628086_converted.input INFO 2017-03-18 23:54:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_628086/mobley_628086_converted.cms WARNING 2017-03-18 23:54:20 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:54:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_628086/mobley_628086_converted.inp INFO 2017-03-18 23:54:20 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_628086/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_628086/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_628086/mobley_628086_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_628086/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -120.73673484 -120.73673484 0.00000000 0.00000000 0.00000000 0.00000000 145.12689344 145.12689344 coulomb total 145.12245840 145.12860917 0.00615077 145.12860888 0.00615048 145.12879298 0.00633458 145.12689344 0.00443504 coulomb-14 265.85261520 265.86534401 0.01272881 0.00000000 -265.85261520 265.86556970 0.01295450 0.00000000 -265.85261520 proper 7.08225680 7.08244414 0.00018734 7.08244424 0.00018744 7.08246278 0.00020598 7.08246600 0.00020920 vdw (SR) 0.00000000 0.97741391 0.97741391 0.00000000 0.00000000 0.00000000 0.00000000 8.30549104 8.30549104 vdw total 8.30524000 8.30550690 0.00026690 8.30550694 0.00026694 8.30564874 0.00040874 8.30549104 0.00025104 vdw-14 7.32785760 7.32809299 0.00023539 0.00000000 -7.32785760 7.32823575 0.00037815 0.00000000 -7.32785760 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.91083280 1.91076088 -0.00007192 1.91076088 -0.00007192 1.91059143 -0.00024137 1.91079096 -0.00004184 bond 1.04558160 1.04542134 -0.00016026 1.04542135 -0.00016025 1.04550200 -0.00007960 1.04541424 -0.00016736 bonded 10.03867120 10.03862636 -0.00004484 10.03862647 -0.00004473 10.03855621 -0.00011499 10.03867120 0.00000000 dihedral 7.08225680 7.08244414 0.00018734 7.08244424 0.00018744 7.08246278 0.00020598 7.08246600 0.00020920 nonbonded 153.42769840 153.43411608 0.00641768 153.43411247 0.00641407 153.43444172 0.00674332 153.43238448 0.00468608 potential 163.46636960 163.47274244 0.00637284 163.47274183 0.00637223 163.47296358 0.00659398 163.47105568 0.00468608 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 163.46636960 Difference in potential energy from amber=>gromacs conversion: 0.00637284 Difference in potential energy from amber=>lammps conversion: 0.00637223 Difference in potential energy from amber=>desmond conversion: 0.00659398 Difference in potential energy from amber=>charmm conversion: 0.00468608 ======================================================================= INFO 2017-03-18 23:54:20 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_628086.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_628086.inpcrd') INFO 2017-03-18 23:54:20 Beginning InterMol conversion INFO 2017-03-18 23:54:20 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:54:20 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_628951.inpcrd INFO 2017-03-18 23:54:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_628951/mobley_628951_converted.input INFO 2017-03-18 23:54:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_628951/mobley_628951_converted.cms INFO 2017-03-18 23:54:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_628951/mobley_628951_converted.rst7 WARNING 2017-03-18 23:54:36 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:54:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_628951/mobley_628951_converted.inp INFO 2017-03-18 23:54:36 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_628951/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_628951/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_628951/mobley_628951_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_628951/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_628951/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 3.19927512 3.19927512 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 11.51043504 11.51043504 coulomb total 11.48717200 11.49880721 0.01163521 11.49880729 0.01163529 11.49878344 0.01161144 11.48717200 0.00000000 11.51043504 0.02326304 coulomb-14 8.29143280 8.29953209 0.00809929 0.00000000 -8.29143280 8.29951545 0.00808265 8.29143280 0.00000000 0.00000000 -8.29143280 improper 0.00000000 0.00016851 0.00016851 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00016736 0.00016736 proper 33.47409200 33.47395581 -0.00013619 33.47412422 0.00003222 33.47412129 0.00002929 33.47409200 0.00000000 33.47396648 -0.00012552 vdw (SR) 0.00000000 -19.12931010 -19.12931010 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 22.03993128 22.03993128 vdw total 22.04005680 22.03996629 -0.00009051 22.03996643 -0.00009037 22.04014801 0.00009121 22.04005680 0.00000000 22.03993128 -0.00012552 vdw-14 41.16930480 41.16927639 -0.00002841 0.00000000 -41.16930480 41.16947078 0.00016598 41.16930480 0.00000000 0.00000000 -41.16930480 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.69949280 3.69938727 -0.00010553 3.69938728 -0.00010552 3.69953677 0.00004397 3.69949280 0.00000000 3.69940912 -0.00008368 bond 2.85641680 2.85639996 -0.00001684 2.85639994 -0.00001686 2.85569726 -0.00071954 2.85641680 0.00000000 2.85641680 0.00000000 bonded 40.03000160 40.02991155 -0.00009005 40.02991143 -0.00009017 40.02935532 -0.00064628 40.03000160 0.00000000 40.02995976 -0.00004184 dihedral 33.47409200 33.47412432 0.00003232 33.47412422 0.00003222 33.47412129 0.00002929 33.47409200 0.00000000 33.47413384 0.00004184 nonbonded 33.52722880 33.53877350 0.01154470 33.53877329 0.01154449 33.53893145 0.01170265 33.52722880 0.00000000 33.55036632 0.02313752 potential 73.55723040 73.56868505 0.01145465 73.56868619 0.01145579 73.56806738 0.01083698 73.55723040 0.00000000 73.58032608 0.02309568 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 73.55723040 Difference in potential energy from amber=>gromacs conversion: 0.01145465 Difference in potential energy from amber=>lammps conversion: 0.01145579 Difference in potential energy from amber=>desmond conversion: 0.01083698 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.02309568 ======================================================================= INFO 2017-03-18 23:54:36 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_628951.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_628951.inpcrd') INFO 2017-03-18 23:54:36 Beginning InterMol conversion INFO 2017-03-18 23:54:36 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:54:36 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:54:36 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6303022.inpcrd INFO 2017-03-18 23:54:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6303022/mobley_6303022_converted.input INFO 2017-03-18 23:54:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6303022/mobley_6303022_converted.cms WARNING 2017-03-18 23:54:52 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:54:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6303022/mobley_6303022_converted.inp INFO 2017-03-18 23:54:52 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6303022/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6303022/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6303022/mobley_6303022_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6303022/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 58.48156942 58.48156942 0.00000000 0.00000000 0.00000000 0.00000000 -112.38408096 -112.38408096 coulomb total -112.37554560 -112.37897987 -0.00343427 -112.37898066 -0.00343506 -112.37910953 -0.00356393 -112.38408096 -0.00853536 coulomb-14 -170.85489520 -170.86054929 -0.00565409 0.00000000 170.85489520 -170.86066284 -0.00576764 0.00000000 170.85489520 improper 0.00000000 0.00013684 0.00013684 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.02092000 0.02063932 -0.00028068 0.02077625 -0.00014375 0.02078001 -0.00013999 0.02062712 -0.00029288 vdw (SR) 0.00000000 -3.19772688 -3.19772688 0.00000000 0.00000000 0.00000000 0.00000000 19.52969864 19.52969864 vdw total 19.52965680 19.52971701 0.00006021 19.52971705 0.00006025 19.53003639 0.00037959 19.52969864 0.00004184 vdw-14 22.72748800 22.72744389 -0.00004411 0.00000000 -22.72748800 22.72778055 0.00029255 0.00000000 -22.72748800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.03677120 2.03669951 -0.00007169 2.03669953 -0.00007167 2.03669865 -0.00007255 2.03668752 -0.00008368 bond 1.57611280 1.57629211 0.00017931 1.57629213 0.00017933 1.57611322 0.00000042 1.57628016 0.00016736 bonded 3.63380400 3.63376778 -0.00003622 3.63376790 -0.00003610 3.63359188 -0.00021212 3.63372032 -0.00008368 dihedral 0.02092000 0.02077616 -0.00014384 0.02077625 -0.00014375 0.02078001 -0.00013999 0.02075264 -0.00016736 nonbonded -92.84588880 -92.84926286 -0.00337406 -92.84926110 -0.00337230 -92.84907314 -0.00318434 -92.85438232 -0.00849352 potential -89.21208480 -89.21549508 -0.00341028 -89.21549476 -0.00340996 -89.21552823 -0.00344343 -89.22062016 -0.00853536 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -89.21208480 Difference in potential energy from amber=>gromacs conversion: -0.00341028 Difference in potential energy from amber=>lammps conversion: -0.00340996 Difference in potential energy from amber=>desmond conversion: -0.00344343 Difference in potential energy from amber=>charmm conversion: -0.00853536 ======================================================================= INFO 2017-03-18 23:54:52 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6303022.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6303022.inpcrd') INFO 2017-03-18 23:54:52 Beginning InterMol conversion INFO 2017-03-18 23:54:52 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:54:53 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:54:53 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6309289.inpcrd INFO 2017-03-18 23:54:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6309289/mobley_6309289_converted.input INFO 2017-03-18 23:54:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6309289/mobley_6309289_converted.cms WARNING 2017-03-18 23:55:08 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:55:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6309289/mobley_6309289_converted.inp INFO 2017-03-18 23:55:08 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6309289/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6309289/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6309289/mobley_6309289_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6309289/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 16.72989032 16.72989032 0.00000000 0.00000000 0.00000000 0.00000000 -7.58893920 -7.58893920 coulomb total -7.60902240 -7.57911543 0.02990697 -7.57911517 0.02990723 -7.57914529 0.02987711 -7.58893920 0.02008320 coulomb-14 -24.31740800 -24.30900575 0.00840225 0.00000000 24.31740800 -24.30906343 0.00834457 0.00000000 24.31740800 proper 10.61187920 10.61192245 0.00004325 10.61192230 0.00004310 10.61192250 0.00004330 10.61204656 0.00016736 vdw (SR) 0.00000000 -2.00834006 -2.00834006 0.00000000 0.00000000 0.00000000 0.00000000 10.93839856 10.93839856 vdw total 10.93823120 10.93840748 0.00017628 10.93840776 0.00017656 10.93815156 -0.00007964 10.93839856 0.00016736 vdw-14 12.94655120 12.94674753 0.00019633 0.00000000 -12.94655120 12.94649283 -0.00005837 0.00000000 -12.94655120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.89577040 1.89564820 -0.00012220 1.89564819 -0.00012221 1.89563144 -0.00013896 1.89556120 -0.00020920 bond 0.74307840 0.74315184 0.00007344 0.74315183 0.00007343 0.74279029 -0.00028811 0.74316208 0.00008368 bonded 13.25072800 13.25072249 -0.00000551 13.25072231 -0.00000569 13.25034424 -0.00038376 13.25076984 0.00004184 dihedral 10.61187920 10.61192245 0.00004325 10.61192230 0.00004310 10.61192250 0.00004330 10.61204656 0.00016736 nonbonded 3.32920880 3.35929204 0.03008324 3.35929251 0.03008371 3.35900626 0.02979746 3.34945936 0.02025056 potential 16.57993680 16.61001453 0.03007773 16.61001516 0.03007836 16.60930722 0.02937042 16.60027104 0.02033424 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 16.57993680 Difference in potential energy from amber=>gromacs conversion: 0.03007773 Difference in potential energy from amber=>lammps conversion: 0.03007836 Difference in potential energy from amber=>desmond conversion: 0.02937042 Difference in potential energy from amber=>charmm conversion: 0.02033424 ======================================================================= INFO 2017-03-18 23:55:08 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6309289.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6309289.inpcrd') INFO 2017-03-18 23:55:08 Beginning InterMol conversion INFO 2017-03-18 23:55:08 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:55:09 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:55:09 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_632905.inpcrd INFO 2017-03-18 23:55:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_632905/mobley_632905_converted.input INFO 2017-03-18 23:55:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_632905/mobley_632905_converted.cms WARNING 2017-03-18 23:55:24 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:55:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_632905/mobley_632905_converted.inp INFO 2017-03-18 23:55:24 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_632905/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_632905/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_632905/mobley_632905_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_632905/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 1.21029708 1.21029708 0.00000000 0.00000000 0.00000000 0.00000000 -80.75492376 -80.75492376 coulomb total -80.75998640 -80.76603566 -0.00604926 -80.76603646 -0.00605006 -80.76583924 -0.00585284 -80.75492376 0.00506264 coulomb-14 -81.97794880 -81.97633274 0.00161606 0.00000000 81.97794880 -81.97620449 0.00174431 0.00000000 81.97794880 improper 0.00000000 0.00118876 0.00118876 0.00000000 0.00000000 0.00000000 0.00000000 0.00117152 0.00117152 proper 19.42338320 19.42205704 -0.00132616 19.42326521 -0.00011799 19.42327425 -0.00010895 19.42208616 -0.00129704 vdw (SR) 0.00000000 14.58551988 14.58551988 0.00000000 0.00000000 0.00000000 0.00000000 45.77894312 45.77894312 vdw total 45.77923600 45.77880430 -0.00043170 45.77880505 -0.00043095 45.77812791 -0.00110809 45.77894312 -0.00029288 vdw-14 31.19339360 31.19328442 -0.00010918 0.00000000 -31.19339360 31.19295403 -0.00043957 0.00000000 -31.19339360 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 7.12409680 7.12426995 0.00017315 7.12427002 0.00017322 7.12376426 -0.00033254 7.12426416 0.00016736 bond 3.79488800 3.79490420 0.00001620 3.79490419 0.00001619 3.79464487 -0.00024313 3.79488800 0.00000000 bonded 30.34236800 30.34241995 0.00005195 30.34243942 0.00007142 30.34168338 -0.00068462 30.34240984 0.00004184 dihedral 19.42338320 19.42324580 -0.00013740 19.42326521 -0.00011799 19.42327425 -0.00010895 19.42325768 -0.00012552 nonbonded -34.98075040 -34.98723136 -0.00648096 -34.98723016 -0.00647976 -34.98771133 -0.00696093 -34.97598064 0.00476976 potential -4.63838240 -4.64481141 -0.00642901 -4.64479061 -0.00640821 -4.64612096 -0.00773856 -4.63352896 0.00485344 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -4.63838240 Difference in potential energy from amber=>gromacs conversion: -0.00642901 Difference in potential energy from amber=>lammps conversion: -0.00640821 Difference in potential energy from amber=>desmond conversion: -0.00773856 Difference in potential energy from amber=>charmm conversion: 0.00485344 ======================================================================= INFO 2017-03-18 23:55:24 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_632905.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_632905.inpcrd') INFO 2017-03-18 23:55:25 Beginning InterMol conversion INFO 2017-03-18 23:55:25 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:55:25 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:55:25 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6334915.inpcrd INFO 2017-03-18 23:55:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6334915/mobley_6334915_converted.input INFO 2017-03-18 23:55:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6334915/mobley_6334915_converted.cms WARNING 2017-03-18 23:55:40 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:55:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6334915/mobley_6334915_converted.inp INFO 2017-03-18 23:55:40 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6334915/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6334915/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6334915/mobley_6334915_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6334915/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -370.48909809 -370.48909809 0.00000000 0.00000000 0.00000000 0.00000000 28.38810528 28.38810528 coulomb total 28.51144960 28.51480912 0.00335952 28.51480893 0.00335933 28.51432443 0.00287483 28.38810528 -0.12334432 coulomb-14 399.00339440 399.00390721 0.00051281 0.00000000 -399.00339440 399.00380611 0.00041171 0.00000000 -399.00339440 proper 29.28256080 29.28251754 -0.00004326 29.28251770 -0.00004310 29.28246570 -0.00009510 29.28247712 -0.00008368 vdw (SR) 0.00000000 -6.16262452 -6.16262452 0.00000000 0.00000000 0.00000000 0.00000000 -0.87976968 -0.87976968 vdw total -0.87989520 -0.88001382 -0.00011862 -0.88001386 -0.00011866 -0.88009666 -0.00020146 -0.87976968 0.00012552 vdw-14 5.28271840 5.28261071 -0.00010769 0.00000000 -5.28271840 5.28251928 -0.00019912 0.00000000 -5.28271840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 14.40132800 14.40136893 0.00004093 14.40136900 0.00004100 14.40114114 -0.00018686 14.40136984 0.00004184 bond 3.50577360 3.50561836 -0.00015524 3.50561837 -0.00015523 3.50495492 -0.00081868 3.50560624 -0.00016736 bonded 47.18966240 47.18950483 -0.00015757 47.18950508 -0.00015732 47.18856176 -0.00110064 47.18945320 -0.00020920 dihedral 29.28256080 29.28251754 -0.00004326 29.28251770 -0.00004310 29.28246570 -0.00009510 29.28247712 -0.00008368 nonbonded 27.63155440 27.63479530 0.00324090 27.63479491 0.00324051 27.63422777 0.00267337 27.50833560 -0.12321880 potential 74.82121680 74.82430013 0.00308333 74.82430041 0.00308361 74.82262806 0.00141126 74.69783064 -0.12338616 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 74.82121680 Difference in potential energy from amber=>gromacs conversion: 0.00308333 Difference in potential energy from amber=>lammps conversion: 0.00308361 Difference in potential energy from amber=>desmond conversion: 0.00141126 Difference in potential energy from amber=>charmm conversion: -0.12338616 ======================================================================= INFO 2017-03-18 23:55:40 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6334915.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6334915.inpcrd') INFO 2017-03-18 23:55:41 Beginning InterMol conversion INFO 2017-03-18 23:55:41 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:55:41 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:55:41 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6338073.inpcrd INFO 2017-03-18 23:55:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6338073/mobley_6338073_converted.input INFO 2017-03-18 23:55:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6338073/mobley_6338073_converted.cms WARNING 2017-03-18 23:55:57 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:55:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6338073/mobley_6338073_converted.inp INFO 2017-03-18 23:55:57 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6338073/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6338073/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6338073/mobley_6338073_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6338073/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 1086.88623958 1086.88623958 0.00000000 0.00000000 0.00000000 0.00000000 -1843.43676064 -1843.43676064 coulomb total -1843.33400160 -1843.39672852 -0.06272692 -1843.39671976 -0.06271816 -1843.39563192 -0.06163032 -1843.43676064 -0.10275904 coulomb-14 -2930.18281200 -2930.28296810 -0.10015610 0.00000000 2930.18281200 -2930.28213179 -0.09931979 0.00000000 2930.18281200 improper 0.00000000 0.00004556 0.00004556 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 5.03460720 5.03444583 -0.00016137 5.03448754 -0.00011966 5.03451180 -0.00009540 5.03443984 -0.00016736 vdw (SR) 0.00000000 41.73468319 41.73468319 0.00000000 0.00000000 0.00000000 0.00000000 91.50207168 91.50207168 vdw total 91.50240640 91.50211936 -0.00028704 91.50212189 -0.00028451 91.50112978 -0.00127662 91.50207168 -0.00033472 vdw-14 49.76742480 49.76743616 0.00001136 0.00000000 -49.76742480 49.76710723 -0.00031757 0.00000000 -49.76742480 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 13.36327760 13.36315099 -0.00012661 13.36315082 -0.00012678 13.36323141 -0.00004619 13.36315208 -0.00012552 bond 8.77426640 8.77422269 -0.00004371 8.77422289 -0.00004351 8.77408779 -0.00017861 8.77422456 -0.00004184 bonded 27.17215120 27.17186508 -0.00028612 27.17186125 -0.00028995 27.17183100 -0.00032020 27.17185832 -0.00029288 dihedral 5.03460720 5.03449139 -0.00011581 5.03448754 -0.00011966 5.03451180 -0.00009540 5.03448168 -0.00012552 nonbonded -1751.83159520 -1751.89460916 -0.06301396 -1751.89460624 -0.06301104 -1751.89450214 -0.06290694 -1751.93468896 -0.10309376 potential -1724.65944400 -1724.72274408 -0.06330008 -1724.72270608 -0.06326208 -1724.72294457 -0.06350057 -1724.76283064 -0.10338664 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -1724.65944400 Difference in potential energy from amber=>gromacs conversion: -0.06330008 Difference in potential energy from amber=>lammps conversion: -0.06326208 Difference in potential energy from amber=>desmond conversion: -0.06350057 Difference in potential energy from amber=>charmm conversion: -0.10338664 ======================================================================= INFO 2017-03-18 23:55:57 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6338073.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6338073.inpcrd') INFO 2017-03-18 23:55:57 Beginning InterMol conversion INFO 2017-03-18 23:55:57 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:55:58 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:55:58 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6353617.inpcrd INFO 2017-03-18 23:55:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6353617/mobley_6353617_converted.input INFO 2017-03-18 23:55:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6353617/mobley_6353617_converted.cms WARNING 2017-03-18 23:56:13 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:56:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6353617/mobley_6353617_converted.inp INFO 2017-03-18 23:56:13 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6353617/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6353617/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6353617/mobley_6353617_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6353617/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 142.92515460 142.92515460 0.00000000 0.00000000 0.00000000 0.00000000 -209.33836488 -209.33836488 coulomb total -209.35062400 -209.35756337 -0.00693937 -209.35756107 -0.00693707 -209.35757948 -0.00695548 -209.33836488 0.01225912 coulomb-14 -352.27062480 -352.28271796 -0.01209316 0.00000000 352.27062480 -352.28272828 -0.01210348 0.00000000 352.27062480 improper 0.00000000 0.00195134 0.00195134 0.00000000 0.00000000 0.00000000 0.00000000 0.00196648 0.00196648 proper 19.42547520 19.42361530 -0.00185990 19.42558608 0.00011088 19.42560917 0.00013397 19.42363424 -0.00184096 vdw (SR) 0.00000000 -0.49047757 -0.49047757 0.00000000 0.00000000 0.00000000 0.00000000 23.82980464 23.82980464 vdw total 23.82997200 23.82982482 -0.00014718 23.82982472 -0.00014728 23.83020838 0.00023638 23.82980464 -0.00016736 vdw-14 24.32033680 24.32030240 -0.00003440 0.00000000 -24.32033680 24.32066566 0.00032886 0.00000000 -24.32033680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 8.28432000 8.28432841 0.00000841 8.28432837 0.00000837 8.28419348 -0.00012652 8.28432000 0.00000000 bond 3.43255360 3.43255779 0.00000419 3.43255778 0.00000418 3.43199276 -0.00056084 3.43255360 0.00000000 bonded 31.14234880 31.14245284 0.00010404 31.14247223 0.00012343 31.14179540 -0.00055340 31.14247432 0.00012552 dihedral 19.42547520 19.42556664 0.00009144 19.42558608 0.00011088 19.42560917 0.00013397 19.42560072 0.00012552 nonbonded -185.52065200 -185.52773854 -0.00708654 -185.52773551 -0.00708351 -185.52737111 -0.00671911 -185.50856024 0.01209176 potential -154.37830320 -154.38528571 -0.00698251 -154.38526538 -0.00696218 -154.38563817 -0.00733497 -154.36608592 0.01221728 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -154.37830320 Difference in potential energy from amber=>gromacs conversion: -0.00698251 Difference in potential energy from amber=>lammps conversion: -0.00696218 Difference in potential energy from amber=>desmond conversion: -0.00733497 Difference in potential energy from amber=>charmm conversion: 0.01221728 ======================================================================= INFO 2017-03-18 23:56:13 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6353617.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6353617.inpcrd') INFO 2017-03-18 23:56:14 Beginning InterMol conversion INFO 2017-03-18 23:56:14 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:56:14 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:56:14 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6358463.inpcrd INFO 2017-03-18 23:56:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6358463/mobley_6358463_converted.input INFO 2017-03-18 23:56:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6358463/mobley_6358463_converted.cms WARNING 2017-03-18 23:56:29 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:56:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6358463/mobley_6358463_converted.inp INFO 2017-03-18 23:56:29 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6358463/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6358463/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6358463/mobley_6358463_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6358463/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -208.27772074 -208.27772074 0.00000000 0.00000000 0.00000000 0.00000000 94.85772336 94.85772336 coulomb total 94.76843680 94.77573002 0.00729322 94.77572951 0.00729271 94.77543119 0.00699439 94.85772336 0.08928656 coulomb-14 303.02912880 303.05345076 0.02432196 0.00000000 -303.02912880 303.05316295 0.02403415 0.00000000 -303.02912880 improper 0.00000000 0.00004299 0.00004299 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00038917 -0.00002923 0.00043213 0.00001373 0.00043343 0.00001503 0.00037656 -0.00004184 vdw (SR) 0.00000000 166.41103185 166.41103185 0.00000000 0.00000000 0.00000000 0.00000000 193.98618104 193.98618104 vdw total 193.98613920 193.98911556 0.00297636 193.98911821 0.00297901 193.98667442 0.00053522 193.98618104 0.00004184 vdw-14 27.57799920 27.57808371 0.00008451 0.00000000 -27.57799920 27.57802313 0.00002393 0.00000000 -27.57799920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.22042480 3.22055760 0.00013280 3.22055760 0.00013280 3.22033698 -0.00008782 3.22050848 0.00008368 bond 5.77099120 5.77104936 0.00005816 5.77104936 0.00005816 5.76988160 -0.00110960 5.77103304 0.00004184 bonded 8.99183440 8.99203912 0.00020472 8.99203909 0.00020469 8.99065201 -0.00118239 8.99195992 0.00012552 dihedral 0.00041840 0.00043216 0.00001376 0.00043213 0.00001373 0.00043343 0.00001503 0.00041840 0.00000000 nonbonded 288.75457600 288.76484558 0.01026958 288.76484354 0.01026754 288.76210561 0.00752961 288.84390440 0.08932840 potential 297.74641040 297.75688471 0.01047431 297.75688295 0.01047255 297.75270355 0.00629315 297.83590616 0.08949576 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 297.74641040 Difference in potential energy from amber=>gromacs conversion: 0.01047431 Difference in potential energy from amber=>lammps conversion: 0.01047255 Difference in potential energy from amber=>desmond conversion: 0.00629315 Difference in potential energy from amber=>charmm conversion: 0.08949576 ======================================================================= INFO 2017-03-18 23:56:29 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6358463.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6358463.inpcrd') INFO 2017-03-18 23:56:30 Beginning InterMol conversion INFO 2017-03-18 23:56:30 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:56:30 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6359156.inpcrd INFO 2017-03-18 23:56:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6359156/mobley_6359156_converted.input INFO 2017-03-18 23:56:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6359156/mobley_6359156_converted.cms INFO 2017-03-18 23:56:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6359156/mobley_6359156_converted.rst7 WARNING 2017-03-18 23:56:45 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:56:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6359156/mobley_6359156_converted.inp INFO 2017-03-18 23:56:45 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6359156/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6359156/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6359156/mobley_6359156_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_6359156/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6359156/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -11.93643002 -11.93643002 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -6.02742856 -6.02742856 coulomb total -6.02496000 -6.03114040 -0.00618040 -6.03114019 -0.00618019 -6.03111684 -0.00615684 -6.02496000 0.00000000 -6.02742856 -0.00246856 coulomb-14 5.90613440 5.90528962 -0.00084478 0.00000000 -5.90613440 5.90527425 -0.00086015 5.90613440 0.00000000 0.00000000 -5.90613440 improper 0.00000000 0.00020747 0.00020747 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00020920 0.00020920 proper 33.47367360 33.47363931 -0.00003429 33.47384682 0.00017322 33.47384473 0.00017113 33.47367360 0.00000000 33.47363176 -0.00004184 vdw (SR) 0.00000000 -9.80544920 -9.80544920 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 25.15609080 25.15609080 vdw total 25.15588160 25.15613735 0.00025575 25.15613724 0.00025564 25.15628623 0.00040463 25.15588160 0.00000000 25.15609080 0.00020920 vdw-14 34.96150400 34.96158655 0.00008255 0.00000000 -34.96150400 34.96172935 0.00022535 34.96150400 0.00000000 0.00000000 -34.96150400 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.47483600 2.47478198 -0.00005402 2.47478198 -0.00005402 2.47453410 -0.00030190 2.47483600 0.00000000 2.47479416 -0.00004184 bond 3.84802480 3.84791572 -0.00010908 3.84791572 -0.00010908 3.84741204 -0.00061276 3.84802480 0.00000000 3.84789928 -0.00012552 bonded 39.79653440 39.79654449 0.00001009 39.79654453 0.00001013 39.79579086 -0.00074354 39.79653440 0.00000000 39.79653440 -0.00000000 dihedral 33.47367360 33.47384678 0.00017318 33.47384682 0.00017322 33.47384473 0.00017113 33.47367360 0.00000000 33.47384096 0.00016736 nonbonded 19.13092160 19.12499695 -0.00592465 19.12499706 -0.00592454 19.12516939 -0.00575221 19.13092160 0.00000000 19.12866224 -0.00225936 potential 58.92745600 58.92154144 -0.00591456 58.92153982 -0.00591618 58.92080930 -0.00664670 58.92745600 0.00000000 58.92523848 -0.00221752 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 58.92745600 Difference in potential energy from amber=>gromacs conversion: -0.00591456 Difference in potential energy from amber=>lammps conversion: -0.00591618 Difference in potential energy from amber=>desmond conversion: -0.00664670 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.00221752 ======================================================================= INFO 2017-03-18 23:56:45 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6359156.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6359156.inpcrd') INFO 2017-03-18 23:56:46 Beginning InterMol conversion INFO 2017-03-18 23:56:46 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:56:46 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:56:46 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_63712.inpcrd INFO 2017-03-18 23:56:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_63712/mobley_63712_converted.input INFO 2017-03-18 23:56:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_63712/mobley_63712_converted.cms WARNING 2017-03-18 23:57:01 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:57:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_63712/mobley_63712_converted.inp INFO 2017-03-18 23:57:02 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_63712/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_63712/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_63712/mobley_63712_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_63712/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 12.57623462 12.57623462 0.00000000 0.00000000 0.00000000 0.00000000 6.56105592 6.56105592 coulomb total 6.56971680 6.56992909 0.00021229 6.56992893 0.00021213 6.56996859 0.00025179 6.56105592 -0.00866088 coulomb-14 -6.00613200 -6.00630554 -0.00017354 0.00000000 6.00613200 -6.00625200 -0.00012000 0.00000000 6.00613200 proper 10.60309280 10.60307175 -0.00002105 10.60307188 -0.00002092 10.60311359 0.00002079 10.60317648 0.00008368 vdw (SR) 0.00000000 -3.51761441 -3.51761441 0.00000000 0.00000000 0.00000000 0.00000000 12.86069552 12.86069552 vdw total 12.86077920 12.86063146 -0.00014774 12.86063192 -0.00014728 12.86074770 -0.00003150 12.86069552 -0.00008368 vdw-14 16.37826800 16.37824587 -0.00002213 0.00000000 -16.37826800 16.37837005 0.00010205 0.00000000 -16.37826800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.82840800 1.82852865 0.00012065 1.82852862 0.00012062 1.82860011 0.00019211 1.82844984 0.00004184 bond 0.73303680 0.73284714 -0.00018966 0.73284714 -0.00018966 0.73314088 0.00010408 0.73282760 -0.00020920 bonded 13.16453760 13.16444754 -0.00009006 13.16444764 -0.00008996 13.16485458 0.00031698 13.16445392 -0.00008368 dihedral 10.60309280 10.60307175 -0.00002105 10.60307188 -0.00002092 10.60311359 0.00002079 10.60317648 0.00008368 nonbonded 19.43049600 19.43056055 0.00006455 19.43056085 0.00006485 19.43071629 0.00022029 19.42175144 -0.00874456 potential 32.59503360 32.59500809 -0.00002551 32.59500850 -0.00002510 32.59551911 0.00048551 32.58620536 -0.00882824 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 32.59503360 Difference in potential energy from amber=>gromacs conversion: -0.00002551 Difference in potential energy from amber=>lammps conversion: -0.00002510 Difference in potential energy from amber=>desmond conversion: 0.00048551 Difference in potential energy from amber=>charmm conversion: -0.00882824 ======================================================================= INFO 2017-03-18 23:57:02 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_63712.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_63712.inpcrd') INFO 2017-03-18 23:57:02 Beginning InterMol conversion INFO 2017-03-18 23:57:02 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:57:02 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_637522.inpcrd INFO 2017-03-18 23:57:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_637522/mobley_637522_converted.input INFO 2017-03-18 23:57:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_637522/mobley_637522_converted.cms INFO 2017-03-18 23:57:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_637522/mobley_637522_converted.rst7 WARNING 2017-03-18 23:57:18 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:57:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_637522/mobley_637522_converted.inp INFO 2017-03-18 23:57:18 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_637522/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_637522/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_637522/mobley_637522_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_637522/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_637522/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -3.18258434 -3.18258434 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -5.85789288 -5.85789288 coulomb total -5.92370720 -5.92419472 -0.00048752 -5.92419464 -0.00048744 -5.92417093 -0.00046373 -5.92370720 0.00000000 -5.85789288 0.06581432 coulomb-14 -2.74135680 -2.74161038 -0.00025358 0.00000000 2.74135680 -2.74153485 -0.00017805 -2.74135680 0.00000000 0.00000000 2.74135680 improper 0.00000000 0.00006983 0.00006983 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00083680 0.00063493 -0.00020187 0.00070481 -0.00013199 0.00068581 -0.00015099 0.00083680 0.00000000 0.00062760 -0.00020920 vdw (SR) 0.00000000 -6.49980481 -6.49980481 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 39.06370680 39.06370680 vdw total 39.06349760 39.06374990 0.00025230 39.06374990 0.00025230 39.06380119 0.00030359 39.06391600 0.00041840 39.06370680 0.00020920 vdw-14 45.56334160 45.56355471 0.00021311 0.00000000 -45.56334160 45.56361021 0.00026861 45.56376000 0.00041840 0.00000000 -45.56334160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.14513680 2.14494340 -0.00019340 2.14494342 -0.00019338 2.14559514 0.00045834 2.14513680 0.00000000 2.14496944 -0.00016736 bond 8.29185120 8.29201129 0.00016009 8.29201145 0.00016025 8.29170823 -0.00014297 8.29185120 0.00000000 8.29201856 0.00016736 bonded 10.43782480 10.43765945 -0.00016535 10.43765967 -0.00016513 10.43798918 0.00016438 10.43782480 0.00000000 10.43769928 -0.00012552 dihedral 0.00083680 0.00070475 -0.00013205 0.00070481 -0.00013199 0.00068581 -0.00015099 0.00083680 0.00000000 0.00071128 -0.00012552 nonbonded 33.13979040 33.13955519 -0.00023521 33.13955526 -0.00023514 33.13963027 -0.00016013 33.14020880 0.00041840 33.20581392 0.06602352 potential 43.57761520 43.57721463 -0.00040057 43.57721354 -0.00040166 43.57749721 -0.00011799 43.57803360 0.00041840 43.64347136 0.06585616 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 43.57761520 Difference in potential energy from amber=>gromacs conversion: -0.00040057 Difference in potential energy from amber=>lammps conversion: -0.00040166 Difference in potential energy from amber=>desmond conversion: -0.00011799 Difference in potential energy from amber=>amber conversion: 0.00041840 Difference in potential energy from amber=>charmm conversion: 0.06585616 ======================================================================= INFO 2017-03-18 23:57:18 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_637522.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_637522.inpcrd') INFO 2017-03-18 23:57:18 Beginning InterMol conversion INFO 2017-03-18 23:57:18 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:57:18 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:57:18 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6416775.inpcrd INFO 2017-03-18 23:57:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6416775/mobley_6416775_converted.input INFO 2017-03-18 23:57:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6416775/mobley_6416775_converted.cms WARNING 2017-03-18 23:57:34 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:57:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6416775/mobley_6416775_converted.inp INFO 2017-03-18 23:57:34 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6416775/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6416775/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6416775/mobley_6416775_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6416775/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 10.90071192 10.90071192 0.00000000 0.00000000 0.00000000 0.00000000 -0.77320320 -0.77320320 coulomb total -0.77613200 -0.77599469 0.00013731 -0.77599468 0.00013732 -0.77601460 0.00011740 -0.77320320 0.00292880 coulomb-14 -11.67628880 -11.67670661 -0.00041781 0.00000000 11.67628880 -11.67671134 -0.00042254 0.00000000 11.67628880 proper 42.50567440 42.50547496 -0.00019944 42.50547775 -0.00019665 42.50545139 -0.00022301 42.50546520 -0.00020920 vdw (SR) 0.00000000 -1.80450674 -1.80450674 0.00000000 0.00000000 0.00000000 0.00000000 7.92273872 7.92273872 vdw total 7.92282240 7.92258492 -0.00023748 7.92258517 -0.00023723 7.92270731 -0.00011509 7.92273872 -0.00008368 vdw-14 9.72738160 9.72709166 -0.00028994 0.00000000 -9.72738160 9.72716349 -0.00021811 0.00000000 -9.72738160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 19.58655920 19.58655932 0.00000012 19.58655920 0.00000000 19.58657179 0.00001259 19.58639184 -0.00016736 bond 1.52841520 1.52829107 -0.00012413 1.52829106 -0.00012414 1.52824910 -0.00016610 1.52828968 -0.00012552 bonded 63.62064880 63.62032535 -0.00032345 63.62032801 -0.00032079 63.62027229 -0.00037651 63.62014672 -0.00050208 dihedral 42.50567440 42.50547496 -0.00019944 42.50547775 -0.00019665 42.50545139 -0.00022301 42.50546520 -0.00020920 nonbonded 7.14669040 7.14659023 -0.00010017 7.14659040 -0.00010000 7.14669271 0.00000231 7.14953552 0.00284512 potential 70.76733920 70.76691558 -0.00042362 70.76691662 -0.00042258 70.76689068 -0.00044852 70.76972408 0.00238488 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 70.76733920 Difference in potential energy from amber=>gromacs conversion: -0.00042362 Difference in potential energy from amber=>lammps conversion: -0.00042258 Difference in potential energy from amber=>desmond conversion: -0.00044852 Difference in potential energy from amber=>charmm conversion: 0.00238488 ======================================================================= INFO 2017-03-18 23:57:34 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6416775.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6416775.inpcrd') INFO 2017-03-18 23:57:34 Beginning InterMol conversion INFO 2017-03-18 23:57:34 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:57:34 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:57:34 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6430250.inpcrd INFO 2017-03-18 23:57:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6430250/mobley_6430250_converted.input INFO 2017-03-18 23:57:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6430250/mobley_6430250_converted.cms WARNING 2017-03-18 23:57:50 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:57:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6430250/mobley_6430250_converted.inp INFO 2017-03-18 23:57:50 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6430250/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6430250/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6430250/mobley_6430250_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6430250/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 4.56890585 4.56890585 0.00000000 0.00000000 0.00000000 0.00000000 -1.00566624 -1.00566624 coulomb total -1.00290480 -1.01679804 -0.01389324 -1.01679802 -0.01389322 -1.01682936 -0.01392456 -1.00566624 -0.00276144 coulomb-14 -5.58396640 -5.58570389 -0.00173749 0.00000000 5.58396640 -5.58571661 -0.00175021 0.00000000 5.58396640 improper 0.00000000 0.00001306 0.00001306 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.04518720 0.04507959 -0.00010761 0.04509264 -0.00009456 0.04509083 -0.00009637 0.04506168 -0.00012552 vdw (SR) 0.00000000 -4.04570975 -4.04570975 0.00000000 0.00000000 0.00000000 0.00000000 16.70068704 16.70068704 vdw total 16.70085440 16.70066522 -0.00018918 16.70066528 -0.00018912 16.70073885 -0.00011555 16.70068704 -0.00016736 vdw-14 20.74636400 20.74637497 0.00001097 0.00000000 -20.74636400 20.74645140 0.00008740 0.00000000 -20.74636400 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.84684160 0.84674298 -0.00009862 0.84674298 -0.00009862 0.84679379 -0.00004781 0.84671608 -0.00012552 bond 1.80037520 1.80024574 -0.00012946 1.80024575 -0.00012945 1.80016735 -0.00020785 1.80024968 -0.00012552 bonded 2.69240400 2.69208138 -0.00032262 2.69208137 -0.00032263 2.69205197 -0.00035203 2.69202744 -0.00037656 dihedral 0.04518720 0.04509265 -0.00009455 0.04509264 -0.00009456 0.04509083 -0.00009637 0.04506168 -0.00012552 nonbonded 15.69794960 15.68386718 -0.01408242 15.68386709 -0.01408251 15.68390949 -0.01404011 15.69502080 -0.00292880 potential 18.39035360 18.37594856 -0.01440504 18.37594851 -0.01440509 18.37589064 -0.01446296 18.38709008 -0.00326352 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 18.39035360 Difference in potential energy from amber=>gromacs conversion: -0.01440504 Difference in potential energy from amber=>lammps conversion: -0.01440509 Difference in potential energy from amber=>desmond conversion: -0.01446296 Difference in potential energy from amber=>charmm conversion: -0.00326352 ======================================================================= INFO 2017-03-18 23:57:50 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6430250.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6430250.inpcrd') INFO 2017-03-18 23:57:50 Beginning InterMol conversion INFO 2017-03-18 23:57:50 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:57:50 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:57:50 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6456034.inpcrd INFO 2017-03-18 23:57:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6456034/mobley_6456034_converted.input INFO 2017-03-18 23:57:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6456034/mobley_6456034_converted.cms WARNING 2017-03-18 23:58:06 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:58:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6456034/mobley_6456034_converted.inp INFO 2017-03-18 23:58:06 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6456034/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6456034/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6456034/mobley_6456034_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6456034/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -117.23892042 -117.23892042 0.00000000 0.00000000 0.00000000 0.00000000 -27.34151952 -27.34151952 coulomb total -27.31775440 -27.31720602 0.00054838 -27.31720588 0.00054852 -27.31717241 0.00058199 -27.34151952 -0.02376512 coulomb-14 89.90746560 89.92171440 0.01424880 0.00000000 -89.90746560 89.92164350 0.01417790 0.00000000 -89.90746560 improper 0.00000000 0.00071768 0.00071768 0.00000000 0.00000000 0.00000000 0.00000000 0.00071128 0.00071128 proper 9.23408800 9.23326935 -0.00081865 9.23398800 -0.00010000 9.23398758 -0.00010042 9.23329304 -0.00079496 vdw (SR) 0.00000000 -5.33414265 -5.33414265 0.00000000 0.00000000 0.00000000 0.00000000 12.40627128 12.40627128 vdw total 12.40597840 12.40606636 0.00008796 12.40606668 0.00008828 12.40597786 -0.00000054 12.40627128 0.00029288 vdw-14 17.74016000 17.74020901 0.00004901 0.00000000 -17.74016000 17.74008900 -0.00007100 0.00000000 -17.74016000 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.95220640 3.95232234 0.00011594 3.95232234 0.00011594 3.95225490 0.00004850 3.95233192 0.00012552 bond 2.11668560 2.11654399 -0.00014161 2.11654397 -0.00014163 2.11703705 0.00035145 2.11656008 -0.00012552 bonded 15.30298000 15.30285335 -0.00012665 15.30285431 -0.00012569 15.30327953 0.00029953 15.30289632 -0.00008368 dihedral 9.23408800 9.23398703 -0.00010097 9.23398800 -0.00010000 9.23398758 -0.00010042 9.23400432 -0.00008368 nonbonded -14.91177600 -14.91113966 0.00063634 -14.91113920 0.00063680 -14.91119455 0.00058145 -14.93524824 -0.02347224 potential 0.39120400 0.39171369 0.00050969 0.39171502 0.00051102 0.39198273 0.00077873 0.36764808 -0.02355592 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 0.39120400 Difference in potential energy from amber=>gromacs conversion: 0.00050969 Difference in potential energy from amber=>lammps conversion: 0.00051102 Difference in potential energy from amber=>desmond conversion: 0.00077873 Difference in potential energy from amber=>charmm conversion: -0.02355592 ======================================================================= INFO 2017-03-18 23:58:06 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6456034.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6456034.inpcrd') INFO 2017-03-18 23:58:06 Beginning InterMol conversion INFO 2017-03-18 23:58:06 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:58:06 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:58:07 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_646007.inpcrd INFO 2017-03-18 23:58:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_646007/mobley_646007_converted.input INFO 2017-03-18 23:58:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_646007/mobley_646007_converted.cms WARNING 2017-03-18 23:58:22 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:58:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_646007/mobley_646007_converted.inp INFO 2017-03-18 23:58:22 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_646007/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_646007/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_646007/mobley_646007_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_646007/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 30.21489864 30.21489864 0.00000000 0.00000000 0.00000000 0.00000000 -1.88706768 -1.88706768 coulomb total -1.85811440 -1.85813042 -0.00001602 -1.85813038 -0.00001598 -1.85815524 -0.00004084 -1.88706768 -0.02895328 coulomb-14 -32.07203360 -32.07302906 -0.00099546 0.00000000 32.07203360 -32.07304973 -0.00101613 0.00000000 32.07203360 proper 36.22339840 36.22337298 -0.00002542 36.22337288 -0.00002552 36.22342045 0.00002205 36.22754056 0.00414216 vdw (SR) 0.00000000 -0.30428485 -0.30428485 0.00000000 0.00000000 0.00000000 0.00000000 0.70337224 0.70337224 vdw total 0.70333040 0.70331733 -0.00001307 0.70331735 -0.00001305 0.70332754 -0.00000286 0.70337224 0.00004184 vdw-14 1.00750720 1.00760218 0.00009498 0.00000000 -1.00750720 1.00761235 0.00010515 0.00000000 -1.00750720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 16.93432160 16.93432304 0.00000144 16.93432286 0.00000126 16.93442582 0.00010422 16.93415424 -0.00016736 bond 1.19244000 1.19228792 -0.00015208 1.19228791 -0.00015209 1.19230339 -0.00013661 1.19227264 -0.00016736 bonded 54.35016000 54.34998394 -0.00017606 54.34998364 -0.00017636 54.35014966 -0.00001034 54.35396744 0.00380744 dihedral 36.22339840 36.22337298 -0.00002542 36.22337288 -0.00002552 36.22342045 0.00002205 36.22754056 0.00414216 nonbonded -1.15478400 -1.15481308 -0.00002908 -1.15481304 -0.00002904 -1.15482770 -0.00004370 -1.18369544 -0.02891144 potential 53.19537600 53.19517085 -0.00020515 53.19517098 -0.00020502 53.19529609 -0.00007991 53.17027200 -0.02510400 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 53.19537600 Difference in potential energy from amber=>gromacs conversion: -0.00020515 Difference in potential energy from amber=>lammps conversion: -0.00020502 Difference in potential energy from amber=>desmond conversion: -0.00007991 Difference in potential energy from amber=>charmm conversion: -0.02510400 ======================================================================= INFO 2017-03-18 23:58:22 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_646007.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_646007.inpcrd') INFO 2017-03-18 23:58:22 Beginning InterMol conversion INFO 2017-03-18 23:58:22 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-18 23:58:23 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6474572.inpcrd INFO 2017-03-18 23:58:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6474572/mobley_6474572_converted.input INFO 2017-03-18 23:58:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6474572/mobley_6474572_converted.cms INFO 2017-03-18 23:58:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6474572/mobley_6474572_converted.rst7 WARNING 2017-03-18 23:58:38 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:58:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6474572/mobley_6474572_converted.inp INFO 2017-03-18 23:58:38 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6474572/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6474572/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6474572/mobley_6474572_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_6474572/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6474572/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 4.46407696 4.46407696 coulomb total 4.45972560 4.45994593 0.00022033 4.45994568 0.00022008 4.45995241 0.00022681 4.45972560 0.00000000 4.46407696 0.00435136 coulomb-14 4.45972560 4.45994593 0.00022033 0.00000000 -4.45972560 4.45995241 0.00022681 4.45972560 0.00000000 0.00000000 -4.45972560 improper 0.00000000 0.00000372 0.00000372 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00000000 0.00004282 0.00004282 0.00004646 0.00004646 0.00004439 0.00004439 0.00000000 0.00000000 0.00004184 0.00004184 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.19882368 0.19882368 vdw total 0.19874000 0.19883560 0.00009560 0.19883560 0.00009560 0.19883863 0.00009863 0.19874000 0.00000000 0.19882368 0.00008368 vdw-14 0.19874000 0.19883560 0.00009560 0.00000000 -0.19874000 0.19883863 0.00009863 0.19874000 0.00000000 0.00000000 -0.19874000 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.23681440 0.23679682 -0.00001758 0.23679682 -0.00001758 0.23687589 0.00006149 0.23681440 0.00000000 0.23681440 0.00000000 bond 0.34936400 0.34947346 0.00010946 0.34947346 0.00010946 0.34943910 0.00007510 0.34936400 0.00000000 0.34948952 0.00012552 bonded 0.58617840 0.58631682 0.00013842 0.58631674 0.00013834 0.58635938 0.00018098 0.58617840 0.00000000 0.58634576 0.00016736 dihedral 0.00000000 0.00004654 0.00004654 0.00004646 0.00004646 0.00004439 0.00004439 0.00000000 0.00000000 0.00004184 0.00004184 nonbonded 4.65846560 4.65878153 0.00031593 4.65878149 0.00031589 4.65879104 0.00032544 4.65846560 0.00000000 4.66290064 0.00443504 potential 5.24464400 5.24509835 0.00045435 5.24509838 0.00045438 5.24514026 0.00049626 5.24464400 0.00000000 5.24924640 0.00460240 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 5.24464400 Difference in potential energy from amber=>gromacs conversion: 0.00045435 Difference in potential energy from amber=>lammps conversion: 0.00045438 Difference in potential energy from amber=>desmond conversion: 0.00049626 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00460240 ======================================================================= INFO 2017-03-18 23:58:38 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6474572.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6474572.inpcrd') INFO 2017-03-18 23:58:38 Beginning InterMol conversion INFO 2017-03-18 23:58:38 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:58:39 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:58:39 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6497672.inpcrd INFO 2017-03-18 23:58:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6497672/mobley_6497672_converted.input INFO 2017-03-18 23:58:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6497672/mobley_6497672_converted.cms WARNING 2017-03-18 23:58:54 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:58:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6497672/mobley_6497672_converted.inp INFO 2017-03-18 23:58:54 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6497672/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6497672/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6497672/mobley_6497672_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6497672/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 5.76988313 5.76988313 0.00000000 0.00000000 0.00000000 0.00000000 -4.95548776 -4.95548776 coulomb total -4.95218240 -4.95260704 -0.00042464 -4.95260708 -0.00042468 -4.95269553 -0.00051313 -4.95548776 -0.00330536 coulomb-14 -10.72191840 -10.72249016 -0.00057176 0.00000000 10.72191840 -10.72254734 -0.00062894 0.00000000 10.72191840 improper 0.00000000 0.00064713 0.00064713 0.00000000 0.00000000 0.00000000 0.00000000 0.00062760 0.00062760 proper 0.00125520 0.00063682 -0.00061838 0.00128431 0.00002911 0.00127985 0.00002465 0.00062760 -0.00062760 vdw (SR) 0.00000000 -0.38820099 -0.38820099 0.00000000 0.00000000 0.00000000 0.00000000 1.85589688 1.85589688 vdw total 1.85560400 1.85584623 0.00024223 1.85584625 0.00024225 1.85586764 0.00026364 1.85589688 0.00029288 vdw-14 2.24387920 2.24404723 0.00016803 0.00000000 -2.24387920 2.24406123 0.00018203 0.00000000 -2.24387920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.94767600 0.94751739 -0.00015861 0.94751738 -0.00015862 0.94739318 -0.00028282 0.94750864 -0.00016736 bond 0.84349440 0.84350025 0.00000585 0.84350026 0.00000586 0.84305922 -0.00043518 0.84349440 0.00000000 bonded 1.79242560 1.79230160 -0.00012400 1.79230196 -0.00012364 1.79173225 -0.00069335 1.79225824 -0.00016736 dihedral 0.00125520 0.00128395 0.00002875 0.00128431 0.00002911 0.00127985 0.00002465 0.00125520 0.00000000 nonbonded -3.09657840 -3.09676080 -0.00018240 -3.09676074 -0.00018234 -3.09682789 -0.00024949 -3.09959088 -0.00301248 potential -1.30415280 -1.30445920 -0.00030640 -1.30445878 -0.00030598 -1.30511880 -0.00096600 -1.30729080 -0.00313800 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -1.30415280 Difference in potential energy from amber=>gromacs conversion: -0.00030640 Difference in potential energy from amber=>lammps conversion: -0.00030598 Difference in potential energy from amber=>desmond conversion: -0.00096600 Difference in potential energy from amber=>charmm conversion: -0.00313800 ======================================================================= INFO 2017-03-18 23:58:54 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6497672.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6497672.inpcrd') INFO 2017-03-18 23:58:54 Beginning InterMol conversion INFO 2017-03-18 23:58:54 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:58:55 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:58:55 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6522117.inpcrd INFO 2017-03-18 23:58:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6522117/mobley_6522117_converted.input INFO 2017-03-18 23:58:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6522117/mobley_6522117_converted.cms WARNING 2017-03-18 23:59:10 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:59:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6522117/mobley_6522117_converted.inp INFO 2017-03-18 23:59:10 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6522117/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6522117/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6522117/mobley_6522117_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6522117/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 168.25547423 168.25547423 0.00000000 0.00000000 0.00000000 0.00000000 -357.79614072 -357.79614072 coulomb total -357.62823680 -357.64353207 -0.01529527 -357.64352932 -0.01529252 -357.64345945 -0.01522265 -357.79614072 -0.16790392 coulomb-14 -525.84930400 -525.89900630 -0.04970230 0.00000000 525.84930400 -525.89911034 -0.04980634 0.00000000 525.84930400 improper 0.00000000 0.00373500 0.00373500 0.00000000 0.00000000 0.00000000 0.00000000 0.00372376 0.00372376 proper 67.26365760 67.25990008 -0.00375752 67.26363668 -0.00002092 67.26372538 0.00006778 67.25989200 -0.00376560 vdw (SR) 0.00000000 -19.86276483 -19.86276483 0.00000000 0.00000000 0.00000000 0.00000000 9.76704592 9.76704592 vdw total 9.76712960 9.76679294 -0.00033666 9.76679279 -0.00033681 9.76714851 0.00001891 9.76704592 -0.00008368 vdw-14 29.62983280 29.62955778 -0.00027502 0.00000000 -29.62983280 29.62982213 -0.00001067 0.00000000 -29.62983280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.49780000 4.49800365 0.00020365 4.49800376 0.00020376 4.49811171 0.00031171 4.49805104 0.00025104 bond 7.06844960 7.06825867 -0.00019093 7.06825881 -0.00019079 7.06840722 -0.00004238 7.06824040 -0.00020920 bonded 78.82990720 78.82989739 -0.00000981 78.82989925 -0.00000795 78.83024430 0.00033710 78.82990720 0.00000000 dihedral 67.26365760 67.26363507 -0.00002253 67.26363668 -0.00002092 67.26372538 0.00006778 67.26361576 -0.00004184 nonbonded -347.86110720 -347.87673913 -0.01563193 -347.87673444 -0.01562724 -347.87631094 -0.01520374 -348.02909480 -0.16798760 potential -269.03120000 -269.04684174 -0.01564174 -269.04683561 -0.01563561 -269.04643980 -0.01523980 -269.19918760 -0.16798760 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -269.03120000 Difference in potential energy from amber=>gromacs conversion: -0.01564174 Difference in potential energy from amber=>lammps conversion: -0.01563561 Difference in potential energy from amber=>desmond conversion: -0.01523980 Difference in potential energy from amber=>charmm conversion: -0.16798760 ======================================================================= INFO 2017-03-18 23:59:10 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6522117.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6522117.inpcrd') INFO 2017-03-18 23:59:11 Beginning InterMol conversion INFO 2017-03-18 23:59:11 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:59:11 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:59:11 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6571751.inpcrd INFO 2017-03-18 23:59:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6571751/mobley_6571751_converted.input INFO 2017-03-18 23:59:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6571751/mobley_6571751_converted.cms WARNING 2017-03-18 23:59:26 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:59:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6571751/mobley_6571751_converted.inp INFO 2017-03-18 23:59:27 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6571751/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6571751/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6571751/mobley_6571751_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6571751/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 12.67765393 12.67765393 0.00000000 0.00000000 0.00000000 0.00000000 -6.87506512 -6.87506512 coulomb total -6.86217840 -6.87462370 -0.01244530 -6.87462371 -0.01244531 -6.87464212 -0.01246372 -6.87506512 -0.01288672 coulomb-14 -19.55266880 -19.55227764 0.00039116 0.00000000 19.55266880 -19.55227249 0.00039631 0.00000000 19.55266880 improper 0.00000000 0.00037501 0.00037501 0.00000000 0.00000000 0.00000000 0.00000000 0.00037656 0.00037656 proper 52.07406400 52.07374294 -0.00032106 52.07413931 0.00007531 52.07410333 0.00003933 52.07414768 0.00008368 vdw (SR) 0.00000000 -2.76921171 -2.76921171 0.00000000 0.00000000 0.00000000 0.00000000 11.64917648 11.64917648 vdw total 11.64909280 11.64914156 0.00004876 11.64914175 0.00004895 11.64914613 0.00005333 11.64917648 0.00008368 vdw-14 14.41848240 14.41835327 -0.00012913 0.00000000 -14.41848240 14.41835583 -0.00012657 0.00000000 -14.41848240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.60621360 2.60604042 -0.00017318 2.60604042 -0.00017318 2.60609921 -0.00011439 2.60592072 -0.00029288 bond 1.70707200 1.70687932 -0.00019268 1.70687933 -0.00019267 1.70659931 -0.00047269 1.70686280 -0.00020920 bonded 56.38734960 56.38703769 -0.00031191 56.38705906 -0.00029054 56.38680186 -0.00054774 56.38730776 -0.00004184 dihedral 52.07406400 52.07411795 0.00005395 52.07413931 0.00007531 52.07410333 0.00003933 52.07452424 0.00046024 nonbonded 4.78691440 4.77451786 -0.01239654 4.77451804 -0.01239636 4.77450401 -0.01241039 4.77411136 -0.01280304 potential 61.17426400 61.16155555 -0.01270845 61.16157811 -0.01268589 61.16125427 -0.01300973 61.16150280 -0.01276120 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 61.17426400 Difference in potential energy from amber=>gromacs conversion: -0.01270845 Difference in potential energy from amber=>lammps conversion: -0.01268589 Difference in potential energy from amber=>desmond conversion: -0.01300973 Difference in potential energy from amber=>charmm conversion: -0.01276120 ======================================================================= INFO 2017-03-18 23:59:27 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6571751.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6571751.inpcrd') INFO 2017-03-18 23:59:27 Beginning InterMol conversion INFO 2017-03-18 23:59:27 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:59:27 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:59:27 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6619554.inpcrd INFO 2017-03-18 23:59:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6619554/mobley_6619554_converted.input INFO 2017-03-18 23:59:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6619554/mobley_6619554_converted.cms WARNING 2017-03-18 23:59:43 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:59:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6619554/mobley_6619554_converted.inp INFO 2017-03-18 23:59:43 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6619554/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6619554/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6619554/mobley_6619554_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6619554/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -15.50860769 -15.50860769 0.00000000 0.00000000 0.00000000 0.00000000 -80.47024440 -80.47024440 coulomb total -80.47631120 -80.47869735 -0.00238615 -80.47869608 -0.00238488 -80.47863930 -0.00232810 -80.47024440 0.00606680 coulomb-14 -64.96957040 -64.97008966 -0.00051926 0.00000000 64.96957040 -64.97006202 -0.00049162 0.00000000 64.96957040 improper 0.00000000 0.00000568 0.00000568 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 14.82976960 14.82973540 -0.00003420 14.82974115 -0.00002845 14.82971182 -0.00005778 14.82972776 -0.00004184 vdw (SR) 0.00000000 -3.54878783 -3.54878783 0.00000000 0.00000000 0.00000000 0.00000000 10.45456080 10.45456080 vdw total 10.45456080 10.45440351 -0.00015729 10.45440348 -0.00015732 10.45452672 -0.00003408 10.45456080 -0.00000000 vdw-14 14.00342960 14.00319134 -0.00023826 0.00000000 -14.00342960 14.00331429 -0.00011531 0.00000000 -14.00342960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.29029760 3.29043285 0.00013525 3.29043287 0.00013527 3.29040577 0.00010817 3.29046496 0.00016736 bond 2.74010160 2.74010940 0.00000780 2.74010938 0.00000778 2.74031258 0.00021098 2.74010160 0.00000000 bonded 20.86016880 20.86028333 0.00011453 20.86028340 0.00011460 20.86043017 0.00026137 20.86029432 0.00012552 dihedral 14.82976960 14.82974108 -0.00002852 14.82974115 -0.00002845 14.82971182 -0.00005778 14.82972776 -0.00004184 nonbonded -70.02175040 -70.02429384 -0.00254344 -70.02429427 -0.00254387 -70.02411258 -0.00236218 -70.01568360 0.00606680 potential -49.16158160 -49.16401052 -0.00242892 -49.16400832 -0.00242672 -49.16377443 -0.00219283 -49.15538928 0.00619232 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -49.16158160 Difference in potential energy from amber=>gromacs conversion: -0.00242892 Difference in potential energy from amber=>lammps conversion: -0.00242672 Difference in potential energy from amber=>desmond conversion: -0.00219283 Difference in potential energy from amber=>charmm conversion: 0.00619232 ======================================================================= INFO 2017-03-18 23:59:43 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6619554.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6619554.inpcrd') INFO 2017-03-18 23:59:43 Beginning InterMol conversion INFO 2017-03-18 23:59:43 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:59:43 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:59:43 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6620221.inpcrd INFO 2017-03-18 23:59:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6620221/mobley_6620221_converted.input INFO 2017-03-18 23:59:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6620221/mobley_6620221_converted.cms WARNING 2017-03-18 23:59:59 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-18 23:59:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6620221/mobley_6620221_converted.inp INFO 2017-03-18 23:59:59 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6620221/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6620221/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6620221/mobley_6620221_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6620221/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -69.69802208 -69.69802208 0.00000000 0.00000000 0.00000000 0.00000000 -185.33889904 -185.33889904 coulomb total -185.29680800 -185.30482402 -0.00801602 -185.30482036 -0.00801236 -185.30515885 -0.00835085 -185.33889904 -0.04209104 coulomb-14 -115.60433840 -115.60680194 -0.00246354 0.00000000 115.60433840 -115.60715507 -0.00281667 0.00000000 115.60433840 improper 0.00000000 0.01484679 0.01484679 0.00000000 0.00000000 0.00000000 0.00000000 0.01485320 0.01485320 proper 38.97856240 38.96380982 -0.01475258 38.97865403 0.00009163 38.97862646 0.00006406 38.96404392 -0.01451848 vdw (SR) 0.00000000 -14.08269328 -14.08269328 0.00000000 0.00000000 0.00000000 0.00000000 17.14293584 17.14293584 vdw total 17.14310320 17.14282038 -0.00028282 17.14282036 -0.00028284 17.14319387 0.00009067 17.14293584 -0.00016736 vdw-14 31.22561040 31.22551366 -0.00009674 0.00000000 -31.22561040 31.22591930 0.00030890 0.00000000 -31.22561040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 53.68072000 53.68070405 -0.00001595 53.68070326 -0.00001674 53.68139153 0.00067153 53.68059448 -0.00012552 bond 15.21051360 15.21047562 -0.00003798 15.21047553 -0.00003807 15.20934869 -0.00116491 15.21047176 -0.00004184 bonded 107.86979600 107.86983629 0.00004029 107.86983282 0.00003682 107.86936668 -0.00042932 107.86996336 0.00016736 dihedral 38.97856240 38.97865662 0.00009422 38.97865403 0.00009163 38.97862646 0.00006406 38.97889712 0.00033472 nonbonded -168.15370480 -168.16200364 -0.00829884 -168.16200167 -0.00829687 -168.16196498 -0.00826018 -168.19596320 -0.04225840 potential -60.28390880 -60.29216735 -0.00825855 -60.29216802 -0.00825922 -60.29280273 -0.00889393 -60.32599984 -0.04209104 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -60.28390880 Difference in potential energy from amber=>gromacs conversion: -0.00825855 Difference in potential energy from amber=>lammps conversion: -0.00825922 Difference in potential energy from amber=>desmond conversion: -0.00889393 Difference in potential energy from amber=>charmm conversion: -0.04209104 ======================================================================= INFO 2017-03-18 23:59:59 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6620221.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6620221.inpcrd') INFO 2017-03-18 23:59:59 Beginning InterMol conversion INFO 2017-03-18 23:59:59 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-18 23:59:59 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-18 23:59:59 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6632459.inpcrd INFO 2017-03-18 23:59:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6632459/mobley_6632459_converted.input INFO 2017-03-18 23:59:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6632459/mobley_6632459_converted.cms WARNING 2017-03-19 00:00:15 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:00:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6632459/mobley_6632459_converted.inp INFO 2017-03-19 00:00:15 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6632459/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6632459/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6632459/mobley_6632459_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6632459/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -31.20903000 -31.20903000 0.00000000 0.00000000 0.00000000 0.00000000 -2.10651848 -2.10651848 coulomb total -2.10329680 -2.10548584 -0.00218904 -2.10548583 -0.00218903 -2.10547876 -0.00218196 -2.10651848 -0.00322168 coulomb-14 29.09846480 29.10354416 0.00507936 0.00000000 -29.09846480 29.10355217 0.00508737 0.00000000 -29.09846480 improper 0.00000000 0.00000707 0.00000707 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 3.18235040 3.18221797 -0.00013243 3.18222505 -0.00012535 3.18225158 -0.00009882 3.18222488 -0.00012552 vdw (SR) 0.00000000 -0.10954995 -0.10954995 0.00000000 0.00000000 0.00000000 0.00000000 3.17527944 3.17527944 vdw total 3.17523760 3.17525007 0.00001247 3.17525011 0.00001251 3.17532396 0.00008636 3.17527944 0.00004184 vdw-14 3.28485840 3.28480002 -0.00005838 0.00000000 -3.28485840 3.28486481 0.00000641 0.00000000 -3.28485840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.24850560 1.24854357 0.00003797 1.24854359 0.00003799 1.24844904 -0.00005656 1.24854744 0.00004184 bond 1.02759040 1.02770300 0.00011260 1.02770299 0.00011259 1.02768336 0.00009296 1.02771592 0.00012552 bonded 5.45844640 5.45847162 0.00002522 5.45847163 0.00002523 5.45838397 -0.00006243 5.45848824 0.00004184 dihedral 3.18235040 3.18222505 -0.00012535 3.18222505 -0.00012535 3.18225158 -0.00009882 3.18222488 -0.00012552 nonbonded 1.07194080 1.06976423 -0.00217657 1.06976433 -0.00217647 1.06984520 -0.00209560 1.06876096 -0.00317984 potential 6.53038720 6.52823585 -0.00215135 6.52823579 -0.00215141 6.52821420 -0.00217300 6.52729104 -0.00309616 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 6.53038720 Difference in potential energy from amber=>gromacs conversion: -0.00215135 Difference in potential energy from amber=>lammps conversion: -0.00215141 Difference in potential energy from amber=>desmond conversion: -0.00217300 Difference in potential energy from amber=>charmm conversion: -0.00309616 ======================================================================= INFO 2017-03-19 00:00:15 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6632459.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6632459.inpcrd') INFO 2017-03-19 00:00:15 Beginning InterMol conversion INFO 2017-03-19 00:00:15 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:00:15 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_667278.inpcrd INFO 2017-03-19 00:00:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_667278/mobley_667278_converted.input INFO 2017-03-19 00:00:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_667278/mobley_667278_converted.cms INFO 2017-03-19 00:00:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_667278/mobley_667278_converted.rst7 WARNING 2017-03-19 00:00:31 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:00:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_667278/mobley_667278_converted.inp INFO 2017-03-19 00:00:31 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_667278/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_667278/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_667278/mobley_667278_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_667278/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_667278/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -4.50830890 -4.50830890 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 8.03721296 8.03721296 coulomb total 8.04541360 8.04329319 -0.00212041 8.04329315 -0.00212045 8.04330198 -0.00211162 8.04541360 0.00000000 8.03721296 -0.00820064 coulomb-14 12.55116320 12.55160209 0.00043889 0.00000000 -12.55116320 12.55161608 0.00045288 12.55116320 0.00000000 0.00000000 -12.55116320 improper 0.00000000 0.00013117 0.00013117 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 33.47367360 33.47355281 -0.00012079 33.47368406 0.00001046 33.47367214 -0.00000146 33.47367360 0.00000000 33.47354808 -0.00012552 vdw (SR) 0.00000000 -16.66471245 -16.66471245 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 32.97159360 32.97159360 vdw total 32.97159360 32.97152602 -0.00006758 32.97152624 -0.00006736 32.97143862 -0.00015498 32.97117520 -0.00041840 32.97159360 0.00000000 vdw-14 49.63646560 49.63623848 -0.00022712 0.00000000 -49.63646560 49.63615138 -0.00031422 49.63604720 -0.00041840 0.00000000 -49.63646560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 6.10069040 6.10085972 0.00016932 6.10085985 0.00016945 6.10089755 0.00020715 6.10069040 0.00000000 6.10089960 0.00020920 bond 4.19236800 4.19236921 0.00000121 4.19236926 0.00000126 4.19234783 -0.00002017 4.19236800 0.00000000 4.19236800 0.00000000 bonded 43.76673200 43.76691292 0.00018092 43.76691317 0.00018117 43.76691752 0.00018552 43.76673200 0.00000000 43.76694120 0.00020920 dihedral 33.47367360 33.47368398 0.00001038 33.47368406 0.00001046 33.47367214 -0.00000146 33.47367360 0.00000000 33.47367360 -0.00000000 nonbonded 41.01700720 41.01481921 -0.00218799 41.01481897 -0.00218823 41.01474060 -0.00226660 41.01658880 -0.00041840 41.00880656 -0.00820064 potential 84.78373920 84.78173213 -0.00200707 84.78173088 -0.00200832 84.78132880 -0.00241040 84.78332080 -0.00041840 84.77578960 -0.00794960 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 84.78373920 Difference in potential energy from amber=>gromacs conversion: -0.00200707 Difference in potential energy from amber=>lammps conversion: -0.00200832 Difference in potential energy from amber=>desmond conversion: -0.00241040 Difference in potential energy from amber=>amber conversion: -0.00041840 Difference in potential energy from amber=>charmm conversion: -0.00794960 ======================================================================= INFO 2017-03-19 00:00:31 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_667278.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_667278.inpcrd') INFO 2017-03-19 00:00:31 Beginning InterMol conversion INFO 2017-03-19 00:00:31 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:00:31 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:00:31 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6688723.inpcrd INFO 2017-03-19 00:00:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6688723/mobley_6688723_converted.input INFO 2017-03-19 00:00:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6688723/mobley_6688723_converted.cms WARNING 2017-03-19 00:00:47 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:00:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6688723/mobley_6688723_converted.inp INFO 2017-03-19 00:00:47 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6688723/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6688723/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6688723/mobley_6688723_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6688723/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -144.33344866 -144.33344866 0.00000000 0.00000000 0.00000000 0.00000000 30.63194264 30.63194264 coulomb total 30.60303120 30.60398095 0.00094975 30.60398055 0.00094935 30.60490019 0.00186899 30.63194264 0.02891144 coulomb-14 174.93136640 174.93742961 0.00606321 0.00000000 -174.93136640 174.93728341 0.00591701 0.00000000 -174.93136640 improper 0.00000000 0.00005228 0.00005228 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 30.12898400 30.12885188 -0.00013212 30.12890409 -0.00007991 30.12890894 -0.00007506 30.12885848 -0.00012552 vdw (SR) 0.00000000 -9.87704556 -9.87704556 0.00000000 0.00000000 0.00000000 0.00000000 15.61167552 15.61167552 vdw total 15.61134080 15.61153603 0.00019523 15.61153619 0.00019539 15.61145862 0.00011782 15.61167552 0.00033472 vdw-14 25.48850960 25.48858159 0.00007199 0.00000000 -25.48850960 25.48851533 0.00000573 0.00000000 -25.48850960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.15520240 1.15500893 -0.00019347 1.15500893 -0.00019347 1.15501988 -0.00018252 1.15507688 -0.00012552 bond 1.62046320 1.62060635 0.00014315 1.62060633 0.00014313 1.62039511 -0.00006809 1.62058872 0.00012552 bonded 32.90464960 32.90451943 -0.00013017 32.90451935 -0.00013025 32.90432392 -0.00032568 32.90456592 -0.00008368 dihedral 30.12898400 30.12890415 -0.00007985 30.12890409 -0.00007991 30.12890894 -0.00007506 30.12890032 -0.00008368 nonbonded 46.21437200 46.21551699 0.00114499 46.21551842 0.00114642 46.21635881 0.00198681 46.24361816 0.02924616 potential 79.11902160 79.12003642 0.00101482 79.12003413 0.00101253 79.12053788 0.00151628 79.14818408 0.02916248 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 79.11902160 Difference in potential energy from amber=>gromacs conversion: 0.00101482 Difference in potential energy from amber=>lammps conversion: 0.00101253 Difference in potential energy from amber=>desmond conversion: 0.00151628 Difference in potential energy from amber=>charmm conversion: 0.02916248 ======================================================================= INFO 2017-03-19 00:00:47 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6688723.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6688723.inpcrd') INFO 2017-03-19 00:00:47 Beginning InterMol conversion INFO 2017-03-19 00:00:47 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:00:47 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:00:47 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6714389.inpcrd INFO 2017-03-19 00:00:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6714389/mobley_6714389_converted.input INFO 2017-03-19 00:00:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6714389/mobley_6714389_converted.cms WARNING 2017-03-19 00:01:03 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:01:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6714389/mobley_6714389_converted.inp INFO 2017-03-19 00:01:03 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6714389/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6714389/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6714389/mobley_6714389_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6714389/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 23.16760296 23.16760296 coulomb total 23.18438080 23.19923785 0.01485705 23.19923777 0.01485697 23.19921919 0.01483839 23.16760296 -0.01677784 coulomb-14 23.18438080 23.19923785 0.01485705 0.00000000 -23.18438080 23.19921919 0.01483839 0.00000000 -23.18438080 proper 4.93586480 4.93578872 -0.00007608 4.93578865 -0.00007615 4.93568116 -0.00018364 4.93578112 -0.00008368 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.06970544 -0.06970544 vdw total -0.06987280 -0.06971380 0.00015900 -0.06971380 0.00015900 -0.06971349 0.00015931 -0.06970544 0.00016736 vdw-14 -0.06987280 -0.06971380 0.00015900 0.00000000 0.06987280 -0.06971349 0.00015931 0.00000000 0.06987280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 19.44137440 19.44137411 -0.00000029 19.44137398 -0.00000042 19.44113173 -0.00024267 19.44154176 0.00016736 bond 1.82464240 1.82484709 0.00020469 1.82484708 0.00020468 1.82438110 -0.00026130 1.82485160 0.00020920 bonded 26.20188160 26.20200992 0.00012832 26.20200971 0.00012811 26.20119399 -0.00068761 26.20217448 0.00029288 dihedral 4.93586480 4.93578872 -0.00007608 4.93578865 -0.00007615 4.93568116 -0.00018364 4.93578112 -0.00008368 nonbonded 23.11450800 23.12952406 0.01501606 23.12952396 0.01501596 23.12950570 0.01499770 23.09789752 -0.01661048 potential 49.31638960 49.33153398 0.01514438 49.33153568 0.01514608 49.33069679 0.01430719 49.30007200 -0.01631760 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 49.31638960 Difference in potential energy from amber=>gromacs conversion: 0.01514438 Difference in potential energy from amber=>lammps conversion: 0.01514608 Difference in potential energy from amber=>desmond conversion: 0.01430719 Difference in potential energy from amber=>charmm conversion: -0.01631760 ======================================================================= INFO 2017-03-19 00:01:03 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6714389.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6714389.inpcrd') INFO 2017-03-19 00:01:03 Beginning InterMol conversion INFO 2017-03-19 00:01:03 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:01:03 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:01:03 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6727159.inpcrd INFO 2017-03-19 00:01:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6727159/mobley_6727159_converted.input INFO 2017-03-19 00:01:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6727159/mobley_6727159_converted.cms WARNING 2017-03-19 00:01:19 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:01:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6727159/mobley_6727159_converted.inp INFO 2017-03-19 00:01:19 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6727159/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6727159/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6727159/mobley_6727159_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6727159/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -75.29875409 -75.29875409 0.00000000 0.00000000 0.00000000 0.00000000 28.02987120 28.02987120 coulomb total 28.04953600 28.05446211 0.00492611 28.05446182 0.00492582 28.05451454 0.00497854 28.02987120 -0.01966480 coulomb-14 103.34647360 103.35321620 0.00674260 0.00000000 -103.34647360 103.35328473 0.00681113 0.00000000 -103.34647360 proper 5.64923680 5.64912682 -0.00010998 5.64912676 -0.00011004 5.64914011 -0.00009669 5.64911128 -0.00012552 vdw (SR) 0.00000000 -0.07429264 -0.07429264 0.00000000 0.00000000 0.00000000 0.00000000 13.90673736 13.90673736 vdw total 13.90677920 13.90663455 -0.00014465 13.90663485 -0.00014435 13.90662972 -0.00014948 13.90673736 -0.00004184 vdw-14 13.98083600 13.98092719 0.00009119 0.00000000 -13.98083600 13.98089002 0.00005402 0.00000000 -13.98083600 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.99320960 3.99317722 -0.00003238 3.99317722 -0.00003238 3.99318336 -0.00002624 3.99320960 0.00000000 bond 2.04472080 2.04488033 0.00015953 2.04488034 0.00015954 2.04459512 -0.00012568 2.04488816 0.00016736 bonded 11.68716720 11.68718437 0.00001717 11.68718431 0.00001711 11.68691859 -0.00024861 11.68720904 0.00004184 dihedral 5.64923680 5.64912682 -0.00010998 5.64912676 -0.00011004 5.64914011 -0.00009669 5.64911128 -0.00012552 nonbonded 41.95631520 41.96109666 0.00478146 41.96109751 0.00478231 41.96114426 0.00482906 41.93660856 -0.01970664 potential 53.64348240 53.64828103 0.00479863 53.64828145 0.00479905 53.64803124 0.00454884 53.62385944 -0.01962296 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 53.64348240 Difference in potential energy from amber=>gromacs conversion: 0.00479863 Difference in potential energy from amber=>lammps conversion: 0.00479905 Difference in potential energy from amber=>desmond conversion: 0.00454884 Difference in potential energy from amber=>charmm conversion: -0.01962296 ======================================================================= INFO 2017-03-19 00:01:19 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6727159.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6727159.inpcrd') INFO 2017-03-19 00:01:19 Beginning InterMol conversion INFO 2017-03-19 00:01:19 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:01:20 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:01:20 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6733657.inpcrd INFO 2017-03-19 00:01:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6733657/mobley_6733657_converted.input INFO 2017-03-19 00:01:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6733657/mobley_6733657_converted.cms WARNING 2017-03-19 00:01:35 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:01:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6733657/mobley_6733657_converted.inp ERROR 2017-03-19 00:01:38 charmm failed. See $RUNPATH/FreeSolv/converted/mobley_6733657/charmm_stderr.txt ERROR 2017-03-19 00:01:38 No energy data (ENER ENR line) found in $RUNPATH/FreeSolv/converted/mobley_6733657/charmm_stdout.txt ERROR 2017-03-19 00:01:38 'NoneType' object is not iterable out, outfile = crm.energies(inpfile, crm.CRM_PATH) TypeError: 'NoneType' object is not iterable INFO 2017-03-19 00:01:38 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6733657/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6733657/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6733657/mobley_6733657_converted.enegrp.dat charmm output energy file: -1 **** CHARMM ENERGIES ENTERED MANUALLY AFTER MANUAL EDITING OF FILE CHARMM FILES ***** **** NOT ALL ENERGY TERMS ENTERED **** Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -1.21211907 -1.21211907 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 coulomb total 6.79858160 6.79864423 0.00006263 6.79864394 0.00006234 6.79871269 0.00013109 6.84067264 -0.04209104 coulomb-14 8.01068640 8.01076330 0.00007690 0.00000000 -8.01068640 8.01081456 0.00012816 0.00000000 -8.01068640 improper 0.00000000 0.11496666 0.11496666 0.00000000 0.00000000 0.00000000 0.00000000 0.11497632 -0.11497632 proper 80.64911040 80.53422328 -0.11488712 80.64918990 0.00007950 80.64910538 -0.00000502 80.5384436 -0.11066680 vdw (SR) 0.00000000 -2.51457641 -2.51457641 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 vdw total 15.51008800 15.50976445 -0.00032355 15.50976458 -0.00032342 15.50972023 -0.00036777 15.51004616 0.00004184 vdw-14 18.02467200 18.02434086 -0.00033114 0.00000000 -18.02467200 18.02426414 -0.00040786 0.00000000 -18.02467200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 233.09398720 233.09400821 0.00002101 233.09400812 0.00002092 233.09456208 0.00057488 233.0936106 0.00037656 bond 20.55515520 20.55520837 0.00005317 20.55520834 0.00005314 20.55414983 -0.00100537 20.55519704 -0.00004184 bonded 334.29825280 334.29840653 0.00015373 334.29840635 0.00015355 334.29781729 -0.00043551 334.3022276 -0.00397480 dihedral 80.64911040 80.64918995 0.00007955 80.64918990 0.00007950 80.64910538 -0.00000502 80.65341992 -0.00430952 nonbonded 22.30866960 22.30840867 -0.00026093 22.30840852 -0.00026108 22.30843292 -0.00023668 22.3507188 -0.04204920 potential 356.60692240 356.60681520 -0.00010720 356.60681362 -0.00010878 356.60585548 -0.00106692 356.6529464 -0.04602400 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 356.60692240 Difference in potential energy from amber=>gromacs conversion: -0.00010720 Difference in potential energy from amber=>lammps conversion: -0.00010878 Difference in potential energy from amber=>desmond conversion: -0.00106692 Difference in potential energy from amber=>charmm conversion: -0.04602400 ======================================================================= INFO 2017-03-19 00:01:38 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6733657.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6733657.inpcrd') INFO 2017-03-19 00:01:38 Beginning InterMol conversion INFO 2017-03-19 00:01:38 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:01:38 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:01:38 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6739648.inpcrd INFO 2017-03-19 00:01:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6739648/mobley_6739648_converted.input INFO 2017-03-19 00:01:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6739648/mobley_6739648_converted.cms WARNING 2017-03-19 00:01:54 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:01:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6739648/mobley_6739648_converted.inp INFO 2017-03-19 00:01:54 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6739648/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6739648/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6739648/mobley_6739648_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6739648/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 37.14991244 37.14991244 0.00000000 0.00000000 0.00000000 0.00000000 68.86198744 68.86198744 coulomb total 68.85232240 68.83264845 -0.01967395 68.83264923 -0.01967317 68.83259262 -0.01972978 68.86198744 0.00966504 coulomb-14 31.66995120 31.68273601 0.01278481 0.00000000 -31.66995120 31.68272248 0.01277128 0.00000000 -31.66995120 proper 14.22099760 14.22119078 0.00019318 14.22119090 0.00019330 14.22129002 0.00029242 14.22120680 0.00020920 vdw (SR) 0.00000000 -1.23898870 -1.23898870 0.00000000 0.00000000 0.00000000 0.00000000 14.79098392 14.79098392 vdw total 14.79127680 14.79096408 -0.00031272 14.79096467 -0.00031213 14.79069690 -0.00057990 14.79098392 -0.00029288 vdw-14 16.03015920 16.02995279 -0.00020641 0.00000000 -16.03015920 16.02967900 -0.00048020 0.00000000 -16.03015920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.80581440 1.80590201 0.00008761 1.80590201 0.00008761 1.80608733 0.00027293 1.80589808 0.00008368 bond 1.12633280 1.12646617 0.00013337 1.12646619 0.00013339 1.12643596 0.00010316 1.12645832 0.00012552 bonded 17.15314480 17.15355896 0.00041416 17.15355910 0.00041430 17.15381331 0.00066851 17.15356320 0.00041840 dihedral 14.22099760 14.22119078 0.00019318 14.22119090 0.00019330 14.22129002 0.00029242 14.22120680 0.00020920 nonbonded 83.64359920 83.62361253 -0.01998667 83.62361223 -0.01998697 83.62328952 -0.02030968 83.65297136 0.00937216 potential 100.79674400 100.77717149 -0.01957251 100.77717125 -0.01957275 100.77707292 -0.01967108 100.80657640 0.00983240 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 100.79674400 Difference in potential energy from amber=>gromacs conversion: -0.01957251 Difference in potential energy from amber=>lammps conversion: -0.01957275 Difference in potential energy from amber=>desmond conversion: -0.01967108 Difference in potential energy from amber=>charmm conversion: 0.00983240 ======================================================================= INFO 2017-03-19 00:01:54 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6739648.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6739648.inpcrd') INFO 2017-03-19 00:01:54 Beginning InterMol conversion INFO 2017-03-19 00:01:54 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:01:55 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:01:55 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6743808.inpcrd INFO 2017-03-19 00:01:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6743808/mobley_6743808_converted.input INFO 2017-03-19 00:01:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6743808/mobley_6743808_converted.cms WARNING 2017-03-19 00:02:10 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:02:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6743808/mobley_6743808_converted.inp INFO 2017-03-19 00:02:10 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6743808/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6743808/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6743808/mobley_6743808_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6743808/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 46.94046045 46.94046045 0.00000000 0.00000000 0.00000000 0.00000000 -93.98912496 -93.98912496 coulomb total -93.97515040 -93.97853282 -0.00338242 -93.97853107 -0.00338067 -93.97907164 -0.00392124 -93.98912496 -0.01397456 coulomb-14 -140.91419120 -140.91899327 -0.00480207 0.00000000 140.91419120 -140.91887435 -0.00468315 0.00000000 140.91419120 improper 0.00000000 0.00007935 0.00007935 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00083680 0.00082629 -0.00001051 0.00090560 0.00006880 0.00090926 0.00007246 0.00083680 0.00000000 vdw (SR) 0.00000000 23.71985418 23.71985418 0.00000000 0.00000000 0.00000000 0.00000000 46.14458288 46.14458288 vdw total 46.14491760 46.14426685 -0.00065075 46.14426908 -0.00064852 46.14411649 -0.00080111 46.14458288 -0.00033472 vdw-14 22.42456640 22.42441268 -0.00015372 0.00000000 -22.42456640 22.42449439 -0.00007201 0.00000000 -22.42456640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.94767600 0.94761083 -0.00006517 0.94761081 -0.00006519 0.94762278 -0.00005322 0.94763416 -0.00004184 bond 1.87694240 1.87689046 -0.00005194 1.87689048 -0.00005192 1.87659752 -0.00034488 1.87690056 -0.00004184 bonded 2.82545520 2.82540693 -0.00004827 2.82540689 -0.00004831 2.82512956 -0.00032564 2.82545520 -0.00000000 dihedral 0.00083680 0.00090564 0.00006884 0.00090560 0.00006880 0.00090926 0.00007246 0.00092048 0.00008368 nonbonded -47.83023280 -47.83426597 -0.00403317 -47.83426618 -0.00403338 -47.83495516 -0.00472236 -47.84454208 -0.01430928 potential -45.00477760 -45.00885904 -0.00408144 -45.00885700 -0.00407940 -45.00988501 -0.00510741 -45.01912872 -0.01435112 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -45.00477760 Difference in potential energy from amber=>gromacs conversion: -0.00408144 Difference in potential energy from amber=>lammps conversion: -0.00407940 Difference in potential energy from amber=>desmond conversion: -0.00510741 Difference in potential energy from amber=>charmm conversion: -0.01435112 ======================================================================= INFO 2017-03-19 00:02:10 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6743808.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6743808.inpcrd') INFO 2017-03-19 00:02:11 Beginning InterMol conversion INFO 2017-03-19 00:02:11 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:02:11 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:02:11 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6794076.inpcrd INFO 2017-03-19 00:02:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6794076/mobley_6794076_converted.input INFO 2017-03-19 00:02:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6794076/mobley_6794076_converted.cms WARNING 2017-03-19 00:02:26 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:02:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6794076/mobley_6794076_converted.inp INFO 2017-03-19 00:02:26 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6794076/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6794076/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6794076/mobley_6794076_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6794076/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -205.54441318 -205.54441318 0.00000000 0.00000000 0.00000000 0.00000000 -51.20354096 -51.20354096 coulomb total -51.09375280 -51.09610175 -0.00234895 -51.09610002 -0.00234722 -51.09623768 -0.00248488 -51.20354096 -0.10978816 coulomb-14 154.44524720 154.44831143 0.00306423 0.00000000 -154.44524720 154.44786178 0.00261458 0.00000000 -154.44524720 improper 0.00000000 0.00161096 0.00161096 0.00000000 0.00000000 0.00000000 0.00000000 0.00163176 0.00163176 proper 19.42422000 19.42275705 -0.00146295 19.42438736 0.00016736 19.42441087 0.00019087 19.42275560 -0.00146440 vdw (SR) 0.00000000 0.57391705 0.57391705 0.00000000 0.00000000 0.00000000 0.00000000 25.44231824 25.44231824 vdw total 25.44248560 25.44230277 -0.00018283 25.44230276 -0.00018284 25.44247329 -0.00001231 25.44231824 -0.00016736 vdw-14 24.86844080 24.86838573 -0.00005507 0.00000000 -24.86844080 24.86863904 0.00019824 0.00000000 -24.86844080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 8.20147680 8.20152901 0.00005221 8.20152910 0.00005230 8.20127300 -0.00020380 8.20151864 0.00004184 bond 3.29531840 3.29538390 0.00006550 3.29538388 0.00006548 3.29451896 -0.00079944 3.29540208 0.00008368 bonded 30.92101520 30.92128092 0.00026572 30.92130034 0.00028514 30.92020283 -0.00081237 30.92130808 0.00029288 dihedral 19.42422000 19.42436801 0.00014801 19.42438736 0.00016736 19.42441087 0.00019087 19.42438736 0.00016736 nonbonded -25.65126720 -25.65379898 -0.00253178 -25.65379810 -0.00253090 -25.65376439 -0.00249719 -25.76122272 -0.10995552 potential 5.26974800 5.26748194 -0.00226606 5.26750203 -0.00224597 5.26638867 -0.00335933 5.16004352 -0.10970448 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 5.26974800 Difference in potential energy from amber=>gromacs conversion: -0.00226606 Difference in potential energy from amber=>lammps conversion: -0.00224597 Difference in potential energy from amber=>desmond conversion: -0.00335933 Difference in potential energy from amber=>charmm conversion: -0.10970448 ======================================================================= INFO 2017-03-19 00:02:26 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6794076.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6794076.inpcrd') INFO 2017-03-19 00:02:27 Beginning InterMol conversion INFO 2017-03-19 00:02:27 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:02:27 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6804509.inpcrd INFO 2017-03-19 00:02:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6804509/mobley_6804509_converted.input INFO 2017-03-19 00:02:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6804509/mobley_6804509_converted.cms INFO 2017-03-19 00:02:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6804509/mobley_6804509_converted.rst7 WARNING 2017-03-19 00:02:42 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:02:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6804509/mobley_6804509_converted.inp INFO 2017-03-19 00:02:42 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6804509/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6804509/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6804509/mobley_6804509_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_6804509/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6804509/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -14.08472232 -14.08472232 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -11.27257464 -11.27257464 coulomb total -11.29805520 -11.30038705 -0.00233185 -11.30038694 -0.00233174 -11.30037707 -0.00232187 -11.29805520 0.00000000 -11.27257464 0.02548056 coulomb-14 2.78528880 2.78433528 -0.00095352 0.00000000 -2.78528880 2.78434158 -0.00094722 2.78528880 0.00000000 0.00000000 -2.78528880 improper 0.00000000 0.00001081 0.00001081 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00000000 0.00010804 0.00010804 0.00011885 0.00011885 0.00011921 0.00011921 0.00000000 0.00000000 0.00012552 0.00012552 vdw (SR) 0.00000000 -2.88015157 -2.88015157 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 16.05731336 16.05731336 vdw total 16.05735520 16.05730816 -0.00004704 16.05730834 -0.00004686 16.05730818 -0.00004702 16.05735520 0.00000000 16.05731336 -0.00004184 vdw-14 18.93762080 18.93745973 -0.00016107 0.00000000 -18.93762080 18.93745578 -0.00016502 18.93762080 0.00000000 0.00000000 -18.93762080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.00243840 3.00254233 0.00010393 3.00254233 0.00010393 3.00261171 0.00017331 3.00243840 0.00000000 3.00256392 0.00012552 bond 0.72843440 0.72842011 -0.00001429 0.72842009 -0.00001431 0.72835567 -0.00007873 0.72843440 0.00000000 0.72843440 0.00000000 bonded 3.73087280 3.73108128 0.00020848 3.73108127 0.00020847 3.73108659 0.00021379 3.73087280 0.00000000 3.73112384 0.00025104 dihedral 0.00000000 0.00011885 0.00011885 0.00011885 0.00011885 0.00011921 0.00011921 0.00000000 0.00000000 0.00012552 0.00012552 nonbonded 4.75930000 4.75692111 -0.00237889 4.75692140 -0.00237860 4.75693112 -0.00236888 4.75930000 0.00000000 4.78473872 0.02543872 potential 8.49017280 8.48800240 -0.00217040 8.48800256 -0.00217024 8.48791913 -0.00225367 8.49017280 0.00000000 8.51586256 0.02568976 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 8.49017280 Difference in potential energy from amber=>gromacs conversion: -0.00217040 Difference in potential energy from amber=>lammps conversion: -0.00217024 Difference in potential energy from amber=>desmond conversion: -0.00225367 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.02568976 ======================================================================= INFO 2017-03-19 00:02:42 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6804509.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6804509.inpcrd') INFO 2017-03-19 00:02:43 Beginning InterMol conversion INFO 2017-03-19 00:02:43 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:02:43 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:02:43 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6812653.inpcrd INFO 2017-03-19 00:02:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6812653/mobley_6812653_converted.input INFO 2017-03-19 00:02:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6812653/mobley_6812653_converted.cms WARNING 2017-03-19 00:02:58 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:02:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6812653/mobley_6812653_converted.inp INFO 2017-03-19 00:02:58 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6812653/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6812653/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6812653/mobley_6812653_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6812653/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 5.36961039 5.36961039 0.00000000 0.00000000 0.00000000 0.00000000 3.33054768 3.33054768 coulomb total 3.30536000 3.32724415 0.02188415 3.32724412 0.02188412 3.32721733 0.02185733 3.33054768 0.02518768 coulomb-14 -2.04764960 -2.04236624 0.00528336 0.00000000 2.04764960 -2.04237225 0.00527735 0.00000000 2.04764960 proper 5.10071440 5.10089964 0.00018524 5.10089975 0.00018535 5.10089494 0.00018054 5.10088176 0.00016736 vdw (SR) 0.00000000 -1.77981873 -1.77981873 0.00000000 0.00000000 0.00000000 0.00000000 5.26974800 5.26974800 vdw total 5.26974800 5.26963456 -0.00011344 5.26963461 -0.00011339 5.26966903 -0.00007897 5.26974800 0.00000000 vdw-14 7.04962160 7.04945329 -0.00016831 0.00000000 -7.04962160 7.04947796 -0.00014364 0.00000000 -7.04962160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.02633520 1.02638030 0.00004510 1.02638030 0.00004510 1.02626926 -0.00006594 1.02633520 0.00000000 bond 1.00583360 1.00575517 -0.00007843 1.00575519 -0.00007841 1.00551580 -0.00031780 1.00574992 -0.00008368 bonded 7.13288320 7.13303511 0.00015191 7.13303525 0.00015205 7.13268000 -0.00020320 7.13296688 0.00008368 dihedral 5.10071440 5.10089964 0.00018524 5.10089975 0.00018535 5.10089494 0.00018054 5.10088176 0.00016736 nonbonded 8.57510800 8.59687871 0.02177071 8.59687861 0.02177061 8.59688636 0.02177836 8.60029568 0.02518768 potential 15.70799120 15.72991382 0.02192262 15.72991369 0.02192249 15.72951922 0.02152802 15.73326256 0.02527136 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 15.70799120 Difference in potential energy from amber=>gromacs conversion: 0.02192262 Difference in potential energy from amber=>lammps conversion: 0.02192249 Difference in potential energy from amber=>desmond conversion: 0.02152802 Difference in potential energy from amber=>charmm conversion: 0.02527136 ======================================================================= INFO 2017-03-19 00:02:58 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6812653.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6812653.inpcrd') INFO 2017-03-19 00:02:59 Beginning InterMol conversion INFO 2017-03-19 00:02:59 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:02:59 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:02:59 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6843802.inpcrd INFO 2017-03-19 00:02:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6843802/mobley_6843802_converted.input INFO 2017-03-19 00:02:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6843802/mobley_6843802_converted.cms WARNING 2017-03-19 00:03:15 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:03:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6843802/mobley_6843802_converted.inp INFO 2017-03-19 00:03:15 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6843802/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6843802/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6843802/mobley_6843802_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6843802/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 19.25953674 19.25953674 0.00000000 0.00000000 0.00000000 0.00000000 32.07646864 32.07646864 coulomb total 32.10257680 32.10525857 0.00268177 32.10525833 0.00268153 32.10525816 0.00268136 32.07646864 -0.02610816 coulomb-14 12.84906400 12.84572183 -0.00334217 0.00000000 -12.84906400 12.84573638 -0.00332762 0.00000000 -12.84906400 improper 0.00000000 0.00010172 0.00010172 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 13.40260720 13.40258405 -0.00002315 13.40269506 0.00008786 13.40260883 0.00000163 13.40218880 -0.00041840 vdw (SR) 0.00000000 3.31730415 3.31730415 0.00000000 0.00000000 0.00000000 0.00000000 29.46456480 29.46456480 vdw total 29.46456480 29.46468375 0.00011895 29.46468404 0.00011924 29.46448232 -0.00008248 29.46456480 0.00000000 vdw-14 26.14707120 26.14737960 0.00030840 0.00000000 -26.14707120 26.14722488 0.00015368 0.00000000 -26.14707120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.68949920 1.68956157 0.00006237 1.68956158 0.00006238 1.68942811 -0.00007109 1.68958288 0.00008368 bond 2.66395280 2.66399634 0.00004354 2.66399636 0.00004356 2.66397190 0.00001910 2.66399464 0.00004184 bonded 17.75605920 17.75624367 0.00018447 17.75625300 0.00019380 17.75600884 -0.00005036 17.75585000 -0.00020920 dihedral 13.40260720 13.40268576 0.00007856 13.40269506 0.00008786 13.40260883 0.00000163 13.40227248 -0.00033472 nonbonded 61.56714160 61.56994232 0.00280072 61.56994070 0.00279910 61.56974048 0.00259888 61.54103344 -0.02610816 potential 79.32320080 79.32618599 0.00298519 79.32619654 0.00299574 79.32567271 0.00247191 79.29692528 -0.02627552 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 79.32320080 Difference in potential energy from amber=>gromacs conversion: 0.00298519 Difference in potential energy from amber=>lammps conversion: 0.00299574 Difference in potential energy from amber=>desmond conversion: 0.00247191 Difference in potential energy from amber=>charmm conversion: -0.02627552 ======================================================================= INFO 2017-03-19 00:03:15 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6843802.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6843802.inpcrd') INFO 2017-03-19 00:03:15 Beginning InterMol conversion INFO 2017-03-19 00:03:15 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:03:15 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:03:15 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6854178.inpcrd INFO 2017-03-19 00:03:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6854178/mobley_6854178_converted.input INFO 2017-03-19 00:03:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6854178/mobley_6854178_converted.cms WARNING 2017-03-19 00:03:31 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:03:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6854178/mobley_6854178_converted.inp INFO 2017-03-19 00:03:31 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6854178/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6854178/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6854178/mobley_6854178_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6854178/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 47.08940078 47.08940078 0.00000000 0.00000000 0.00000000 0.00000000 -60.45382104 -60.45382104 coulomb total -60.45168720 -60.45354013 -0.00185293 -60.45354071 -0.00185351 -60.45348799 -0.00180079 -60.45382104 -0.00213384 coulomb-14 -107.53926000 -107.54294091 -0.00368091 0.00000000 107.53926000 -107.54298209 -0.00372209 0.00000000 107.53926000 improper 0.00000000 0.00001519 0.00001519 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 20.55850240 20.55867882 0.00017642 20.55869194 0.00018954 20.55865645 0.00015405 20.55854424 0.00004184 vdw (SR) 0.00000000 1.51308311 1.51308311 0.00000000 0.00000000 0.00000000 0.00000000 11.07078032 11.07078032 vdw total 11.07044560 11.07065948 0.00021388 11.07065940 0.00021380 11.07064516 0.00019956 11.07078032 0.00033472 vdw-14 9.55751120 9.55757637 0.00006517 0.00000000 -9.55751120 9.55755618 0.00004498 0.00000000 -9.55751120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.78612560 2.78622157 0.00009597 2.78622158 0.00009598 2.78633377 0.00020817 2.78629296 0.00016736 bond 1.57862320 1.57846499 -0.00015821 1.57846500 -0.00015820 1.57838814 -0.00023506 1.57845584 -0.00016736 bonded 24.92325120 24.92338057 0.00012937 24.92337852 0.00012732 24.92337837 0.00012717 24.92329304 0.00004184 dihedral 20.55850240 20.55869401 0.00019161 20.55869194 0.00018954 20.55865645 0.00015405 20.55854424 0.00004184 nonbonded -49.38124160 -49.38288065 -0.00163905 -49.38288173 -0.00164013 -49.38284284 -0.00160124 -49.38304072 -0.00179912 potential -24.45799040 -24.45950008 -0.00150968 -24.45950166 -0.00151126 -24.45949572 -0.00150532 -24.45974768 -0.00175728 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -24.45799040 Difference in potential energy from amber=>gromacs conversion: -0.00150968 Difference in potential energy from amber=>lammps conversion: -0.00151126 Difference in potential energy from amber=>desmond conversion: -0.00150532 Difference in potential energy from amber=>charmm conversion: -0.00175728 ======================================================================= INFO 2017-03-19 00:03:31 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6854178.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6854178.inpcrd') INFO 2017-03-19 00:03:31 Beginning InterMol conversion INFO 2017-03-19 00:03:31 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:03:31 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:03:31 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6861308.inpcrd INFO 2017-03-19 00:03:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6861308/mobley_6861308_converted.input INFO 2017-03-19 00:03:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6861308/mobley_6861308_converted.cms WARNING 2017-03-19 00:03:47 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:03:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6861308/mobley_6861308_converted.inp INFO 2017-03-19 00:03:47 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6861308/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6861308/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6861308/mobley_6861308_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6861308/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 106.06616209 106.06616209 0.00000000 0.00000000 0.00000000 0.00000000 -266.79334576 -266.79334576 coulomb total -266.71451920 -266.71128384 0.00323536 -266.71128078 0.00323842 -266.71110380 0.00341540 -266.79334576 -0.07882656 coulomb-14 -372.77473520 -372.77744593 -0.00271073 0.00000000 372.77473520 -372.77789538 -0.00316018 0.00000000 372.77473520 improper 0.00000000 0.09880740 0.09880740 0.00000000 0.00000000 0.00000000 0.00000000 0.09882608 0.09882608 proper 18.22592240 18.12721402 -0.09870838 18.22606675 0.00014435 18.22593859 0.00001619 18.12726368 -0.09865872 vdw (SR) 0.00000000 13.81931856 13.81931856 0.00000000 0.00000000 0.00000000 0.00000000 43.28465152 43.28465152 vdw total 43.28431680 43.28447477 0.00015797 43.28447579 0.00015899 43.28422852 -0.00008828 43.28465152 0.00033472 vdw-14 29.46498320 29.46515621 0.00017301 0.00000000 -29.46498320 29.46526081 0.00027761 0.00000000 -29.46498320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.62666720 4.62677950 0.00011230 4.62677933 0.00011213 4.62683937 0.00017217 4.62683456 0.00016736 bond 17.05649440 17.05649314 -0.00000126 17.05649314 -0.00000126 17.05623641 -0.00025799 17.05649440 0.00000000 bonded 39.90908400 39.90929406 0.00021006 39.90933922 0.00025522 39.90901438 -0.00006962 39.90941872 0.00033472 dihedral 18.22592240 18.22602142 0.00009902 18.22606675 0.00014435 18.22593859 0.00001619 18.22608976 0.00016736 nonbonded -223.43020240 -223.42680907 0.00339333 -223.42680499 0.00339741 -223.42687528 0.00332712 -223.50869424 -0.07849184 potential -183.52111840 -183.51751501 0.00360339 -183.51746577 0.00365263 -183.51793730 0.00318110 -183.59931736 -0.07819896 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -183.52111840 Difference in potential energy from amber=>gromacs conversion: 0.00360339 Difference in potential energy from amber=>lammps conversion: 0.00365263 Difference in potential energy from amber=>desmond conversion: 0.00318110 Difference in potential energy from amber=>charmm conversion: -0.07819896 ======================================================================= INFO 2017-03-19 00:03:47 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6861308.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6861308.inpcrd') INFO 2017-03-19 00:03:47 Beginning InterMol conversion INFO 2017-03-19 00:03:47 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:03:47 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:03:47 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6896128.inpcrd INFO 2017-03-19 00:03:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6896128/mobley_6896128_converted.input INFO 2017-03-19 00:03:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6896128/mobley_6896128_converted.cms WARNING 2017-03-19 00:04:03 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:04:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6896128/mobley_6896128_converted.inp INFO 2017-03-19 00:04:03 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6896128/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6896128/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6896128/mobley_6896128_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6896128/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 3.49735547 3.49735547 0.00000000 0.00000000 0.00000000 0.00000000 -1.33703904 -1.33703904 coulomb total -1.34766640 -1.34216720 0.00549920 -1.34216720 0.00549920 -1.34218969 0.00547671 -1.33703904 0.01062736 coulomb-14 -4.83963280 -4.83952267 0.00011013 0.00000000 4.83963280 -4.83952113 0.00011167 0.00000000 4.83963280 proper 10.68760960 10.68754373 -0.00006587 10.68754391 -0.00006569 10.68754609 -0.00006351 10.68752592 -0.00008368 vdw (SR) 0.00000000 8.01415413 8.01415413 0.00000000 0.00000000 0.00000000 0.00000000 20.42285712 20.42285712 vdw total 20.42294080 20.42260625 -0.00033455 20.42260650 -0.00033430 20.42283026 -0.00011054 20.42285712 -0.00008368 vdw-14 12.40848880 12.40845212 -0.00003668 0.00000000 -12.40848880 12.40853650 0.00004770 0.00000000 -12.40848880 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.91954720 4.91940483 -0.00014237 4.91940494 -0.00014226 4.91956975 0.00002255 4.91937984 -0.00016736 bond 1.10415760 1.10430787 0.00015027 1.10430789 0.00015029 1.10425923 0.00010163 1.10432496 0.00016736 bonded 16.71131440 16.71125643 -0.00005797 16.71125674 -0.00005766 16.71137506 0.00006066 16.71123072 -0.00008368 dihedral 10.68760960 10.68754373 -0.00006587 10.68754391 -0.00006569 10.68754609 -0.00006351 10.68752592 -0.00008368 nonbonded 19.07527440 19.08043905 0.00516465 19.08043955 0.00516515 19.08064057 0.00536617 19.08581808 0.01054368 potential 35.78658880 35.79169548 0.00510668 35.79169579 0.00510699 35.79193281 0.00534401 35.79704880 0.01046000 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 35.78658880 Difference in potential energy from amber=>gromacs conversion: 0.00510668 Difference in potential energy from amber=>lammps conversion: 0.00510699 Difference in potential energy from amber=>desmond conversion: 0.00534401 Difference in potential energy from amber=>charmm conversion: 0.01046000 ======================================================================= INFO 2017-03-19 00:04:03 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6896128.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6896128.inpcrd') INFO 2017-03-19 00:04:03 Beginning InterMol conversion INFO 2017-03-19 00:04:03 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:04:03 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:04:03 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6911232.inpcrd INFO 2017-03-19 00:04:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6911232/mobley_6911232_converted.input INFO 2017-03-19 00:04:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6911232/mobley_6911232_converted.cms WARNING 2017-03-19 00:04:19 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:04:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6911232/mobley_6911232_converted.inp INFO 2017-03-19 00:04:19 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6911232/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6911232/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6911232/mobley_6911232_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6911232/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 8.04048816 8.04048816 0.00000000 0.00000000 0.00000000 0.00000000 -8.48824816 -8.48824816 coulomb total -8.49059120 -8.48225391 0.00833729 -8.48225374 0.00833746 -8.48223374 0.00835746 -8.48824816 0.00234304 coulomb-14 -16.52303440 -16.52274208 0.00029232 0.00000000 16.52303440 -16.52271269 0.00032171 0.00000000 16.52303440 proper 3.17230880 3.17234203 0.00003323 3.17234202 0.00003322 3.17233675 0.00002795 3.17235064 0.00004184 vdw (SR) 0.00000000 -0.49595416 -0.49595416 0.00000000 0.00000000 0.00000000 0.00000000 3.01653848 3.01653848 vdw total 3.01666400 3.01650330 -0.00016070 3.01650338 -0.00016062 3.01645886 -0.00020514 3.01653848 -0.00012552 vdw-14 3.51246800 3.51245747 -0.00001053 0.00000000 -3.51246800 3.51241135 -0.00005665 0.00000000 -3.51246800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.39748000 0.39768644 0.00020644 0.39768643 0.00020643 0.39770362 0.00022362 0.39768920 0.00020920 bond 1.47737040 1.47720877 -0.00016163 1.47720877 -0.00016163 1.47726230 -0.00010810 1.47720304 -0.00016736 bonded 5.04715920 5.04723723 0.00007803 5.04723723 0.00007803 5.04730267 0.00014347 5.04724288 0.00008368 dihedral 3.17230880 3.17234203 0.00003323 3.17234202 0.00003322 3.17233675 0.00002795 3.17235064 0.00004184 nonbonded -5.47392720 -5.46575061 0.00817659 -5.46575041 0.00817679 -5.46577489 0.00815231 -5.47170968 0.00221752 potential -0.42676800 -0.41851337 0.00825463 -0.41851322 0.00825478 -0.41848921 0.00827879 -0.42446680 0.00230120 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -0.42676800 Difference in potential energy from amber=>gromacs conversion: 0.00825463 Difference in potential energy from amber=>lammps conversion: 0.00825478 Difference in potential energy from amber=>desmond conversion: 0.00827879 Difference in potential energy from amber=>charmm conversion: 0.00230120 ======================================================================= INFO 2017-03-19 00:04:19 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6911232.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6911232.inpcrd') INFO 2017-03-19 00:04:19 Beginning InterMol conversion INFO 2017-03-19 00:04:19 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:04:19 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:04:19 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6917738.inpcrd INFO 2017-03-19 00:04:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6917738/mobley_6917738_converted.input INFO 2017-03-19 00:04:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6917738/mobley_6917738_converted.cms WARNING 2017-03-19 00:04:35 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:04:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6917738/mobley_6917738_converted.inp INFO 2017-03-19 00:04:35 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6917738/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6917738/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6917738/mobley_6917738_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6917738/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -78.90660504 -78.90660504 0.00000000 0.00000000 0.00000000 0.00000000 71.84392424 71.84392424 coulomb total 71.87024160 71.89989039 0.02964879 71.89988942 0.02964782 71.89996850 0.02972690 71.84392424 -0.02631736 coulomb-14 150.79930960 150.80649543 0.00718583 0.00000000 -150.79930960 150.80653537 0.00722577 0.00000000 -150.79930960 proper 8.09813200 8.09800632 -0.00012568 8.09800648 -0.00012552 8.09802418 -0.00010782 8.09800648 -0.00012552 vdw (SR) 0.00000000 -0.73492036 -0.73492036 0.00000000 0.00000000 0.00000000 0.00000000 2.30810360 2.30810360 vdw total 2.30831280 2.30805692 -0.00025588 2.30805699 -0.00025581 2.30807168 -0.00024112 2.30810360 -0.00020920 vdw-14 3.04302320 3.04297728 -0.00004592 0.00000000 -3.04302320 3.04298292 -0.00004028 0.00000000 -3.04302320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 22.79987120 22.79965620 -0.00021500 22.79965614 -0.00021506 22.79940464 -0.00046656 22.79982936 -0.00004184 bond 4.35345200 4.35340757 -0.00004443 4.35340765 -0.00004435 4.35269742 -0.00075458 4.35341016 -0.00004184 bonded 35.25145520 35.25107009 -0.00038511 35.25107027 -0.00038493 35.25012624 -0.00132896 35.25124600 -0.00020920 dihedral 8.09813200 8.09800632 -0.00012568 8.09800648 -0.00012552 8.09802418 -0.00010782 8.09800648 -0.00012552 nonbonded 74.17855440 74.20794732 0.02939292 74.20794700 0.02939260 74.20804018 0.02948578 74.15202784 -0.02652656 potential 109.43000960 109.45901740 0.02900780 109.45901727 0.02900767 109.45814951 0.02813991 109.40323200 -0.02677760 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 109.43000960 Difference in potential energy from amber=>gromacs conversion: 0.02900780 Difference in potential energy from amber=>lammps conversion: 0.02900767 Difference in potential energy from amber=>desmond conversion: 0.02813991 Difference in potential energy from amber=>charmm conversion: -0.02677760 ======================================================================= INFO 2017-03-19 00:04:35 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6917738.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6917738.inpcrd') INFO 2017-03-19 00:04:35 Beginning InterMol conversion INFO 2017-03-19 00:04:35 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:04:35 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:04:35 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6929123.inpcrd INFO 2017-03-19 00:04:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6929123/mobley_6929123_converted.input INFO 2017-03-19 00:04:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6929123/mobley_6929123_converted.cms WARNING 2017-03-19 00:04:51 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:04:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6929123/mobley_6929123_converted.inp INFO 2017-03-19 00:04:51 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6929123/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6929123/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6929123/mobley_6929123_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6929123/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -30.13773916 -30.13773916 0.00000000 0.00000000 0.00000000 0.00000000 -53.60231184 -53.60231184 coulomb total -53.59411120 -53.58578976 0.00832144 -53.58578922 0.00832198 -53.58571613 0.00839507 -53.60231184 -0.00820064 coulomb-14 -23.45341200 -23.44805059 0.00536141 0.00000000 23.45341200 -23.44805824 0.00535376 0.00000000 23.45341200 improper 0.00000000 0.00000002 0.00000002 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 3.46435200 3.46454932 0.00019732 3.46454928 0.00019728 3.46453911 0.00018711 3.46456120 0.00020920 vdw (SR) 0.00000000 -0.76959286 -0.76959286 0.00000000 0.00000000 0.00000000 0.00000000 7.84604600 7.84604600 vdw total 7.84625520 7.84597316 -0.00028204 7.84597320 -0.00028200 7.84582907 -0.00042613 7.84604600 -0.00020920 vdw-14 8.61569280 8.61556602 -0.00012678 0.00000000 -8.61569280 8.61543322 -0.00025958 0.00000000 -8.61569280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.66978640 3.66972759 -0.00005881 3.66972757 -0.00005883 3.67021707 0.00043067 3.66978640 0.00000000 bond 1.53218080 1.53211454 -0.00006626 1.53211453 -0.00006627 1.53228516 0.00010436 1.53209712 -0.00008368 bonded 8.66631920 8.66639146 0.00007226 8.66639137 0.00007217 8.66704134 0.00072214 8.66644472 0.00012552 dihedral 3.46435200 3.46454934 0.00019734 3.46454928 0.00019728 3.46453911 0.00018711 3.46456120 0.00020920 nonbonded -45.74785600 -45.73981660 0.00803940 -45.73981435 0.00804165 -45.73988706 0.00796894 -45.75626584 -0.00840984 potential -37.08153680 -37.07342513 0.00811167 -37.07342444 0.00811236 -37.07288102 0.00865578 -37.08977928 -0.00824248 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -37.08153680 Difference in potential energy from amber=>gromacs conversion: 0.00811167 Difference in potential energy from amber=>lammps conversion: 0.00811236 Difference in potential energy from amber=>desmond conversion: 0.00865578 Difference in potential energy from amber=>charmm conversion: -0.00824248 ======================================================================= INFO 2017-03-19 00:04:51 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6929123.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6929123.inpcrd') INFO 2017-03-19 00:04:51 Beginning InterMol conversion INFO 2017-03-19 00:04:51 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:04:52 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:04:52 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6935906.inpcrd INFO 2017-03-19 00:04:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6935906/mobley_6935906_converted.input INFO 2017-03-19 00:04:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6935906/mobley_6935906_converted.cms WARNING 2017-03-19 00:05:07 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:05:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6935906/mobley_6935906_converted.inp INFO 2017-03-19 00:05:07 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6935906/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6935906/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6935906/mobley_6935906_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6935906/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 120.09314021 120.09314021 0.00000000 0.00000000 0.00000000 0.00000000 -199.14480200 -199.14480200 coulomb total -199.09856880 -199.10562228 -0.00705348 -199.10561884 -0.00705004 -199.10584227 -0.00727347 -199.14480200 -0.04623320 coulomb-14 -319.19401280 -319.19876249 -0.00474969 0.00000000 319.19401280 -319.19883988 -0.00482708 0.00000000 319.19401280 improper 0.00000000 0.00449174 0.00449174 0.00000000 0.00000000 0.00000000 0.00000000 0.00447688 0.00447688 proper 95.44582640 95.44152684 -0.00429956 95.44602723 0.00020083 95.44622346 0.00039706 95.44168424 -0.00414216 vdw (SR) 0.00000000 45.85153059 45.85153059 0.00000000 0.00000000 0.00000000 0.00000000 76.39996552 76.39996552 vdw total 76.39984000 76.39930444 -0.00053556 76.39930445 -0.00053555 76.39945762 -0.00038238 76.39996552 0.00012552 vdw-14 30.54780240 30.54777385 -0.00002855 0.00000000 -30.54780240 30.54771583 -0.00008657 0.00000000 -30.54780240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 16.09291920 16.09298825 0.00006905 16.09298824 0.00006904 16.09304384 0.00012464 16.09296104 0.00004184 bond 3.45431040 3.45426752 -0.00004288 3.45426751 -0.00004289 3.45466910 0.00035870 3.45426856 -0.00004184 bonded 114.99305600 114.99327435 0.00021835 114.99328298 0.00022698 114.99393640 0.00088040 114.99339072 0.00033472 dihedral 95.44582640 95.44601858 0.00019218 95.44602723 0.00020083 95.44622346 0.00039706 95.44616112 0.00033472 nonbonded -122.69872880 -122.70631784 -0.00758904 -122.70631439 -0.00758559 -122.70638464 -0.00765584 -122.74483648 -0.04610768 potential -7.70567280 -7.71304349 -0.00737069 -7.71303246 -0.00735966 -7.71263339 -0.00696059 -7.75144576 -0.04577296 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -7.70567280 Difference in potential energy from amber=>gromacs conversion: -0.00737069 Difference in potential energy from amber=>lammps conversion: -0.00735966 Difference in potential energy from amber=>desmond conversion: -0.00696059 Difference in potential energy from amber=>charmm conversion: -0.04577296 ======================================================================= INFO 2017-03-19 00:05:07 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6935906.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6935906.inpcrd') INFO 2017-03-19 00:05:08 Beginning InterMol conversion INFO 2017-03-19 00:05:08 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:05:08 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:05:08 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6973347.inpcrd INFO 2017-03-19 00:05:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6973347/mobley_6973347_converted.input INFO 2017-03-19 00:05:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6973347/mobley_6973347_converted.cms WARNING 2017-03-19 00:05:23 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:05:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6973347/mobley_6973347_converted.inp INFO 2017-03-19 00:05:23 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6973347/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6973347/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6973347/mobley_6973347_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6973347/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 9.62154331 9.62154331 0.00000000 0.00000000 0.00000000 0.00000000 -130.24193688 -130.24193688 coulomb total -130.19394640 -130.20286351 -0.00891711 -130.20286250 -0.00891610 -130.20297217 -0.00902577 -130.24193688 -0.04799048 coulomb-14 -139.81505440 -139.82440682 -0.00935242 0.00000000 139.81505440 -139.82443744 -0.00938304 0.00000000 139.81505440 improper 0.00000000 0.00000475 0.00000475 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 20.94384880 20.94372153 -0.00012727 20.94372746 -0.00012134 20.94374148 -0.00010732 20.94372328 -0.00012552 vdw (SR) 0.00000000 -1.55238104 -1.55238104 0.00000000 0.00000000 0.00000000 0.00000000 6.38859144 6.38859144 vdw total 6.38854960 6.38850839 -0.00004121 6.38850860 -0.00004100 6.38864675 0.00009715 6.38859144 0.00004184 vdw-14 7.94081360 7.94088943 0.00007583 0.00000000 -7.94081360 7.94098586 0.00017226 0.00000000 -7.94081360 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.05601760 2.05595038 -0.00006722 2.05595036 -0.00006724 2.05583179 -0.00018581 2.05601760 0.00000000 bond 1.73677840 1.73681259 0.00003419 1.73681258 0.00003418 1.73662260 -0.00015580 1.73682024 0.00004184 bonded 24.73664480 24.73648925 -0.00015555 24.73649041 -0.00015439 24.73619587 -0.00044893 24.73656112 -0.00008368 dihedral 20.94384880 20.94372628 -0.00012252 20.94372746 -0.00012134 20.94374148 -0.00010732 20.94372328 -0.00012552 nonbonded -123.80539680 -123.81435513 -0.00895833 -123.81435474 -0.00895794 -123.81432542 -0.00892862 -123.85334544 -0.04794864 potential -99.06875200 -99.07786587 -0.00911387 -99.07786475 -0.00911275 -99.07816307 -0.00941107 -99.11678432 -0.04803232 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -99.06875200 Difference in potential energy from amber=>gromacs conversion: -0.00911387 Difference in potential energy from amber=>lammps conversion: -0.00911275 Difference in potential energy from amber=>desmond conversion: -0.00941107 Difference in potential energy from amber=>charmm conversion: -0.04803232 ======================================================================= INFO 2017-03-19 00:05:23 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6973347.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6973347.inpcrd') INFO 2017-03-19 00:05:24 Beginning InterMol conversion INFO 2017-03-19 00:05:24 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:05:24 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:05:24 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6978427.inpcrd INFO 2017-03-19 00:05:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6978427/mobley_6978427_converted.input INFO 2017-03-19 00:05:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6978427/mobley_6978427_converted.cms WARNING 2017-03-19 00:05:40 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:05:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6978427/mobley_6978427_converted.inp INFO 2017-03-19 00:05:40 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6978427/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6978427/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6978427/mobley_6978427_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6978427/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -60.60146589 -60.60146589 0.00000000 0.00000000 0.00000000 0.00000000 -22.03796480 -22.03796480 coulomb total -22.02499440 -22.02854523 -0.00355083 -22.02854494 -0.00355054 -22.02814679 -0.00315239 -22.03796480 -0.01297040 coulomb-14 38.58359280 38.57292066 -0.01067214 0.00000000 -38.58359280 38.57287281 -0.01071999 0.00000000 -38.58359280 improper 0.00000000 0.00000269 0.00000269 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 15.16281600 15.16291857 0.00010257 15.16292144 0.00010544 15.16279077 -0.00002523 15.16327624 0.00046024 vdw (SR) 0.00000000 -1.77291126 -1.77291126 0.00000000 0.00000000 0.00000000 0.00000000 24.77438448 24.77438448 vdw total 24.77430080 24.77416785 -0.00013295 24.77416817 -0.00013263 24.77376279 -0.00053801 24.77438448 0.00008368 vdw-14 26.54706160 26.54707912 0.00001752 0.00000000 -26.54706160 26.54692303 -0.00013857 0.00000000 -26.54706160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 6.21031120 6.21021206 -0.00009914 6.21021204 -0.00009916 6.21059764 0.00028644 6.21018568 -0.00012552 bond 2.00037040 2.00023268 -0.00013772 2.00023266 -0.00013774 2.00120438 0.00083398 2.00024488 -0.00012552 bonded 23.37349760 23.37336600 -0.00013160 23.37336614 -0.00013146 23.37459279 0.00109519 23.37370680 0.00020920 dihedral 15.16281600 15.16292126 0.00010526 15.16292144 0.00010544 15.16279077 -0.00002523 15.16327624 0.00046024 nonbonded 2.74930640 2.74562262 -0.00368378 2.74562335 -0.00368305 2.74561600 -0.00369040 2.73641968 -0.01288672 potential 26.12280400 26.11898862 -0.00381538 26.11898945 -0.00381455 26.12011879 -0.00268521 26.11008464 -0.01271936 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 26.12280400 Difference in potential energy from amber=>gromacs conversion: -0.00381538 Difference in potential energy from amber=>lammps conversion: -0.00381455 Difference in potential energy from amber=>desmond conversion: -0.00268521 Difference in potential energy from amber=>charmm conversion: -0.01271936 ======================================================================= INFO 2017-03-19 00:05:40 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6978427.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6978427.inpcrd') INFO 2017-03-19 00:05:40 Beginning InterMol conversion INFO 2017-03-19 00:05:40 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:05:40 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:05:40 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6981465.inpcrd INFO 2017-03-19 00:05:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6981465/mobley_6981465_converted.input INFO 2017-03-19 00:05:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6981465/mobley_6981465_converted.cms WARNING 2017-03-19 00:05:56 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:05:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6981465/mobley_6981465_converted.inp INFO 2017-03-19 00:05:56 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6981465/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6981465/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6981465/mobley_6981465_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6981465/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 55.11598951 55.11598951 0.00000000 0.00000000 0.00000000 0.00000000 -151.92794360 -151.92794360 coulomb total -151.91811120 -151.92319195 -0.00508075 -151.92319058 -0.00507938 -151.92324915 -0.00513795 -151.92794360 -0.00983240 coulomb-14 -207.03226960 -207.03918145 -0.00691185 0.00000000 207.03226960 -207.03931085 -0.00704125 0.00000000 207.03226960 improper 0.00000000 0.00001313 0.00001313 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 31.63773440 31.63778194 0.00004754 31.63779423 0.00005983 31.63781335 0.00007895 31.63765072 -0.00008368 vdw (SR) 0.00000000 0.60761593 0.60761593 0.00000000 0.00000000 0.00000000 0.00000000 11.96038240 11.96038240 vdw total 11.96038240 11.96020884 -0.00017356 11.96020876 -0.00017364 11.96020454 -0.00017786 11.96038240 0.00000000 vdw-14 11.35286560 11.35259291 -0.00027269 0.00000000 -11.35286560 11.35262899 -0.00023661 0.00000000 -11.35286560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.60202960 2.60183971 -0.00018989 2.60183973 -0.00018987 2.60196769 -0.00006191 2.60190408 -0.00012552 bond 2.17986400 2.17996304 0.00009904 2.17996304 0.00009904 2.17962304 -0.00024096 2.17994768 0.00008368 bonded 36.41962800 36.41959782 -0.00003018 36.41959700 -0.00003100 36.41940409 -0.00022391 36.41950248 -0.00012552 dihedral 31.63773440 31.63779507 0.00006067 31.63779423 0.00005983 31.63781335 0.00007895 31.63765072 -0.00008368 nonbonded -139.95772880 -139.96298311 -0.00525431 -139.96297972 -0.00525092 -139.96304461 -0.00531581 -139.96756120 -0.00983240 potential -103.53810080 -103.54338528 -0.00528448 -103.54338519 -0.00528439 -103.54368184 -0.00558104 -103.54805872 -0.00995792 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -103.53810080 Difference in potential energy from amber=>gromacs conversion: -0.00528448 Difference in potential energy from amber=>lammps conversion: -0.00528439 Difference in potential energy from amber=>desmond conversion: -0.00558104 Difference in potential energy from amber=>charmm conversion: -0.00995792 ======================================================================= INFO 2017-03-19 00:05:56 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6981465.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6981465.inpcrd') INFO 2017-03-19 00:05:56 Beginning InterMol conversion INFO 2017-03-19 00:05:56 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:05:56 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:05:56 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6988468.inpcrd INFO 2017-03-19 00:05:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6988468/mobley_6988468_converted.input INFO 2017-03-19 00:05:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6988468/mobley_6988468_converted.cms WARNING 2017-03-19 00:06:12 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:06:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6988468/mobley_6988468_converted.inp INFO 2017-03-19 00:06:12 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6988468/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6988468/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6988468/mobley_6988468_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6988468/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -2.63907576 -2.63907576 0.00000000 0.00000000 0.00000000 0.00000000 -100.38508024 -100.38508024 coulomb total -100.38545680 -100.38368495 0.00177185 -100.38368278 0.00177402 -100.38391082 0.00154598 -100.38508024 0.00037656 coulomb-14 -97.74116880 -97.74460918 -0.00344038 0.00000000 97.74116880 -97.74487331 -0.00370451 0.00000000 97.74116880 improper 0.00000000 0.00010469 0.00010469 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.02092000 0.02090174 -0.00001826 0.02100649 0.00008649 0.02101250 0.00009250 0.02092000 0.00000000 vdw (SR) 0.00000000 -3.16477804 -3.16477804 0.00000000 0.00000000 0.00000000 0.00000000 19.97960416 19.97960416 vdw total 19.97943680 19.97961464 0.00017784 19.97961462 0.00017782 19.98005338 0.00061658 19.97960416 0.00016736 vdw-14 23.14421440 23.14439267 0.00017827 0.00000000 -23.14421440 23.14483280 0.00061840 0.00000000 -23.14421440 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.08446880 2.08434527 -0.00012353 2.08434529 -0.00012351 2.08426333 -0.00020547 2.08434328 -0.00012552 bond 1.52674160 1.52672342 -0.00001818 1.52672340 -0.00001820 1.52651536 -0.00022624 1.52674160 0.00000000 bonded 3.63213040 3.63207512 -0.00005528 3.63207518 -0.00005522 3.63179119 -0.00033921 3.63213040 0.00000000 dihedral 0.02092000 0.02100643 0.00008643 0.02100649 0.00008649 0.02101250 0.00009250 0.02104552 0.00012552 nonbonded -80.40602000 -80.40407031 0.00194969 -80.40407026 0.00194974 -80.40385744 0.00216256 -80.40547608 0.00054392 potential -76.77388960 -76.77199519 0.00189441 -76.77199425 0.00189535 -76.77212144 0.00176816 -76.77342936 0.00046024 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -76.77388960 Difference in potential energy from amber=>gromacs conversion: 0.00189441 Difference in potential energy from amber=>lammps conversion: 0.00189535 Difference in potential energy from amber=>desmond conversion: 0.00176816 Difference in potential energy from amber=>charmm conversion: 0.00046024 ======================================================================= INFO 2017-03-19 00:06:12 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6988468.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6988468.inpcrd') INFO 2017-03-19 00:06:12 Beginning InterMol conversion INFO 2017-03-19 00:06:12 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:06:12 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:06:12 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7009711.inpcrd INFO 2017-03-19 00:06:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7009711/mobley_7009711_converted.input INFO 2017-03-19 00:06:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7009711/mobley_7009711_converted.cms WARNING 2017-03-19 00:06:28 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:06:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7009711/mobley_7009711_converted.inp INFO 2017-03-19 00:06:28 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7009711/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7009711/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7009711/mobley_7009711_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7009711/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 109.97529372 109.97529372 0.00000000 0.00000000 0.00000000 0.00000000 -117.34032184 -117.34032184 coulomb total -117.33902480 -117.33706025 0.00196455 -117.33705832 0.00196648 -117.33768969 0.00133511 -117.34032184 -0.00129704 coulomb-14 -227.29789200 -227.31235397 -0.01446197 0.00000000 227.29789200 -227.31239500 -0.01450300 0.00000000 227.29789200 improper 0.00000000 0.00001677 0.00001677 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00000000 0.00015246 0.00015246 0.00016922 0.00016922 0.00016958 0.00016958 0.00016736 0.00016736 vdw (SR) 0.00000000 -2.94884511 -2.94884511 0.00000000 0.00000000 0.00000000 0.00000000 17.20038216 17.20038216 vdw total 17.20042400 17.20033114 -0.00009286 17.20033112 -0.00009288 17.20041694 -0.00000706 17.20038216 -0.00004184 vdw-14 20.14930720 20.14917624 -0.00013096 0.00000000 -20.14930720 20.14926051 -0.00004669 0.00000000 -20.14930720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.63471280 0.63490218 0.00018938 0.63490217 0.00018937 0.63480605 0.00009325 0.63492200 0.00020920 bond 2.16061760 2.16069174 0.00007414 2.16069174 0.00007414 2.16082867 0.00021107 2.16070128 0.00008368 bonded 2.79533040 2.79576315 0.00043275 2.79576313 0.00043273 2.79580431 0.00047391 2.79579064 0.00046024 dihedral 0.00000000 0.00016923 0.00016923 0.00016922 0.00016922 0.00016958 0.00016958 0.00016736 0.00016736 nonbonded -100.13860080 -100.13672912 0.00187168 -100.13672637 0.00187443 -100.13727274 0.00132806 -100.13993968 -0.00133888 potential -97.34327040 -97.34096597 0.00230443 -97.34096502 0.00230538 -97.34152400 0.00174640 -97.34419088 -0.00092048 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -97.34327040 Difference in potential energy from amber=>gromacs conversion: 0.00230443 Difference in potential energy from amber=>lammps conversion: 0.00230538 Difference in potential energy from amber=>desmond conversion: 0.00174640 Difference in potential energy from amber=>charmm conversion: -0.00092048 ======================================================================= INFO 2017-03-19 00:06:28 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7009711.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7009711.inpcrd') INFO 2017-03-19 00:06:28 Beginning InterMol conversion INFO 2017-03-19 00:06:28 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:06:28 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:06:28 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7010316.inpcrd INFO 2017-03-19 00:06:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7010316/mobley_7010316_converted.input INFO 2017-03-19 00:06:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7010316/mobley_7010316_converted.cms WARNING 2017-03-19 00:06:44 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:06:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7010316/mobley_7010316_converted.inp INFO 2017-03-19 00:06:44 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7010316/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7010316/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7010316/mobley_7010316_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7010316/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 19.13215439 19.13215439 0.00000000 0.00000000 0.00000000 0.00000000 -29.43649016 -29.43649016 coulomb total -29.40473360 -29.40563579 -0.00090219 -29.40563525 -0.00090165 -29.40578839 -0.00105479 -29.43649016 -0.03175656 coulomb-14 -48.53607360 -48.53779018 -0.00171658 0.00000000 48.53607360 -48.53780410 -0.00173050 0.00000000 48.53607360 proper 19.89743040 19.89736718 -0.00006322 19.89736722 -0.00006318 19.89744065 0.00001025 19.89743040 0.00000000 vdw (SR) 0.00000000 -2.99679120 -2.99679120 0.00000000 0.00000000 0.00000000 0.00000000 9.92101712 9.92101712 vdw total 9.92110080 9.92095756 -0.00014324 9.92095813 -0.00014267 9.92101087 -0.00008993 9.92101712 -0.00008368 vdw-14 12.91768160 12.91774876 0.00006716 0.00000000 -12.91768160 12.91781607 0.00013447 0.00000000 -12.91768160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.39073760 2.39091122 0.00017362 2.39091124 0.00017364 2.39095961 0.00022201 2.39082128 0.00008368 bond 1.07026720 1.07037079 0.00010359 1.07037080 0.00010360 1.07032660 0.00005940 1.07035088 0.00008368 bonded 23.35843520 23.35864918 0.00021398 23.35864925 0.00021405 23.35872686 0.00029166 23.35860256 0.00016736 dihedral 19.89743040 19.89736718 -0.00006322 19.89736722 -0.00006318 19.89744065 0.00001025 19.89743040 0.00000000 nonbonded -19.48363280 -19.48467823 -0.00104543 -19.48467754 -0.00104474 -19.48477751 -0.00114471 -19.51547304 -0.03184024 potential 3.87480240 3.87397095 -0.00083145 3.87397162 -0.00083078 3.87389469 -0.00090771 3.84321320 -0.03158920 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 3.87480240 Difference in potential energy from amber=>gromacs conversion: -0.00083145 Difference in potential energy from amber=>lammps conversion: -0.00083078 Difference in potential energy from amber=>desmond conversion: -0.00090771 Difference in potential energy from amber=>charmm conversion: -0.03158920 ======================================================================= INFO 2017-03-19 00:06:44 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7010316.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7010316.inpcrd') INFO 2017-03-19 00:06:44 Beginning InterMol conversion INFO 2017-03-19 00:06:44 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:06:44 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:06:44 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7015518.inpcrd INFO 2017-03-19 00:06:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7015518/mobley_7015518_converted.input INFO 2017-03-19 00:06:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7015518/mobley_7015518_converted.cms WARNING 2017-03-19 00:07:00 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:07:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7015518/mobley_7015518_converted.inp INFO 2017-03-19 00:07:00 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7015518/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7015518/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7015518/mobley_7015518_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7015518/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 4.20460424 4.20460424 0.00000000 0.00000000 0.00000000 0.00000000 13.22687920 13.22687920 coulomb total 13.22227680 13.22950148 0.00722468 13.22950131 0.00722451 13.22948801 0.00721121 13.22687920 0.00460240 coulomb-14 9.02070400 9.02489724 0.00419324 0.00000000 -9.02070400 9.02489290 0.00418890 0.00000000 -9.02070400 proper 0.00376560 0.00362639 -0.00013921 0.00362639 -0.00013921 0.00362807 -0.00013753 0.00364008 -0.00012552 vdw (SR) 0.00000000 -0.00283928 -0.00283928 0.00000000 0.00000000 0.00000000 0.00000000 3.02022040 3.02022040 vdw total 3.02001120 3.02019756 0.00018636 3.02019764 0.00018644 3.02017789 0.00016669 3.02022040 0.00020920 vdw-14 3.02294000 3.02303684 0.00009684 0.00000000 -3.02294000 3.02301351 0.00007351 0.00000000 -3.02294000 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.20334240 0.20339291 0.00005051 0.20339291 0.00005051 0.20332439 -0.00001801 0.20342608 0.00008368 bond 0.83721840 0.83727755 0.00005915 0.83727756 0.00005916 0.83733323 0.00011483 0.83726024 0.00004184 bonded 1.04432640 1.04429684 -0.00002956 1.04429686 -0.00002954 1.04428569 -0.00004071 1.04432640 0.00000000 dihedral 0.00376560 0.00362639 -0.00013921 0.00362639 -0.00013921 0.00362807 -0.00013753 0.00364008 -0.00012552 nonbonded 16.24228800 16.24969904 0.00741104 16.24969912 0.00741112 16.24966589 0.00737789 16.24709960 0.00481160 potential 17.28661440 17.29399588 0.00738148 17.29399581 0.00738141 17.29394247 0.00732807 17.29142600 0.00481160 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 17.28661440 Difference in potential energy from amber=>gromacs conversion: 0.00738148 Difference in potential energy from amber=>lammps conversion: 0.00738141 Difference in potential energy from amber=>desmond conversion: 0.00732807 Difference in potential energy from amber=>charmm conversion: 0.00481160 ======================================================================= INFO 2017-03-19 00:07:00 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7015518.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7015518.inpcrd') INFO 2017-03-19 00:07:00 Beginning InterMol conversion INFO 2017-03-19 00:07:00 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:07:00 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7017274.inpcrd INFO 2017-03-19 00:07:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7017274/mobley_7017274_converted.input INFO 2017-03-19 00:07:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7017274/mobley_7017274_converted.cms INFO 2017-03-19 00:07:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7017274/mobley_7017274_converted.rst7 WARNING 2017-03-19 00:07:16 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:07:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7017274/mobley_7017274_converted.inp INFO 2017-03-19 00:07:16 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7017274/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7017274/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7017274/mobley_7017274_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_7017274/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7017274/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -14.55336250 -14.55336250 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 12.14163328 12.14163328 coulomb total 12.18464480 12.17056567 -0.01407913 12.17056564 -0.01407916 12.17046267 -0.01418213 12.18464480 0.00000000 12.14163328 -0.04301152 coulomb-14 26.72362640 26.72392817 0.00030177 0.00000000 -26.72362640 26.72394392 0.00031752 26.72362640 0.00000000 0.00000000 -26.72362640 improper 0.00000000 0.00014717 0.00014717 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00016736 0.00016736 proper 0.00167360 0.00154217 -0.00013143 0.00168914 0.00001554 0.00168585 0.00001225 0.00167360 0.00000000 0.00154808 -0.00012552 vdw (SR) 0.00000000 -3.75789554 -3.75789554 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 41.27813064 41.27813064 vdw total 41.27850720 41.27815162 -0.00035558 41.27815156 -0.00035564 41.27809149 -0.00041571 41.27808880 -0.00041840 41.27813064 -0.00037656 vdw-14 45.03615760 45.03604716 -0.00011044 0.00000000 -45.03615760 45.03607266 -0.00008494 45.03615760 0.00000000 0.00000000 -45.03615760 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 8.39519600 8.39515055 -0.00004545 8.39515039 -0.00004561 8.39540616 0.00021016 8.39519600 0.00000000 8.39515416 -0.00004184 bond 15.95610240 15.95615652 0.00005412 15.95615637 0.00005397 15.95604115 -0.00006125 15.95610240 0.00000000 15.95614424 0.00004184 bonded 24.35297200 24.35299641 0.00002441 24.35299591 0.00002391 24.35313316 0.00016116 24.35297200 0.00000000 24.35301384 0.00004184 dihedral 0.00167360 0.00168934 0.00001574 0.00168914 0.00001554 0.00168585 0.00001225 0.00167360 0.00000000 0.00171544 0.00004184 nonbonded 53.46315200 53.44871728 -0.01443472 53.44871720 -0.01443480 53.44855416 -0.01459784 53.46273360 -0.00041840 53.41976392 -0.04338808 potential 77.81612400 77.80171370 -0.01441030 77.80171430 -0.01440970 77.80156033 -0.01456367 77.81570560 -0.00041840 77.77277776 -0.04334624 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 77.81612400 Difference in potential energy from amber=>gromacs conversion: -0.01441030 Difference in potential energy from amber=>lammps conversion: -0.01440970 Difference in potential energy from amber=>desmond conversion: -0.01456367 Difference in potential energy from amber=>amber conversion: -0.00041840 Difference in potential energy from amber=>charmm conversion: -0.04334624 ======================================================================= INFO 2017-03-19 00:07:16 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7017274.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7017274.inpcrd') INFO 2017-03-19 00:07:16 Beginning InterMol conversion INFO 2017-03-19 00:07:16 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:07:17 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7039935.inpcrd INFO 2017-03-19 00:07:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7039935/mobley_7039935_converted.input INFO 2017-03-19 00:07:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7039935/mobley_7039935_converted.cms INFO 2017-03-19 00:07:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7039935/mobley_7039935_converted.rst7 WARNING 2017-03-19 00:07:32 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:07:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7039935/mobley_7039935_converted.inp INFO 2017-03-19 00:07:32 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7039935/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7039935/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7039935/mobley_7039935_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_7039935/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7039935/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 5.54033343 5.54033343 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -45.08720240 -45.08720240 coulomb total -45.11816400 -45.10501839 0.01314561 -45.10501787 0.01314613 -45.10534573 0.01281827 -45.11816400 0.00000000 -45.08720240 0.03096160 coulomb-14 -50.64188080 -50.64535183 -0.00347103 0.00000000 50.64188080 -50.64530038 -0.00341958 -50.64188080 0.00000000 0.00000000 50.64188080 improper 0.00000000 0.00006219 0.00006219 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00052950 0.00011110 0.00059164 0.00017324 0.00057733 0.00015893 0.00041840 0.00000000 0.00054392 0.00012552 vdw (SR) 0.00000000 -2.80152166 -2.80152166 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 29.77485024 29.77485024 vdw total 29.77459920 29.77482403 0.00022483 29.77482430 0.00022510 29.77493731 0.00033811 29.77459920 0.00000000 29.77485024 0.00025104 vdw-14 32.57620560 32.57634569 0.00014009 0.00000000 -32.57620560 32.57650279 0.00029719 32.57620560 0.00000000 0.00000000 -32.57620560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.77652640 1.77646623 -0.00006017 1.77646623 -0.00006017 1.77628372 -0.00024268 1.77652640 0.00000000 1.77648456 -0.00004184 bond 4.74591120 4.74603371 0.00012251 4.74603379 0.00012259 4.74573024 -0.00018096 4.74591120 0.00000000 4.74603672 0.00012552 bonded 6.52285600 6.52309164 0.00023564 6.52309167 0.00023567 6.52259129 -0.00026471 6.52285600 0.00000000 6.52310704 0.00025104 dihedral 0.00041840 0.00059169 0.00017329 0.00059164 0.00017324 0.00057733 0.00015893 0.00041840 0.00000000 0.00058576 0.00016736 nonbonded -15.34356480 -15.33019436 0.01337044 -15.33019399 0.01337081 -15.33040842 0.01315638 -15.34356480 0.00000000 -15.31235216 0.03121264 potential -8.82070880 -8.80710273 0.01360607 -8.80710201 0.01360679 -8.80790216 0.01280664 -8.82070880 0.00000000 -8.78924512 0.03146368 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -8.82070880 Difference in potential energy from amber=>gromacs conversion: 0.01360607 Difference in potential energy from amber=>lammps conversion: 0.01360679 Difference in potential energy from amber=>desmond conversion: 0.01280664 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.03146368 ======================================================================= INFO 2017-03-19 00:07:32 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7039935.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7039935.inpcrd') INFO 2017-03-19 00:07:33 Beginning InterMol conversion INFO 2017-03-19 00:07:33 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:07:33 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:07:33 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7047032.inpcrd INFO 2017-03-19 00:07:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7047032/mobley_7047032_converted.input INFO 2017-03-19 00:07:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7047032/mobley_7047032_converted.cms WARNING 2017-03-19 00:07:48 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:07:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7047032/mobley_7047032_converted.inp INFO 2017-03-19 00:07:48 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7047032/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7047032/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7047032/mobley_7047032_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7047032/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 25.94000224 25.94000224 0.00000000 0.00000000 0.00000000 0.00000000 -41.71431264 -41.71431264 coulomb total -41.71238800 -41.71251617 -0.00012817 -41.71251561 -0.00012761 -41.71257180 -0.00018380 -41.71431264 -0.00192464 coulomb-14 -67.64356480 -67.65251841 -0.00895361 0.00000000 67.64356480 -67.65254325 -0.00897845 0.00000000 67.64356480 proper 9.46671840 9.46664038 -0.00007802 9.46664058 -0.00007782 9.46665221 -0.00006619 9.46663472 -0.00008368 vdw (SR) 0.00000000 -0.41753181 -0.41753181 0.00000000 0.00000000 0.00000000 0.00000000 5.13100656 5.13100656 vdw total 5.13083920 5.13092249 0.00008329 5.13092246 0.00008326 5.13098524 0.00014604 5.13100656 0.00016736 vdw-14 5.54840240 5.54845429 0.00005189 0.00000000 -5.54840240 5.54851169 0.00010929 0.00000000 -5.54840240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.85225680 1.85208114 -0.00017566 1.85208116 -0.00017564 1.85193284 -0.00032396 1.85204760 -0.00020920 bond 0.47990480 0.47990724 0.00000244 0.47990723 0.00000243 0.47980193 -0.00010287 0.47990480 0.00000000 bonded 11.79888000 11.79862876 -0.00025124 11.79862896 -0.00025104 11.79838697 -0.00049303 11.79858712 -0.00029288 dihedral 9.46671840 9.46664038 -0.00007802 9.46664058 -0.00007782 9.46665221 -0.00006619 9.46663472 -0.00008368 nonbonded -36.58154880 -36.58159368 -0.00004488 -36.58159315 -0.00004435 -36.58158657 -0.00003777 -36.58330608 -0.00175728 potential -24.78266880 -24.78296492 -0.00029612 -24.78296419 -0.00029539 -24.78323397 -0.00056517 -24.78467712 -0.00200832 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -24.78266880 Difference in potential energy from amber=>gromacs conversion: -0.00029612 Difference in potential energy from amber=>lammps conversion: -0.00029539 Difference in potential energy from amber=>desmond conversion: -0.00056517 Difference in potential energy from amber=>charmm conversion: -0.00200832 ======================================================================= INFO 2017-03-19 00:07:48 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7047032.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7047032.inpcrd') INFO 2017-03-19 00:07:49 Beginning InterMol conversion INFO 2017-03-19 00:07:49 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:07:49 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7066554.inpcrd INFO 2017-03-19 00:07:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7066554/mobley_7066554_converted.input INFO 2017-03-19 00:07:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7066554/mobley_7066554_converted.cms INFO 2017-03-19 00:08:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7066554/mobley_7066554_converted.rst7 WARNING 2017-03-19 00:08:04 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:08:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7066554/mobley_7066554_converted.inp INFO 2017-03-19 00:08:04 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7066554/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7066554/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7066554/mobley_7066554_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_7066554/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7066554/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 17.35281437 17.35281437 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -67.26424336 -67.26424336 coulomb total -67.23688000 -67.25521369 -0.01833369 -67.25521429 -0.01833429 -67.25572587 -0.01884587 -67.23688000 0.00000000 -67.26424336 -0.02736336 coulomb-14 -84.60801120 -84.60802806 -0.00001686 0.00000000 84.60801120 -84.60798819 0.00002301 -84.60801120 0.00000000 0.00000000 84.60801120 improper 0.00000000 0.00002000 0.00002000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00041840 0.00030790 -0.00011050 0.00032790 -0.00009050 0.00033168 -0.00008672 0.00041840 0.00000000 0.00029288 -0.00012552 vdw (SR) 0.00000000 -1.56478456 -1.56478456 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 14.30948920 14.30948920 vdw total 14.30928000 14.30947666 0.00019666 14.30947665 0.00019665 14.30951894 0.00023894 14.30928000 0.00000000 14.30948920 0.00020920 vdw-14 15.87409600 15.87426122 0.00016522 0.00000000 -15.87409600 15.87430039 0.00020439 15.87409600 0.00000000 0.00000000 -15.87409600 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.28785920 0.28790495 0.00004575 0.28790494 0.00004574 0.28786571 0.00000651 0.28785920 0.00000000 0.28790104 0.00004184 bond 0.83136080 0.83121663 -0.00014417 0.83121662 -0.00014418 0.83102717 -0.00033363 0.83136080 0.00000000 0.83123528 -0.00012552 bonded 1.11963840 1.11944948 -0.00018892 1.11944946 -0.00018894 1.11922456 -0.00041384 1.11963840 0.00000000 1.11942920 -0.00020920 dihedral 0.00041840 0.00032790 -0.00009050 0.00032790 -0.00009050 0.00033168 -0.00008672 0.00041840 0.00000000 0.00029288 -0.00012552 nonbonded -52.92760000 -52.94573703 -0.01813703 -52.94573764 -0.01813764 -52.94620692 -0.01860692 -52.92760000 0.00000000 -52.95475416 -0.02715416 potential -51.80796160 -51.82628755 -0.01832595 -51.82628752 -0.01832592 -51.82703436 -0.01907276 -51.80796160 0.00000000 -51.83532496 -0.02736336 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -51.80796160 Difference in potential energy from amber=>gromacs conversion: -0.01832595 Difference in potential energy from amber=>lammps conversion: -0.01832592 Difference in potential energy from amber=>desmond conversion: -0.01907276 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.02736336 ======================================================================= INFO 2017-03-19 00:08:04 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7066554.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7066554.inpcrd') INFO 2017-03-19 00:08:05 Beginning InterMol conversion INFO 2017-03-19 00:08:05 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:08:05 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:08:05 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7099614.inpcrd INFO 2017-03-19 00:08:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7099614/mobley_7099614_converted.input INFO 2017-03-19 00:08:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7099614/mobley_7099614_converted.cms WARNING 2017-03-19 00:08:20 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:08:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7099614/mobley_7099614_converted.inp INFO 2017-03-19 00:08:21 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7099614/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7099614/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7099614/mobley_7099614_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7099614/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -1.14537775 -1.14537775 0.00000000 0.00000000 0.00000000 0.00000000 16.70872032 16.70872032 coulomb total 16.71508000 16.71531594 0.00023594 16.71531556 0.00023556 16.71528327 0.00020327 16.70872032 -0.00635968 coulomb-14 17.86024080 17.86069370 0.00045290 0.00000000 -17.86024080 17.86069669 0.00045589 0.00000000 -17.86024080 improper 0.00000000 0.00261864 0.00261864 0.00000000 0.00000000 0.00000000 0.00000000 0.00263592 0.00263592 proper 0.01882800 0.01612409 -0.00270391 0.01874241 -0.00008559 0.01872090 -0.00010710 0.01610840 -0.00271960 vdw (SR) 0.00000000 -0.23695698 -0.23695698 0.00000000 0.00000000 0.00000000 0.00000000 0.25417800 0.25417800 vdw total 0.25438720 0.25417188 -0.00021532 0.25417189 -0.00021531 0.25415881 -0.00022839 0.25417800 -0.00020920 vdw-14 0.49120160 0.49112886 -0.00007274 0.00000000 -0.49120160 0.49112013 -0.00008147 0.00000000 -0.49120160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.49117760 1.49098803 -0.00018957 1.49098802 -0.00018958 1.49084609 -0.00033151 1.49096840 -0.00020920 bond 0.98072960 0.98065105 -0.00007855 0.98065107 -0.00007853 0.98055132 -0.00017828 0.98064592 -0.00008368 bonded 2.49073520 2.49038183 -0.00035337 2.49038150 -0.00035370 2.49011831 -0.00061689 2.49035864 -0.00037656 dihedral 0.01882800 0.01874274 -0.00008526 0.01874241 -0.00008559 0.01872090 -0.00010710 0.01874432 -0.00008368 nonbonded 16.96946720 16.96948782 0.00002062 16.96948770 0.00002050 16.96944208 -0.00002512 16.96289832 -0.00656888 potential 19.46020240 19.45986965 -0.00033275 19.45986894 -0.00033346 19.45954417 -0.00065823 19.45329880 -0.00690360 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 19.46020240 Difference in potential energy from amber=>gromacs conversion: -0.00033275 Difference in potential energy from amber=>lammps conversion: -0.00033346 Difference in potential energy from amber=>desmond conversion: -0.00065823 Difference in potential energy from amber=>charmm conversion: -0.00690360 ======================================================================= INFO 2017-03-19 00:08:21 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7099614.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7099614.inpcrd') INFO 2017-03-19 00:08:21 Beginning InterMol conversion INFO 2017-03-19 00:08:21 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:08:21 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:08:21 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7106722.inpcrd INFO 2017-03-19 00:08:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7106722/mobley_7106722_converted.input INFO 2017-03-19 00:08:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7106722/mobley_7106722_converted.cms WARNING 2017-03-19 00:08:37 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:08:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7106722/mobley_7106722_converted.inp INFO 2017-03-19 00:08:37 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7106722/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7106722/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7106722/mobley_7106722_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7106722/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 7.90748820 7.90748820 0.00000000 0.00000000 0.00000000 0.00000000 -1.93936768 -1.93936768 coulomb total -1.92589520 -1.94134423 -0.01544903 -1.94134420 -0.01544900 -1.94139219 -0.01549699 -1.93936768 -0.01347248 coulomb-14 -9.84871760 -9.84883243 -0.00011483 0.00000000 9.84871760 -9.84883396 -0.00011636 0.00000000 9.84871760 proper 5.51367520 5.51384226 0.00016706 5.51384005 0.00016485 5.51384524 0.00017004 5.51384256 0.00016736 vdw (SR) 0.00000000 5.91123263 5.91123263 0.00000000 0.00000000 0.00000000 0.00000000 14.84621272 14.84621272 vdw total 14.84608720 14.84602378 -0.00006342 14.84602402 -0.00006318 14.84601457 -0.00007263 14.84621272 0.00012552 vdw-14 8.93493200 8.93479116 -0.00014084 0.00000000 -8.93493200 8.93467912 -0.00025288 0.00000000 -8.93493200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.89449120 2.89457856 0.00008736 2.89457856 0.00008736 2.89437543 -0.00011577 2.89457488 0.00008368 bond 0.63429440 0.63424558 -0.00004882 0.63424557 -0.00004883 0.63429287 -0.00000153 0.63425256 -0.00004184 bonded 9.04246080 9.04266640 0.00020560 9.04266418 0.00020338 9.04251354 0.00005274 9.04267000 0.00020920 dihedral 5.51367520 5.51384226 0.00016706 5.51384005 0.00016485 5.51384524 0.00017004 5.51384256 0.00016736 nonbonded 12.92019200 12.90467955 -0.01551245 12.90467982 -0.01551218 12.90462237 -0.01556963 12.90684504 -0.01334696 potential 21.96265280 21.94734595 -0.01530685 21.94734396 -0.01530884 21.94708878 -0.01556402 21.94947320 -0.01317960 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 21.96265280 Difference in potential energy from amber=>gromacs conversion: -0.01530685 Difference in potential energy from amber=>lammps conversion: -0.01530884 Difference in potential energy from amber=>desmond conversion: -0.01556402 Difference in potential energy from amber=>charmm conversion: -0.01317960 ======================================================================= INFO 2017-03-19 00:08:37 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7106722.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7106722.inpcrd') INFO 2017-03-19 00:08:37 Beginning InterMol conversion INFO 2017-03-19 00:08:37 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:08:37 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:08:37 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7142697.inpcrd INFO 2017-03-19 00:08:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7142697/mobley_7142697_converted.input INFO 2017-03-19 00:08:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7142697/mobley_7142697_converted.cms WARNING 2017-03-19 00:08:53 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:08:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7142697/mobley_7142697_converted.inp INFO 2017-03-19 00:08:53 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7142697/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7142697/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7142697/mobley_7142697_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7142697/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 9.70854548 9.70854548 0.00000000 0.00000000 0.00000000 0.00000000 0.46743648 0.46743648 coulomb total 0.46986320 0.44361941 -0.02624379 0.44361939 -0.02624381 0.44354132 -0.02632188 0.46743648 -0.00242672 coulomb-14 -9.25919200 -9.26492607 -0.00573407 0.00000000 9.25919200 -9.26500270 -0.00581070 0.00000000 9.25919200 proper 8.37720480 8.37735765 0.00015285 8.37735752 0.00015272 8.37741952 0.00021472 8.37737216 0.00016736 vdw (SR) 0.00000000 -1.74897091 -1.74897091 0.00000000 0.00000000 0.00000000 0.00000000 3.55999824 3.55999824 vdw total 3.56016560 3.55991435 -0.00025125 3.55991439 -0.00025121 3.55992677 -0.00023883 3.55999824 -0.00016736 vdw-14 5.30907760 5.30888526 -0.00019234 0.00000000 -5.30907760 5.30888334 -0.00019426 0.00000000 -5.30907760 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 21.18024480 21.18034850 0.00010370 21.18034856 0.00010376 21.18022944 -0.00001536 21.18049584 0.00025104 bond 2.52127840 2.52111112 -0.00016728 2.52111112 -0.00016728 2.52057856 -0.00069984 2.52111104 -0.00016736 bonded 32.07872800 32.07881726 0.00008926 32.07881720 0.00008920 32.07822753 -0.00050047 32.07897904 0.00025104 dihedral 8.37720480 8.37735765 0.00015285 8.37735752 0.00015272 8.37741952 0.00021472 8.37737216 0.00016736 nonbonded 4.03002880 4.00353376 -0.02649504 4.00353379 -0.02649501 4.00346809 -0.02656071 4.02743472 -0.00259408 potential 36.10875680 36.08235102 -0.02640578 36.08235116 -0.02640564 36.08165515 -0.02710165 36.10641376 -0.00234304 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 36.10875680 Difference in potential energy from amber=>gromacs conversion: -0.02640578 Difference in potential energy from amber=>lammps conversion: -0.02640564 Difference in potential energy from amber=>desmond conversion: -0.02710165 Difference in potential energy from amber=>charmm conversion: -0.00234304 ======================================================================= INFO 2017-03-19 00:08:53 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7142697.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7142697.inpcrd') INFO 2017-03-19 00:08:53 Beginning InterMol conversion INFO 2017-03-19 00:08:53 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:08:53 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7150646.inpcrd INFO 2017-03-19 00:08:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7150646/mobley_7150646_converted.input INFO 2017-03-19 00:08:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7150646/mobley_7150646_converted.cms INFO 2017-03-19 00:09:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7150646/mobley_7150646_converted.rst7 WARNING 2017-03-19 00:09:09 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:09:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7150646/mobley_7150646_converted.inp INFO 2017-03-19 00:09:09 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7150646/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7150646/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7150646/mobley_7150646_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_7150646/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7150646/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -6.06830351 -6.06830351 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -9.51077592 -9.51077592 coulomb total -9.48847520 -9.51177084 -0.02329564 -9.51177088 -0.02329568 -9.51182174 -0.02334654 -9.48847520 0.00000000 -9.51077592 -0.02230072 coulomb-14 -3.43464560 -3.44346734 -0.00882174 0.00000000 3.43464560 -3.44352462 -0.00887902 -3.43464560 0.00000000 0.00000000 3.43464560 improper 0.00000000 0.00002679 0.00002679 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00024910 -0.00016930 0.00027587 -0.00014253 0.00027582 -0.00014258 0.00041840 0.00000000 0.00025104 -0.00016736 vdw (SR) 0.00000000 -1.82557940 -1.82557940 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 13.25403336 13.25403336 vdw total 13.25407520 13.25404043 -0.00003477 13.25404047 -0.00003473 13.25412981 0.00005461 13.25407520 0.00000000 13.25403336 -0.00004184 vdw-14 15.07955440 15.07961983 0.00006543 0.00000000 -15.07955440 15.07971306 0.00015866 15.07955440 0.00000000 0.00000000 -15.07955440 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.50331120 1.50331597 0.00000477 1.50331597 0.00000477 1.50318456 -0.00012664 1.50331120 0.00000000 1.50339488 0.00008368 bond 0.82424800 0.82431677 0.00006877 0.82431678 0.00006878 0.82422699 -0.00002101 0.82424800 0.00000000 0.82433168 0.00008368 bonded 2.32797760 2.32790864 -0.00006896 2.32790863 -0.00006897 2.32768738 -0.00029022 2.32797760 0.00000000 2.32801944 0.00004184 dihedral 0.00041840 0.00027589 -0.00014251 0.00027587 -0.00014253 0.00027582 -0.00014258 0.00041840 0.00000000 0.00029288 -0.00012552 nonbonded 3.76560000 3.74226959 -0.02333041 3.74226972 -0.02333028 3.74230808 -0.02329192 3.76560000 0.00000000 3.74325744 -0.02234256 potential 6.09357760 6.07017823 -0.02339937 6.07017816 -0.02339944 6.06992616 -0.02365144 6.09357760 0.00000000 6.07119320 -0.02238440 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 6.09357760 Difference in potential energy from amber=>gromacs conversion: -0.02339937 Difference in potential energy from amber=>lammps conversion: -0.02339944 Difference in potential energy from amber=>desmond conversion: -0.02365144 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.02238440 ======================================================================= INFO 2017-03-19 00:09:09 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7150646.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7150646.inpcrd') INFO 2017-03-19 00:09:09 Beginning InterMol conversion INFO 2017-03-19 00:09:09 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:09:09 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:09:09 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7157427.inpcrd INFO 2017-03-19 00:09:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7157427/mobley_7157427_converted.input INFO 2017-03-19 00:09:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7157427/mobley_7157427_converted.cms WARNING 2017-03-19 00:09:25 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:09:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7157427/mobley_7157427_converted.inp INFO 2017-03-19 00:09:25 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7157427/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7157427/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7157427/mobley_7157427_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7157427/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 7.87424187 7.87424187 0.00000000 0.00000000 0.00000000 0.00000000 3.66819648 3.66819648 coulomb total 3.68819600 3.67609774 -0.01209826 3.67609771 -0.01209829 3.67605366 -0.01214234 3.66819648 -0.01999952 coulomb-14 -4.19487840 -4.19814413 -0.00326573 0.00000000 4.19487840 -4.19814435 -0.00326595 0.00000000 4.19487840 proper 10.03490560 10.03471542 -0.00019018 10.03471523 -0.00019037 10.03470887 -0.00019673 10.03473824 -0.00016736 vdw (SR) 0.00000000 -3.06914176 -3.06914176 0.00000000 0.00000000 0.00000000 0.00000000 4.74197824 4.74197824 vdw total 4.74214560 4.74184430 -0.00030130 4.74184435 -0.00030125 4.74188335 -0.00026225 4.74197824 -0.00016736 vdw-14 7.81110960 7.81098606 -0.00012354 0.00000000 -7.81110960 7.81102102 -0.00008858 0.00000000 -7.81110960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.14720480 3.14717574 -0.00002906 3.14717576 -0.00002904 3.14721864 0.00001384 3.14716296 -0.00004184 bond 0.95604400 0.95608212 0.00003812 0.95608212 0.00003812 0.95599353 -0.00005047 0.95608584 0.00004184 bonded 14.13815440 14.13797329 -0.00018111 14.13797311 -0.00018129 14.13792104 -0.00023336 14.13798704 -0.00016736 dihedral 10.03490560 10.03471542 -0.00019018 10.03471523 -0.00019037 10.03470887 -0.00019673 10.03473824 -0.00016736 nonbonded 8.43034160 8.41794205 -0.01239955 8.41794190 -0.01239970 8.41793700 -0.01240460 8.41017472 -0.02016688 potential 22.56849600 22.55591533 -0.01258067 22.55591555 -0.01258045 22.55577568 -0.01272032 22.54811992 -0.02037608 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 22.56849600 Difference in potential energy from amber=>gromacs conversion: -0.01258067 Difference in potential energy from amber=>lammps conversion: -0.01258045 Difference in potential energy from amber=>desmond conversion: -0.01272032 Difference in potential energy from amber=>charmm conversion: -0.02037608 ======================================================================= INFO 2017-03-19 00:09:25 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7157427.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7157427.inpcrd') INFO 2017-03-19 00:09:25 Beginning InterMol conversion INFO 2017-03-19 00:09:25 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:09:26 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:09:26 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7176248.inpcrd INFO 2017-03-19 00:09:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7176248/mobley_7176248_converted.input INFO 2017-03-19 00:09:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7176248/mobley_7176248_converted.cms WARNING 2017-03-19 00:09:41 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:09:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7176248/mobley_7176248_converted.inp INFO 2017-03-19 00:09:41 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7176248/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7176248/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7176248/mobley_7176248_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7176248/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 171.04187038 171.04187038 0.00000000 0.00000000 0.00000000 0.00000000 -107.40871920 -107.40871920 coulomb total -107.45265120 -107.44724567 0.00540553 -107.44724547 0.00540573 -107.44684423 0.00580697 -107.40871920 0.04393200 coulomb-14 -278.48704000 -278.48911605 -0.00207605 0.00000000 278.48704000 -278.48884205 -0.00180205 0.00000000 278.48704000 improper 0.00000000 0.00140716 0.00140716 0.00000000 0.00000000 0.00000000 0.00000000 0.00142256 0.00142256 proper 75.43500960 75.43360496 -0.00140464 75.43501378 0.00000418 75.43500834 -0.00000126 75.43362888 -0.00138072 vdw (SR) 0.00000000 -15.03248150 -15.03248150 0.00000000 0.00000000 0.00000000 0.00000000 24.26887360 24.26887360 vdw total 24.26887360 24.26872888 -0.00014472 24.26872883 -0.00014477 24.26831399 -0.00055961 24.26887360 0.00000000 vdw-14 39.30114880 39.30121038 0.00006158 0.00000000 -39.30114880 39.30110424 -0.00004456 0.00000000 -39.30114880 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 13.09717520 13.09725568 0.00008048 13.09725553 0.00008033 13.09808731 0.00091211 13.09725888 0.00008368 bond 29.24699680 29.24688846 -0.00010834 29.24688843 -0.00010837 29.24951599 0.00251919 29.24687128 -0.00012552 bonded 117.77918160 117.77915627 -0.00002533 117.77915775 -0.00002385 117.78261164 0.00343004 117.77918160 0.00000000 dihedral 75.43500960 75.43501212 0.00000252 75.43501378 0.00000418 75.43500834 -0.00000126 75.43505144 0.00004184 nonbonded -83.18377760 -83.17851679 0.00526081 -83.17851413 0.00526347 -83.17853024 0.00524736 -83.13984560 0.04393200 potential 34.59540400 34.60063947 0.00523547 34.60064111 0.00523711 34.60369962 0.00829562 34.63937784 0.04397384 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 34.59540400 Difference in potential energy from amber=>gromacs conversion: 0.00523547 Difference in potential energy from amber=>lammps conversion: 0.00523711 Difference in potential energy from amber=>desmond conversion: 0.00829562 Difference in potential energy from amber=>charmm conversion: 0.04397384 ======================================================================= INFO 2017-03-19 00:09:41 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7176248.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7176248.inpcrd') INFO 2017-03-19 00:09:42 Beginning InterMol conversion INFO 2017-03-19 00:09:42 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:09:42 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7176290.inpcrd INFO 2017-03-19 00:09:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7176290/mobley_7176290_converted.input INFO 2017-03-19 00:09:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7176290/mobley_7176290_converted.cms INFO 2017-03-19 00:09:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7176290/mobley_7176290_converted.rst7 WARNING 2017-03-19 00:09:57 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:09:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7176290/mobley_7176290_converted.inp INFO 2017-03-19 00:09:57 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7176290/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7176290/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7176290/mobley_7176290_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_7176290/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7176290/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -15.92901921 -15.92901921 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -33.51300320 -33.51300320 coulomb total -33.49835920 -33.51323185 -0.01487265 -33.51323165 -0.01487245 -33.51352649 -0.01516729 -33.49835920 0.00000000 -33.51300320 -0.01464400 coulomb-14 -17.58367840 -17.58421264 -0.00053424 0.00000000 17.58367840 -17.58415249 -0.00047409 -17.58367840 0.00000000 0.00000000 17.58367840 improper 0.00000000 0.00002504 0.00002504 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00024038 -0.00017802 0.00026540 -0.00015300 0.00026809 -0.00015031 0.00041840 0.00000000 0.00025104 -0.00016736 vdw (SR) 0.00000000 1.61662863 1.61662863 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 26.02343400 26.02343400 vdw total 26.02364320 26.02335839 -0.00028481 26.02335827 -0.00028493 26.02328279 -0.00036041 26.02322480 -0.00041840 26.02343400 -0.00020920 vdw-14 24.40694560 24.40672976 -0.00021584 0.00000000 -24.40694560 24.40669443 -0.00025117 24.40652720 -0.00041840 0.00000000 -24.40694560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.23260640 1.23276519 0.00015879 1.23276518 0.00015878 1.23270314 0.00009674 1.23260640 0.00000000 1.23277376 0.00016736 bond 11.95285120 11.95295638 0.00010518 11.95295622 0.00010502 11.95301136 0.00016016 11.95285120 0.00000000 11.95297672 0.00012552 bonded 13.18587600 13.18598699 0.00011099 13.18598680 0.00011080 13.18598259 0.00010659 13.18587600 0.00000000 13.18604336 0.00016736 dihedral 0.00041840 0.00026542 -0.00015298 0.00026540 -0.00015300 0.00026809 -0.00015031 0.00041840 0.00000000 0.00029288 -0.00012552 nonbonded -7.47471600 -7.48987346 -0.01515746 -7.48987296 -0.01515696 -7.49024370 -0.01552770 -7.47513440 -0.00041840 -7.48956920 -0.01485320 potential 5.71116000 5.69611353 -0.01504647 5.69611392 -0.01504608 5.69567594 -0.01548406 5.71074160 -0.00041840 5.69643232 -0.01472768 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 5.71116000 Difference in potential energy from amber=>gromacs conversion: -0.01504647 Difference in potential energy from amber=>lammps conversion: -0.01504608 Difference in potential energy from amber=>desmond conversion: -0.01548406 Difference in potential energy from amber=>amber conversion: -0.00041840 Difference in potential energy from amber=>charmm conversion: -0.01472768 ======================================================================= INFO 2017-03-19 00:09:57 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7176290.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7176290.inpcrd') INFO 2017-03-19 00:09:58 Beginning InterMol conversion INFO 2017-03-19 00:09:58 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:09:58 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:09:58 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_718988.inpcrd INFO 2017-03-19 00:09:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_718988/mobley_718988_converted.input INFO 2017-03-19 00:09:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_718988/mobley_718988_converted.cms WARNING 2017-03-19 00:10:14 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:10:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_718988/mobley_718988_converted.inp INFO 2017-03-19 00:10:14 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_718988/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_718988/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_718988/mobley_718988_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_718988/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 12.70910723 12.70910723 0.00000000 0.00000000 0.00000000 0.00000000 0.93608632 0.93608632 coulomb total 0.93721600 0.92076752 -0.01644848 0.92076752 -0.01644848 0.92069857 -0.01651743 0.93608632 -0.00112968 coulomb-14 -11.78507280 -11.78833971 -0.00326691 0.00000000 11.78507280 -11.78837059 -0.00329779 0.00000000 11.78507280 proper 11.80264560 11.80244733 -0.00019827 11.80244728 -0.00019832 11.80247581 -0.00016979 11.80243640 -0.00020920 vdw (SR) 0.00000000 -3.10289007 -3.10289007 0.00000000 0.00000000 0.00000000 0.00000000 5.05059008 5.05059008 vdw total 5.05050640 5.05046517 -0.00004123 5.05046540 -0.00004100 5.05045400 -0.00005240 5.05059008 0.00008368 vdw-14 8.15336080 8.15335524 -0.00000556 0.00000000 -8.15336080 8.15333783 -0.00002297 0.00000000 -8.15336080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 23.22078160 23.22095799 0.00017639 23.22095816 0.00017656 23.22102599 0.00024439 23.22107448 0.00029288 bond 2.30454720 2.30457340 0.00002620 2.30457339 0.00002619 2.30513038 0.00058318 2.30458904 0.00004184 bonded 37.32797440 37.32797872 0.00000432 37.32797884 0.00000444 37.32863218 0.00065778 37.32809992 0.00012552 dihedral 11.80264560 11.80244733 -0.00019827 11.80244728 -0.00019832 11.80247581 -0.00016979 11.80243640 -0.00020920 nonbonded 5.98772240 5.97123270 -0.01648970 5.97123284 -0.01648956 5.97115258 -0.01656982 5.98667640 -0.00104600 potential 43.31569680 43.29921142 -0.01648538 43.29921184 -0.01648496 43.29970764 -0.01598916 43.31477632 -0.00092048 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 43.31569680 Difference in potential energy from amber=>gromacs conversion: -0.01648538 Difference in potential energy from amber=>lammps conversion: -0.01648496 Difference in potential energy from amber=>desmond conversion: -0.01598916 Difference in potential energy from amber=>charmm conversion: -0.00092048 ======================================================================= INFO 2017-03-19 00:10:14 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_718988.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_718988.inpcrd') INFO 2017-03-19 00:10:14 Beginning InterMol conversion INFO 2017-03-19 00:10:14 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:10:14 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7200804.inpcrd INFO 2017-03-19 00:10:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7200804/mobley_7200804_converted.input INFO 2017-03-19 00:10:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7200804/mobley_7200804_converted.cms INFO 2017-03-19 00:10:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7200804/mobley_7200804_converted.rst7 WARNING 2017-03-19 00:10:29 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:10:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7200804/mobley_7200804_converted.inp INFO 2017-03-19 00:10:30 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7200804/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7200804/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7200804/mobley_7200804_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_7200804/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7200804/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -54.08484735 -54.08484735 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -16.07710368 -16.07710368 coulomb total -16.07199920 -16.07977409 -0.00777489 -16.07977391 -0.00777471 -16.07963253 -0.00763333 -16.07199920 0.00000000 -16.07710368 -0.00510448 coulomb-14 38.00327200 38.00507326 0.00180126 0.00000000 -38.00327200 38.00499702 0.00172502 38.00327200 0.00000000 0.00000000 -38.00327200 improper 0.00000000 0.00002948 0.00002948 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00035256 -0.00006584 0.00038198 -0.00003642 0.00037857 -0.00003983 0.00041840 0.00000000 0.00033472 -0.00008368 vdw (SR) 0.00000000 -1.24866511 -1.24866511 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 16.20438096 16.20438096 vdw total 16.20463200 16.20442790 -0.00020410 16.20442782 -0.00020418 16.20444505 -0.00018695 16.20463200 0.00000000 16.20438096 -0.00025104 vdw-14 17.45313760 17.45309301 -0.00004459 0.00000000 -17.45313760 17.45310814 -0.00002946 17.45313760 0.00000000 0.00000000 -17.45313760 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.26317360 0.26307099 -0.00010261 0.26307099 -0.00010261 0.26301922 -0.00015438 0.26317360 0.00000000 0.26308992 -0.00008368 bond 0.77906080 0.77915600 0.00009520 0.77915599 0.00009519 0.77896916 -0.00009164 0.77906080 0.00000000 0.77914448 0.00008368 bonded 1.04265280 1.04260904 -0.00004376 1.04260896 -0.00004384 1.04236695 -0.00028585 1.04265280 0.00000000 1.04261096 -0.00004184 dihedral 0.00041840 0.00038205 -0.00003635 0.00038198 -0.00003642 0.00037857 -0.00003983 0.00041840 0.00000000 0.00037656 -0.00004184 nonbonded 0.13263280 0.12465381 -0.00797899 0.12465401 -0.00797879 0.12481252 -0.00782028 0.13263280 0.00000000 0.12727728 -0.00535552 potential 1.17528560 1.16726285 -0.00802275 1.16726299 -0.00802261 1.16713354 -0.00815206 1.17528560 0.00000000 1.16993008 -0.00535552 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 1.17528560 Difference in potential energy from amber=>gromacs conversion: -0.00802275 Difference in potential energy from amber=>lammps conversion: -0.00802261 Difference in potential energy from amber=>desmond conversion: -0.00815206 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.00535552 ======================================================================= INFO 2017-03-19 00:10:30 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7200804.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7200804.inpcrd') INFO 2017-03-19 00:10:30 Beginning InterMol conversion INFO 2017-03-19 00:10:30 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:10:30 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:10:30 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7203421.inpcrd INFO 2017-03-19 00:10:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7203421/mobley_7203421_converted.input INFO 2017-03-19 00:10:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7203421/mobley_7203421_converted.cms WARNING 2017-03-19 00:10:46 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:10:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7203421/mobley_7203421_converted.inp INFO 2017-03-19 00:10:46 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7203421/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7203421/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7203421/mobley_7203421_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7203421/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 2.30527643 2.30527643 0.00000000 0.00000000 0.00000000 0.00000000 -199.18952896 -199.18952896 coulomb total -199.12576480 -199.13013857 -0.00437377 -199.13013708 -0.00437228 -199.13031336 -0.00454856 -199.18952896 -0.06376416 coulomb-14 -201.42361760 -201.43541500 -0.01179740 0.00000000 201.42361760 -201.43552275 -0.01190515 0.00000000 201.42361760 improper 0.00000000 0.03516790 0.03516790 0.00000000 0.00000000 0.00000000 0.00000000 0.03518744 0.03518744 proper 24.86844080 24.83343069 -0.03501011 24.86860188 0.00016108 24.86861703 0.00017623 24.83342072 -0.03502008 vdw (SR) 0.00000000 -2.53699858 -2.53699858 0.00000000 0.00000000 0.00000000 0.00000000 6.26139784 6.26139784 vdw total 6.26135600 6.26127029 -0.00008571 6.26127023 -0.00008577 6.26124086 -0.00011514 6.26139784 0.00004184 vdw-14 8.79853360 8.79826887 -0.00026473 0.00000000 -8.79853360 8.79825419 -0.00027941 0.00000000 -8.79853360 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.92498640 4.92495219 -0.00003421 4.92495209 -0.00003431 4.92513723 0.00015083 4.92494456 -0.00004184 bond 3.67480720 3.67460934 -0.00019786 3.67460934 -0.00019786 3.67489169 0.00008449 3.67459800 -0.00020920 bonded 33.46823440 33.46816012 -0.00007428 33.46816331 -0.00007109 33.46864595 0.00041155 33.46815072 -0.00008368 dihedral 24.86844080 24.86859859 0.00015779 24.86860188 0.00016108 24.86861703 0.00017623 24.86860816 0.00016736 nonbonded -192.86440880 -192.86886828 -0.00445948 -192.86886476 -0.00445596 -192.86907250 -0.00466370 -192.92813112 -0.06372232 potential -159.39617440 -159.40070816 -0.00453376 -159.40070149 -0.00452709 -159.40049898 -0.00432458 -159.45998040 -0.06380600 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -159.39617440 Difference in potential energy from amber=>gromacs conversion: -0.00453376 Difference in potential energy from amber=>lammps conversion: -0.00452709 Difference in potential energy from amber=>desmond conversion: -0.00432458 Difference in potential energy from amber=>charmm conversion: -0.06380600 ======================================================================= INFO 2017-03-19 00:10:46 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7203421.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7203421.inpcrd') INFO 2017-03-19 00:10:46 Beginning InterMol conversion INFO 2017-03-19 00:10:46 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:10:46 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:10:46 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7227357.inpcrd INFO 2017-03-19 00:10:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7227357/mobley_7227357_converted.input INFO 2017-03-19 00:10:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7227357/mobley_7227357_converted.cms WARNING 2017-03-19 00:11:02 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:11:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7227357/mobley_7227357_converted.inp INFO 2017-03-19 00:11:02 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7227357/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7227357/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7227357/mobley_7227357_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7227357/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -17.95096500 -17.95096500 0.00000000 0.00000000 0.00000000 0.00000000 -23.87482448 -23.87482448 coulomb total -23.90946800 -23.88621187 0.02325613 -23.88621165 0.02325635 -23.88632981 0.02313819 -23.87482448 0.03464352 coulomb-14 -5.93082000 -5.93524687 -0.00442687 0.00000000 5.93082000 -5.93520747 -0.00438747 0.00000000 5.93082000 proper 9.63784400 9.63774013 -0.00010387 9.63774024 -0.00010376 9.63773580 -0.00010820 9.63776032 -0.00008368 vdw (SR) 0.00000000 0.09010233 0.09010233 0.00000000 0.00000000 0.00000000 0.00000000 7.70383184 7.70383184 vdw total 7.70358080 7.70366466 0.00008386 7.70366490 0.00008410 7.70357837 -0.00000243 7.70383184 0.00025104 vdw-14 7.61362480 7.61356233 -0.00006247 0.00000000 -7.61362480 7.61349966 -0.00012514 0.00000000 -7.61362480 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.21752000 2.21743770 -0.00008230 2.21743770 -0.00008230 2.21706844 -0.00045156 2.21739448 -0.00012552 bond 0.59245440 0.59233349 -0.00012091 0.59233348 -0.00012092 0.59231437 -0.00014003 0.59232888 -0.00012552 bonded 12.44781840 12.44751132 -0.00030708 12.44751142 -0.00030698 12.44711861 -0.00069979 12.44748368 -0.00033472 dihedral 9.63784400 9.63774013 -0.00010387 9.63774024 -0.00010376 9.63773580 -0.00010820 9.63776032 -0.00008368 nonbonded -16.20588720 -16.18254721 0.02333999 -16.18254676 0.02334044 -16.18275144 0.02313576 -16.17099264 0.03489456 potential -3.75806880 -3.73503588 0.02303292 -3.73503546 0.02303334 -3.73567900 0.02238980 -3.72355080 0.03451800 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -3.75806880 Difference in potential energy from amber=>gromacs conversion: 0.02303292 Difference in potential energy from amber=>lammps conversion: 0.02303334 Difference in potential energy from amber=>desmond conversion: 0.02238980 Difference in potential energy from amber=>charmm conversion: 0.03451800 ======================================================================= INFO 2017-03-19 00:11:02 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7227357.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7227357.inpcrd') INFO 2017-03-19 00:11:02 Beginning InterMol conversion INFO 2017-03-19 00:11:02 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:11:02 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7239499.inpcrd INFO 2017-03-19 00:11:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7239499/mobley_7239499_converted.input INFO 2017-03-19 00:11:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7239499/mobley_7239499_converted.cms INFO 2017-03-19 00:11:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7239499/mobley_7239499_converted.rst7 WARNING 2017-03-19 00:11:18 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:11:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7239499/mobley_7239499_converted.inp INFO 2017-03-19 00:11:18 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7239499/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7239499/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7239499/mobley_7239499_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_7239499/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7239499/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -23.42304756 -23.42304756 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 33.05724008 33.05724008 coulomb total 33.00841280 33.00939655 0.00098375 33.00939604 0.00098324 33.00933152 0.00091872 33.00841280 0.00000000 33.05724008 0.04882728 coulomb-14 56.43044480 56.43244410 0.00199930 0.00000000 -56.43044480 56.43237990 0.00193510 56.43044480 0.00000000 0.00000000 -56.43044480 improper 0.00000000 0.00010324 0.00010324 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00083680 0.00083089 -0.00000591 0.00093411 0.00009731 0.00092672 0.00008992 0.00083680 0.00000000 0.00083680 0.00000000 vdw (SR) 0.00000000 -8.28950040 -8.28950040 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 40.76864496 40.76864496 vdw total 40.76889600 40.76866071 -0.00023529 40.76866086 -0.00023514 40.76868462 -0.00021138 40.76889600 0.00000000 40.76864496 -0.00025104 vdw-14 49.05823680 49.05816111 -0.00007569 0.00000000 -49.05823680 49.05818994 -0.00004686 49.05823680 0.00000000 0.00000000 -49.05823680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 7.39145440 7.39154246 0.00008806 7.39154226 0.00008786 7.39228568 0.00083128 7.39145440 0.00000000 7.39153808 0.00008368 bond 1.51962880 1.51971755 0.00008875 1.51971754 0.00008874 1.51993152 0.00030272 1.51962880 0.00000000 1.51971248 0.00008368 bonded 8.91192000 8.91219415 0.00027415 8.91219392 0.00027392 8.91314391 0.00122391 8.91192000 0.00000000 8.91217104 0.00025104 dihedral 0.00083680 0.00093414 0.00009734 0.00093411 0.00009731 0.00092672 0.00008992 0.00083680 0.00000000 0.00092048 0.00008368 nonbonded 73.77730880 73.77805726 0.00074846 73.77805774 0.00074894 73.77801615 0.00070735 73.77730880 0.00000000 73.82588504 0.04857624 potential 82.68922880 82.69025141 0.00102261 82.69024970 0.00102090 82.69101411 0.00178531 82.68922880 0.00000000 82.73805608 0.04882728 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 82.68922880 Difference in potential energy from amber=>gromacs conversion: 0.00102261 Difference in potential energy from amber=>lammps conversion: 0.00102090 Difference in potential energy from amber=>desmond conversion: 0.00178531 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.04882728 ======================================================================= INFO 2017-03-19 00:11:18 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7239499.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7239499.inpcrd') INFO 2017-03-19 00:11:18 Beginning InterMol conversion INFO 2017-03-19 00:11:18 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:11:18 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:11:18 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7261305.inpcrd INFO 2017-03-19 00:11:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7261305/mobley_7261305_converted.input INFO 2017-03-19 00:11:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7261305/mobley_7261305_converted.cms WARNING 2017-03-19 00:11:34 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:11:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7261305/mobley_7261305_converted.inp INFO 2017-03-19 00:11:34 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7261305/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7261305/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7261305/mobley_7261305_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7261305/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 216.74743392 216.74743392 coulomb total 216.70400400 216.66818427 -0.03581973 216.66818059 -0.03582341 216.66815214 -0.03585186 216.74743392 0.04342992 coulomb-14 216.70400400 216.66818427 -0.03581973 0.00000000 -216.70400400 216.66815214 -0.03585186 0.00000000 -216.70400400 proper 34.64770400 34.64788738 0.00018338 34.64788726 0.00018326 34.64789810 0.00019410 34.64787136 0.00016736 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00443504 -0.00443504 vdw total -0.00460240 -0.00445559 0.00014681 -0.00445559 0.00014681 -0.00445559 0.00014681 -0.00443504 0.00016736 vdw-14 -0.00460240 -0.00445559 0.00014681 0.00000000 0.00460240 -0.00445559 0.00014681 0.00000000 0.00460240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 6.91824400 6.91839868 0.00015468 6.91839881 0.00015481 6.91854387 0.00029987 6.91849504 0.00025104 bond 1.82673440 1.82659577 -0.00013863 1.82659578 -0.00013862 1.82719244 0.00045804 1.82660888 -0.00012552 bonded 43.39268240 43.39288183 0.00019943 43.39288185 0.00019945 43.39363440 0.00095200 43.39297528 0.00029288 dihedral 34.64770400 34.64788738 0.00018338 34.64788726 0.00018326 34.64789810 0.00019410 34.64787136 0.00016736 nonbonded 216.69940160 216.66372868 -0.03567292 216.66372463 -0.03567697 216.66369655 -0.03570505 216.74299888 0.04359728 potential 260.09208400 260.05661051 -0.03547349 260.05660786 -0.03547614 260.05732668 -0.03475732 260.13593232 0.04384832 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 260.09208400 Difference in potential energy from amber=>gromacs conversion: -0.03547349 Difference in potential energy from amber=>lammps conversion: -0.03547614 Difference in potential energy from amber=>desmond conversion: -0.03475732 Difference in potential energy from amber=>charmm conversion: 0.04384832 ======================================================================= INFO 2017-03-19 00:11:34 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7261305.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7261305.inpcrd') INFO 2017-03-19 00:11:34 Beginning InterMol conversion INFO 2017-03-19 00:11:34 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:11:34 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:11:34 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7295828.inpcrd INFO 2017-03-19 00:11:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7295828/mobley_7295828_converted.input INFO 2017-03-19 00:11:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7295828/mobley_7295828_converted.cms WARNING 2017-03-19 00:11:50 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:11:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7295828/mobley_7295828_converted.inp INFO 2017-03-19 00:11:50 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7295828/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7295828/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7295828/mobley_7295828_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7295828/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 4.58216727 4.58216727 0.00000000 0.00000000 0.00000000 0.00000000 -31.03159832 -31.03159832 coulomb total -31.02143120 -31.02970609 -0.00827489 -31.02970590 -0.00827470 -31.02970196 -0.00827076 -31.03159832 -0.01016712 coulomb-14 -35.61002400 -35.61187336 -0.00184936 0.00000000 35.61002400 -35.61184069 -0.00181669 0.00000000 35.61002400 improper 0.00000000 0.00010929 0.00010929 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00292880 0.00302669 0.00009789 0.00313590 0.00020710 0.00313366 0.00020486 0.00301248 0.00008368 vdw (SR) 0.00000000 13.94278475 13.94278475 0.00000000 0.00000000 0.00000000 0.00000000 39.91029736 39.91029736 vdw total 39.91033920 39.91019403 -0.00014517 39.91019443 -0.00014477 39.91029573 -0.00004347 39.91029736 -0.00004184 vdw-14 25.96757760 25.96740928 -0.00016832 0.00000000 -25.96757760 25.96739392 -0.00018368 0.00000000 -25.96757760 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.34392480 0.34392639 0.00000159 0.34392639 0.00000159 0.34397410 0.00004930 0.34392480 0.00000000 bond 1.26231280 1.26237842 0.00006562 1.26237841 0.00006561 1.26239692 0.00008412 1.26239648 0.00008368 bonded 1.60916640 1.60944080 0.00027440 1.60944070 0.00027430 1.60950468 0.00033828 1.60945928 0.00029288 dihedral 0.00292880 0.00313599 0.00020719 0.00313590 0.00020710 0.00313366 0.00020486 0.00313800 0.00020920 nonbonded 8.88890800 8.88048794 -0.00842006 8.88048854 -0.00841946 8.88059376 -0.00831424 8.87869904 -0.01020896 potential 10.49807440 10.48992874 -0.00814566 10.48992941 -0.00814499 10.49004932 -0.00802508 10.48811648 -0.00995792 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 10.49807440 Difference in potential energy from amber=>gromacs conversion: -0.00814566 Difference in potential energy from amber=>lammps conversion: -0.00814499 Difference in potential energy from amber=>desmond conversion: -0.00802508 Difference in potential energy from amber=>charmm conversion: -0.00995792 ======================================================================= INFO 2017-03-19 00:11:50 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7295828.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7295828.inpcrd') INFO 2017-03-19 00:11:50 Beginning InterMol conversion INFO 2017-03-19 00:11:50 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:11:50 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:11:50 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7298388.inpcrd INFO 2017-03-19 00:11:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7298388/mobley_7298388_converted.input INFO 2017-03-19 00:11:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7298388/mobley_7298388_converted.cms WARNING 2017-03-19 00:12:06 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:12:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7298388/mobley_7298388_converted.inp INFO 2017-03-19 00:12:06 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7298388/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7298388/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7298388/mobley_7298388_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7298388/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -23.33564201 -23.33564201 0.00000000 0.00000000 0.00000000 0.00000000 7.87479008 7.87479008 coulomb total 7.87721680 7.87768861 0.00047181 7.87768834 0.00047154 7.87787427 0.00065747 7.87479008 -0.00242672 coulomb-14 31.21222160 31.21333061 0.00110901 0.00000000 -31.21222160 31.21330814 0.00108654 0.00000000 -31.21222160 improper 0.00000000 0.00004017 0.00004017 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00046510 0.00004670 0.00050529 0.00008689 0.00051124 0.00009284 0.00046024 0.00004184 vdw (SR) 0.00000000 1.29651837 1.29651837 0.00000000 0.00000000 0.00000000 0.00000000 27.55511272 27.55511272 vdw total 27.55498720 27.55501569 0.00002849 27.55501565 0.00002845 27.55505916 0.00007196 27.55511272 0.00012552 vdw-14 26.25836560 26.25849732 0.00013172 0.00000000 -26.25836560 26.25852108 0.00015548 0.00000000 -26.25836560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.42799920 1.42800062 0.00000142 1.42800062 0.00000142 1.42788049 -0.00011871 1.42799920 0.00000000 bond 12.45283920 12.45288732 0.00004812 12.45288732 0.00004812 12.45157521 -0.00126399 12.45288104 0.00004184 bonded 13.88125680 13.88139321 0.00013641 13.88139323 0.00013643 13.87996695 -0.00128985 13.88138232 0.00012552 dihedral 0.00041840 0.00050527 0.00008687 0.00050529 0.00008689 0.00051124 0.00009284 0.00050208 0.00008368 nonbonded 35.43220400 35.43270429 0.00050029 35.43270441 0.00050041 35.43293343 0.00072943 35.42990280 -0.00230120 potential 49.31346080 49.31409751 0.00063671 49.31409677 0.00063597 49.31282943 -0.00063137 49.31128512 -0.00217568 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 49.31346080 Difference in potential energy from amber=>gromacs conversion: 0.00063671 Difference in potential energy from amber=>lammps conversion: 0.00063597 Difference in potential energy from amber=>desmond conversion: -0.00063137 Difference in potential energy from amber=>charmm conversion: -0.00217568 ======================================================================= INFO 2017-03-19 00:12:06 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7298388.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7298388.inpcrd') INFO 2017-03-19 00:12:06 Beginning InterMol conversion INFO 2017-03-19 00:12:06 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:12:06 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:12:06 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7326706.inpcrd INFO 2017-03-19 00:12:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7326706/mobley_7326706_converted.input INFO 2017-03-19 00:12:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7326706/mobley_7326706_converted.cms WARNING 2017-03-19 00:12:22 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:12:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7326706/mobley_7326706_converted.inp INFO 2017-03-19 00:12:22 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7326706/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7326706/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7326706/mobley_7326706_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7326706/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 385.03231360 385.03231360 0.00000000 0.00000000 0.00000000 0.00000000 -526.71823712 -526.71823712 coulomb total -526.70409520 -526.72071531 -0.01662011 -526.72070568 -0.01661048 -526.72033498 -0.01623978 -526.71823712 -0.01414192 coulomb-14 -911.71452000 -911.75302891 -0.03850891 0.00000000 911.71452000 -911.75288310 -0.03836310 0.00000000 911.71452000 improper 0.00000000 0.00004296 0.00004296 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 41.47431840 41.47421604 -0.00010236 41.47425899 -0.00005941 41.47430112 -0.00001728 41.47423472 -0.00008368 vdw (SR) 0.00000000 -16.26116245 -16.26116245 0.00000000 0.00000000 0.00000000 0.00000000 15.55908264 15.55908264 vdw total 15.55904080 15.55891494 -0.00012586 15.55891486 -0.00012594 15.55919310 0.00015230 15.55908264 0.00004184 vdw-14 31.82015680 31.82007739 -0.00007941 0.00000000 -31.82015680 31.82019341 0.00003661 0.00000000 -31.82015680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 8.29185120 8.29170635 -0.00014485 8.29170643 -0.00014477 8.29203241 0.00018121 8.29180936 -0.00004184 bond 6.37097680 6.37115614 0.00017934 6.37115629 0.00017949 6.36972566 -0.00125114 6.37114416 0.00016736 bonded 56.13714640 56.13712148 -0.00002492 56.13712171 -0.00002469 56.13605919 -0.00108721 56.13723008 0.00008368 dihedral 41.47431840 41.47425899 -0.00005941 41.47425899 -0.00005941 41.47430112 -0.00001728 41.47427656 -0.00004184 nonbonded -511.14505440 -511.16180037 -0.01674597 -511.16179040 -0.01673600 -511.16114188 -0.01608748 -511.15915448 -0.01410008 potential -455.00790800 -455.02467889 -0.01677089 -455.02468584 -0.01677784 -455.02540549 -0.01749749 -455.02196624 -0.01405824 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -455.00790800 Difference in potential energy from amber=>gromacs conversion: -0.01677089 Difference in potential energy from amber=>lammps conversion: -0.01677784 Difference in potential energy from amber=>desmond conversion: -0.01749749 Difference in potential energy from amber=>charmm conversion: -0.01405824 ======================================================================= INFO 2017-03-19 00:12:22 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7326706.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7326706.inpcrd') INFO 2017-03-19 00:12:22 Beginning InterMol conversion INFO 2017-03-19 00:12:22 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:12:23 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:12:23 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7326982.inpcrd INFO 2017-03-19 00:12:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7326982/mobley_7326982_converted.input INFO 2017-03-19 00:12:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7326982/mobley_7326982_converted.cms WARNING 2017-03-19 00:12:38 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:12:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7326982/mobley_7326982_converted.inp INFO 2017-03-19 00:12:38 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7326982/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7326982/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7326982/mobley_7326982_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7326982/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 51.25752364 51.25752364 0.00000000 0.00000000 0.00000000 0.00000000 -49.97921888 -49.97921888 coulomb total -49.95779680 -49.96896428 -0.01116748 -49.96896390 -0.01116710 -49.96910992 -0.01131312 -49.97921888 -0.02142208 coulomb-14 -101.23773760 -101.22648791 0.01124969 0.00000000 101.23773760 -101.22650733 0.01123027 0.00000000 101.23773760 proper 7.85462320 7.85482555 0.00020235 7.85482571 0.00020251 7.85483520 0.00021200 7.85483240 0.00020920 vdw (SR) 0.00000000 -0.12418236 -0.12418236 0.00000000 0.00000000 0.00000000 0.00000000 2.51282672 2.51282672 vdw total 2.51291040 2.51278459 -0.00012581 2.51278463 -0.00012577 2.51279491 -0.00011549 2.51282672 -0.00008368 vdw-14 2.63717520 2.63696695 -0.00020825 0.00000000 -2.63717520 2.63697806 -0.00019714 0.00000000 -2.63717520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.31252080 1.31234798 -0.00017282 1.31234796 -0.00017284 1.31245376 -0.00006704 1.31235344 -0.00016736 bond 0.61714000 0.61702538 -0.00011462 0.61702540 -0.00011460 0.61725683 0.00011683 0.61701448 -0.00012552 bonded 9.78428400 9.78419890 -0.00008510 9.78419906 -0.00008494 9.78454579 0.00026179 9.78420032 -0.00008368 dihedral 7.85462320 7.85482555 0.00020235 7.85482571 0.00020251 7.85483520 0.00021200 7.85483240 0.00020920 nonbonded -47.44488640 -47.45617969 -0.01129329 -47.45617902 -0.01129262 -47.45631501 -0.01142861 -47.46639216 -0.02150576 potential -37.66060240 -37.67198078 -0.01137838 -37.67198037 -0.01137797 -37.67178899 -0.01118659 -37.68215000 -0.02154760 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -37.66060240 Difference in potential energy from amber=>gromacs conversion: -0.01137838 Difference in potential energy from amber=>lammps conversion: -0.01137797 Difference in potential energy from amber=>desmond conversion: -0.01118659 Difference in potential energy from amber=>charmm conversion: -0.02154760 ======================================================================= INFO 2017-03-19 00:12:38 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7326982.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7326982.inpcrd') INFO 2017-03-19 00:12:39 Beginning InterMol conversion INFO 2017-03-19 00:12:39 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:12:39 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:12:39 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7360181.inpcrd INFO 2017-03-19 00:12:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7360181/mobley_7360181_converted.input INFO 2017-03-19 00:12:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7360181/mobley_7360181_converted.cms WARNING 2017-03-19 00:12:54 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:12:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7360181/mobley_7360181_converted.inp INFO 2017-03-19 00:12:54 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7360181/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7360181/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7360181/mobley_7360181_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7360181/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -184.11122427 -184.11122427 0.00000000 0.00000000 0.00000000 0.00000000 206.85285968 206.85285968 coulomb total 206.89712640 206.90577869 0.00865229 206.90577473 0.00864833 206.90604878 0.00892238 206.85285968 -0.04426672 coulomb-14 391.00316800 391.01700296 0.01383496 0.00000000 -391.00316800 391.01677395 0.01360595 0.00000000 -391.00316800 proper 54.50789680 54.50777606 -0.00012074 54.50779638 -0.00010042 54.50776751 -0.00012929 54.50781312 -0.00008368 vdw (SR) 0.00000000 53.31608194 53.31608194 0.00000000 0.00000000 0.00000000 0.00000000 75.11020568 75.11020568 vdw total 75.11033120 75.11035710 0.00002590 75.11035630 0.00002510 75.11069985 0.00036865 75.11020568 -0.00012552 vdw-14 21.79445600 21.79427516 -0.00018084 0.00000000 -21.79445600 21.79409915 -0.00035685 0.00000000 -21.79445600 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.84546640 5.84545124 -0.00001516 5.84545134 -0.00001506 5.84534732 -0.00011908 5.84559192 0.00012552 bond 1.72004240 1.71985769 -0.00018471 1.71985768 -0.00018472 1.71949830 -0.00054410 1.71987504 -0.00016736 bonded 62.07340560 62.07308499 -0.00032061 62.07310540 -0.00030020 62.07261313 -0.00079247 62.07328008 -0.00012552 dihedral 54.50789680 54.50777606 -0.00012074 54.50779638 -0.00010042 54.50776751 -0.00012929 54.50781312 -0.00008368 nonbonded 282.00745760 282.01613579 0.00867819 282.01613522 0.00867762 282.01674863 0.00929103 281.96306536 -0.04439224 potential 344.08086320 344.08922078 0.00835758 344.08923957 0.00837637 344.08928936 0.00842616 344.03634544 -0.04451776 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 344.08086320 Difference in potential energy from amber=>gromacs conversion: 0.00835758 Difference in potential energy from amber=>lammps conversion: 0.00837637 Difference in potential energy from amber=>desmond conversion: 0.00842616 Difference in potential energy from amber=>charmm conversion: -0.04451776 ======================================================================= INFO 2017-03-19 00:12:54 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7360181.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7360181.inpcrd') INFO 2017-03-19 00:12:55 Beginning InterMol conversion INFO 2017-03-19 00:12:55 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:12:55 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:12:55 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7364468.inpcrd INFO 2017-03-19 00:12:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7364468/mobley_7364468_converted.input INFO 2017-03-19 00:12:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7364468/mobley_7364468_converted.cms WARNING 2017-03-19 00:13:11 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:13:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7364468/mobley_7364468_converted.inp INFO 2017-03-19 00:13:11 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7364468/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7364468/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7364468/mobley_7364468_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7364468/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 136.77609675 136.77609675 0.00000000 0.00000000 0.00000000 0.00000000 -90.53841280 -90.53841280 coulomb total -90.50452240 -90.50759279 -0.00307039 -90.50759346 -0.00307106 -90.50771688 -0.00319448 -90.53841280 -0.03389040 coulomb-14 -227.27571680 -227.28368954 -0.00797274 0.00000000 227.27571680 -227.28374757 -0.00803077 0.00000000 227.27571680 improper 0.00000000 0.29157039 0.29157039 0.00000000 0.00000000 0.00000000 0.00000000 0.29158296 0.29158296 proper 13.39758640 13.10595855 -0.29162785 13.39753577 -0.00005063 13.39758661 0.00000021 13.10617080 -0.29141560 vdw (SR) 0.00000000 -4.12181734 -4.12181734 0.00000000 0.00000000 0.00000000 0.00000000 19.12452008 19.12452008 vdw total 19.12464560 19.12440375 -0.00024185 19.12440418 -0.00024142 19.12452346 -0.00012214 19.12452008 -0.00012552 vdw-14 23.24630400 23.24622110 -0.00008290 0.00000000 -23.24630400 23.24631467 0.00001067 0.00000000 -23.24630400 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 6.28185760 6.28165173 -0.00020587 6.28165175 -0.00020585 6.28158773 -0.00026987 6.28156472 -0.00029288 bond 1.96438800 1.96446875 0.00008075 1.96446875 0.00008075 1.96444463 0.00005663 1.96447168 0.00008368 bonded 21.64383200 21.64364942 -0.00018258 21.64365627 -0.00017573 21.64361897 -0.00021303 21.64379016 -0.00004184 dihedral 13.39758640 13.39752894 -0.00005746 13.39753577 -0.00005063 13.39758661 0.00000021 13.39775376 0.00016736 nonbonded -71.37987680 -71.38318904 -0.00331224 -71.38318634 -0.00330954 -71.38319342 -0.00331662 -71.41389272 -0.03401592 potential -49.73604480 -49.73953962 -0.00349482 -49.73953007 -0.00348527 -49.73967400 -0.00362920 -49.77010256 -0.03405776 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -49.73604480 Difference in potential energy from amber=>gromacs conversion: -0.00349482 Difference in potential energy from amber=>lammps conversion: -0.00348527 Difference in potential energy from amber=>desmond conversion: -0.00362920 Difference in potential energy from amber=>charmm conversion: -0.03405776 ======================================================================= INFO 2017-03-19 00:13:11 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7364468.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7364468.inpcrd') INFO 2017-03-19 00:13:11 Beginning InterMol conversion INFO 2017-03-19 00:13:11 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:13:11 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:13:11 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7375018.inpcrd INFO 2017-03-19 00:13:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7375018/mobley_7375018_converted.input INFO 2017-03-19 00:13:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7375018/mobley_7375018_converted.cms WARNING 2017-03-19 00:13:27 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:13:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7375018/mobley_7375018_converted.inp INFO 2017-03-19 00:13:27 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7375018/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7375018/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7375018/mobley_7375018_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7375018/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -0.29240843 -0.29240843 0.00000000 0.00000000 0.00000000 0.00000000 -59.87312368 -59.87312368 coulomb total -59.77387920 -59.78324729 -0.00936809 -59.78324718 -0.00936798 -59.78324895 -0.00936975 -59.87312368 -0.09924448 coulomb-14 -59.49313280 -59.49083886 0.00229394 0.00000000 59.49313280 -59.49078432 0.00234848 0.00000000 59.49313280 improper 0.00000000 0.00502658 0.00502658 0.00000000 0.00000000 0.00000000 0.00000000 0.00502080 0.00502080 proper 24.52116880 24.51596254 -0.00520626 24.52099014 -0.00017866 24.52096027 -0.00020853 24.51598064 -0.00518816 vdw (SR) 0.00000000 -5.34383200 -5.34383200 0.00000000 0.00000000 0.00000000 0.00000000 9.76286192 9.76286192 vdw total 9.76294560 9.76266444 -0.00028116 9.76266444 -0.00028116 9.76257996 -0.00036564 9.76286192 -0.00008368 vdw-14 15.10675040 15.10649644 -0.00025396 0.00000000 -15.10675040 15.10642622 -0.00032418 0.00000000 -15.10675040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 8.85585440 8.85598105 0.00012665 8.85598118 0.00012678 8.85675111 0.00089671 8.85593808 0.00008368 bond 1.89367840 1.89365812 -0.00002028 1.89365811 -0.00002029 1.89395254 0.00027414 1.89367840 0.00000000 bonded 35.27070160 35.27062829 -0.00007331 35.27062943 -0.00007217 35.27166392 0.00096232 35.27061792 -0.00008368 dihedral 24.52116880 24.52098912 -0.00017968 24.52099014 -0.00017866 24.52096027 -0.00020853 24.52100144 -0.00016736 nonbonded -50.01093360 -50.02058285 -0.00964925 -50.02058190 -0.00964830 -50.02066899 -0.00973539 -50.11026176 -0.09932816 potential -14.74023200 -14.74995456 -0.00972256 -14.74995269 -0.00972069 -14.74916794 -0.00893594 -14.83968568 -0.09945368 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -14.74023200 Difference in potential energy from amber=>gromacs conversion: -0.00972256 Difference in potential energy from amber=>lammps conversion: -0.00972069 Difference in potential energy from amber=>desmond conversion: -0.00893594 Difference in potential energy from amber=>charmm conversion: -0.09945368 ======================================================================= INFO 2017-03-19 00:13:27 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7375018.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7375018.inpcrd') INFO 2017-03-19 00:13:27 Beginning InterMol conversion INFO 2017-03-19 00:13:27 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:13:27 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:13:27 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7378987.inpcrd INFO 2017-03-19 00:13:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7378987/mobley_7378987_converted.input INFO 2017-03-19 00:13:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7378987/mobley_7378987_converted.cms WARNING 2017-03-19 00:13:43 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:13:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7378987/mobley_7378987_converted.inp INFO 2017-03-19 00:13:43 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7378987/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7378987/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7378987/mobley_7378987_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7378987/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 259.92855260 259.92855260 0.00000000 0.00000000 0.00000000 0.00000000 -705.77184768 -705.77184768 coulomb total -705.80983840 -705.82925829 -0.01941989 -705.82925216 -0.01941376 -705.82906890 -0.01923050 -705.77184768 0.03799072 coulomb-14 -965.69858000 -965.75781090 -0.05923090 0.00000000 965.69858000 -965.75830660 -0.05972660 0.00000000 965.69858000 improper 0.00000000 0.00018439 0.00018439 0.00000000 0.00000000 0.00000000 0.00000000 0.00016736 0.00016736 proper 0.00125520 0.00113304 -0.00012216 0.00131741 0.00006221 0.00132374 0.00006854 0.00112968 -0.00012552 vdw (SR) 0.00000000 -0.38080941 -0.38080941 0.00000000 0.00000000 0.00000000 0.00000000 28.09033000 28.09033000 vdw total 28.09012080 28.09019159 0.00007079 28.09019193 0.00007113 28.09011226 -0.00000854 28.09033000 0.00020920 vdw-14 28.47086480 28.47100100 0.00013620 0.00000000 -28.47086480 28.47101580 0.00015100 0.00000000 -28.47086480 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 27.62444160 27.62431971 -0.00012189 27.62431985 -0.00012175 27.62401638 -0.00042522 27.61502760 -0.00941400 bond 46.03111280 46.03127685 0.00016405 46.03127598 0.00016318 46.03375165 0.00263885 46.03128016 0.00016736 bonded 73.65680960 73.65691399 0.00010439 73.65691323 0.00010363 73.65909177 0.00228217 73.64760480 -0.00920480 dihedral 0.00125520 0.00131743 0.00006223 0.00131741 0.00006221 0.00132374 0.00006854 0.00129704 0.00004184 nonbonded -677.71971760 -677.73906671 -0.01934911 -677.73904768 -0.01933008 -677.73895665 -0.01923905 -677.68151768 0.03819992 potential -604.06290800 -604.08215272 -0.01924472 -604.08215440 -0.01924640 -604.07994106 -0.01703306 -604.03391288 0.02899512 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -604.06290800 Difference in potential energy from amber=>gromacs conversion: -0.01924472 Difference in potential energy from amber=>lammps conversion: -0.01924640 Difference in potential energy from amber=>desmond conversion: -0.01703306 Difference in potential energy from amber=>charmm conversion: 0.02899512 ======================================================================= INFO 2017-03-19 00:13:43 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7378987.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7378987.inpcrd') INFO 2017-03-19 00:13:43 Beginning InterMol conversion INFO 2017-03-19 00:13:43 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:13:43 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:13:43 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7393673.inpcrd INFO 2017-03-19 00:13:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7393673/mobley_7393673_converted.input INFO 2017-03-19 00:13:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7393673/mobley_7393673_converted.cms WARNING 2017-03-19 00:13:59 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:13:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7393673/mobley_7393673_converted.inp INFO 2017-03-19 00:13:59 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7393673/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7393673/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7393673/mobley_7393673_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7393673/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -69.54117733 -69.54117733 0.00000000 0.00000000 0.00000000 0.00000000 -82.28932208 -82.28932208 coulomb total -82.18254640 -82.18851093 -0.00596453 -82.18850860 -0.00596220 -82.18815041 -0.00560401 -82.28932208 -0.10677568 coulomb-14 -12.64237440 -12.64733360 -0.00495920 0.00000000 12.64237440 -12.64728010 -0.00490570 0.00000000 12.64237440 improper 0.00000000 0.00006325 0.00006325 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00460240 0.00436791 -0.00023449 0.00443119 -0.00017121 0.00443782 -0.00016458 0.00435136 -0.00025104 vdw (SR) 0.00000000 17.54787621 17.54787621 0.00000000 0.00000000 0.00000000 0.00000000 57.72894920 57.72894920 vdw total 57.72915840 57.72871566 -0.00044274 57.72871490 -0.00044350 57.72868473 -0.00047367 57.72894920 -0.00020920 vdw-14 40.18104400 40.18083945 -0.00020455 0.00000000 -40.18104400 40.18076024 -0.00028376 0.00000000 -40.18104400 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.29408720 2.29409007 0.00000287 2.29409009 0.00000289 2.29436674 0.00027954 2.29408720 0.00000000 bond 5.85174240 5.85153636 -0.00020604 5.85153655 -0.00020585 5.85101836 -0.00072404 5.85153320 -0.00020920 bonded 8.15043200 8.15005759 -0.00037441 8.15005782 -0.00037418 8.14982292 -0.00060908 8.15005544 -0.00037656 dihedral 0.00460240 0.00443116 -0.00017124 0.00443119 -0.00017121 0.00443782 -0.00016458 0.00443504 -0.00016736 nonbonded -24.45338800 -24.45979527 -0.00640727 -24.45979370 -0.00640570 -24.45946568 -0.00607768 -24.56037288 -0.10698488 potential -16.30295600 -16.30973768 -0.00678168 -16.30973617 -0.00678017 -16.30975421 -0.00679821 -16.41027560 -0.10731960 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -16.30295600 Difference in potential energy from amber=>gromacs conversion: -0.00678168 Difference in potential energy from amber=>lammps conversion: -0.00678017 Difference in potential energy from amber=>desmond conversion: -0.00679821 Difference in potential energy from amber=>charmm conversion: -0.10731960 ======================================================================= INFO 2017-03-19 00:13:59 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7393673.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7393673.inpcrd') INFO 2017-03-19 00:13:59 Beginning InterMol conversion INFO 2017-03-19 00:13:59 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:13:59 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:13:59 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7415647.inpcrd INFO 2017-03-19 00:14:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7415647/mobley_7415647_converted.input INFO 2017-03-19 00:14:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7415647/mobley_7415647_converted.cms WARNING 2017-03-19 00:14:15 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:14:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7415647/mobley_7415647_converted.inp INFO 2017-03-19 00:14:15 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7415647/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7415647/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7415647/mobley_7415647_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7415647/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -188.46937322 -188.46937322 0.00000000 0.00000000 0.00000000 0.00000000 37.05680936 37.05680936 coulomb total 37.05141200 37.05771294 0.00630094 37.05771269 0.00630069 37.05809427 0.00668227 37.05680936 0.00539736 coulomb-14 225.51048720 225.52708616 0.01659896 0.00000000 -225.51048720 225.52717759 0.01669039 0.00000000 -225.51048720 improper 0.00000000 0.01695843 0.01695843 0.00000000 0.00000000 0.00000000 0.00000000 0.01694520 0.01694520 proper 33.49501200 33.47815493 -0.01685707 33.49511451 0.00010251 33.49513129 0.00011929 33.47815048 -0.01686152 vdw (SR) 0.00000000 -2.52402890 -2.52402890 0.00000000 0.00000000 0.00000000 0.00000000 29.86171008 29.86171008 vdw total 29.86204480 29.86159286 -0.00045194 29.86159293 -0.00045187 29.86161970 -0.00042510 29.86171008 -0.00033472 vdw-14 32.38583360 32.38562175 -0.00021185 0.00000000 -32.38583360 32.38562264 -0.00021096 0.00000000 -32.38583360 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 9.63407840 9.63393912 -0.00013928 9.63393907 -0.00013933 9.63340001 -0.00067839 9.63395288 -0.00012552 bond 18.91711920 18.91715898 0.00003978 18.91715895 0.00003975 18.91761588 0.00049668 18.91716104 0.00004184 bonded 62.04620960 62.04621146 0.00000186 62.04621253 0.00000293 62.04614717 -0.00006243 62.04620960 -0.00000000 dihedral 33.49501200 33.49511336 0.00010136 33.49511451 0.00010251 33.49513129 0.00011929 33.49509568 0.00008368 nonbonded 66.91345680 66.91930579 0.00584899 66.91930603 0.00584923 66.91971396 0.00625716 66.91851944 0.00506264 potential 128.95966640 128.96551726 0.00585086 128.96551982 0.00585342 128.96573236 0.00606596 128.96477088 0.00510448 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 128.95966640 Difference in potential energy from amber=>gromacs conversion: 0.00585086 Difference in potential energy from amber=>lammps conversion: 0.00585342 Difference in potential energy from amber=>desmond conversion: 0.00606596 Difference in potential energy from amber=>charmm conversion: 0.00510448 ======================================================================= INFO 2017-03-19 00:14:15 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7415647.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7415647.inpcrd') INFO 2017-03-19 00:14:15 Beginning InterMol conversion INFO 2017-03-19 00:14:15 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:14:16 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:14:16 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7417968.inpcrd INFO 2017-03-19 00:14:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7417968/mobley_7417968_converted.input INFO 2017-03-19 00:14:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7417968/mobley_7417968_converted.cms WARNING 2017-03-19 00:14:31 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:14:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7417968/mobley_7417968_converted.inp INFO 2017-03-19 00:14:31 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7417968/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7417968/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7417968/mobley_7417968_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7417968/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -66.38284880 -66.38284880 0.00000000 0.00000000 0.00000000 0.00000000 -102.94568824 -102.94568824 coulomb total -102.96531120 -102.96905840 -0.00374720 -102.96905588 -0.00374468 -102.96891254 -0.00360134 -102.94568824 0.01962296 coulomb-14 -36.58489600 -36.58620960 -0.00131360 0.00000000 36.58489600 -36.58607145 -0.00117545 0.00000000 36.58489600 improper 0.00000000 0.00001568 0.00001568 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 26.58346240 26.58329276 -0.00016964 26.58330968 -0.00015272 26.58327132 -0.00019108 26.58329504 -0.00016736 vdw (SR) 0.00000000 -4.23844201 -4.23844201 0.00000000 0.00000000 0.00000000 0.00000000 7.88922488 7.88922488 vdw total 7.88935040 7.88907043 -0.00027997 7.88907049 -0.00027991 7.88896062 -0.00038978 7.88922488 -0.00012552 vdw-14 12.12774240 12.12751244 -0.00022996 0.00000000 -12.12774240 12.12740914 -0.00033326 0.00000000 -12.12774240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.49324560 2.49317277 -0.00007283 2.49317276 -0.00007284 2.49265848 -0.00058712 2.49324560 0.00000000 bond 2.98444720 2.98462484 0.00017764 2.98462485 0.00017765 2.98455588 0.00010868 2.98461456 0.00016736 bonded 32.06115520 32.06110605 -0.00004915 32.06110729 -0.00004791 32.06048568 -0.00066952 32.06115520 0.00000000 dihedral 26.58346240 26.58330844 -0.00015396 26.58330968 -0.00015272 26.58327132 -0.00019108 26.58329504 -0.00016736 nonbonded -95.07596080 -95.07998797 -0.00402717 -95.07998581 -0.00402501 -95.07995192 -0.00399112 -95.05646336 0.01949744 potential -63.01480560 -63.01888193 -0.00407633 -63.01888082 -0.00407522 -63.01953896 -0.00473336 -62.99530816 0.01949744 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -63.01480560 Difference in potential energy from amber=>gromacs conversion: -0.00407633 Difference in potential energy from amber=>lammps conversion: -0.00407522 Difference in potential energy from amber=>desmond conversion: -0.00473336 Difference in potential energy from amber=>charmm conversion: 0.01949744 ======================================================================= INFO 2017-03-19 00:14:31 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7417968.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7417968.inpcrd') INFO 2017-03-19 00:14:32 Beginning InterMol conversion INFO 2017-03-19 00:14:32 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:14:32 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:14:32 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7455579.inpcrd INFO 2017-03-19 00:14:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7455579/mobley_7455579_converted.input INFO 2017-03-19 00:14:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7455579/mobley_7455579_converted.cms WARNING 2017-03-19 00:14:47 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:14:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7455579/mobley_7455579_converted.inp INFO 2017-03-19 00:14:47 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7455579/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7455579/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7455579/mobley_7455579_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7455579/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -32.16483359 -32.16483359 0.00000000 0.00000000 0.00000000 0.00000000 -21.92357424 -21.92357424 coulomb total -21.93043600 -21.92410270 0.00633330 -21.92410226 0.00633374 -21.92399164 0.00644436 -21.92357424 0.00686176 coulomb-14 10.23197200 10.24073089 0.00875889 0.00000000 -10.23197200 10.24073928 0.00876728 0.00000000 -10.23197200 improper 0.00000000 0.00002187 0.00002187 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 8.39728800 8.39742790 0.00013990 8.39744992 0.00016192 8.39746143 0.00017343 8.39741352 0.00012552 vdw (SR) 0.00000000 -1.61608456 -1.61608456 0.00000000 0.00000000 0.00000000 0.00000000 9.17542832 9.17542832 vdw total 9.17551200 9.17530812 -0.00020388 9.17530824 -0.00020376 9.17514198 -0.00037002 9.17542832 -0.00008368 vdw-14 10.79137280 10.79139268 0.00001988 0.00000000 -10.79137280 10.79123084 -0.00014196 0.00000000 -10.79137280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.21414880 3.21430576 0.00015696 3.21430574 0.00015694 3.21425878 0.00010998 3.21435800 0.00020920 bond 1.47067600 1.47087908 0.00020308 1.47087909 0.00020309 1.47130970 0.00063370 1.47088520 0.00020920 bonded 13.08211280 13.08263461 0.00052181 13.08263475 0.00052195 13.08302991 0.00091711 13.08269856 0.00058576 dihedral 8.39728800 8.39744976 0.00016176 8.39744992 0.00016192 8.39746143 0.00017343 8.39745536 0.00016736 nonbonded -12.75492400 -12.74879458 0.00612942 -12.74879402 0.00612998 -12.74884966 0.00607434 -12.74814592 0.00677808 potential 0.32718880 0.33384003 0.00665123 0.33384040 0.00665160 0.33413153 0.00694273 0.33451080 0.00732200 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 0.32718880 Difference in potential energy from amber=>gromacs conversion: 0.00665123 Difference in potential energy from amber=>lammps conversion: 0.00665160 Difference in potential energy from amber=>desmond conversion: 0.00694273 Difference in potential energy from amber=>charmm conversion: 0.00732200 ======================================================================= INFO 2017-03-19 00:14:47 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7455579.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7455579.inpcrd') INFO 2017-03-19 00:14:48 Beginning InterMol conversion INFO 2017-03-19 00:14:48 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:14:48 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:14:48 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7463408.inpcrd INFO 2017-03-19 00:14:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7463408/mobley_7463408_converted.input INFO 2017-03-19 00:14:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7463408/mobley_7463408_converted.cms WARNING 2017-03-19 00:15:03 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:15:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7463408/mobley_7463408_converted.inp INFO 2017-03-19 00:15:03 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7463408/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7463408/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7463408/mobley_7463408_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7463408/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 86.15403120 86.15403120 0.00000000 0.00000000 0.00000000 0.00000000 -182.66381680 -182.66381680 coulomb total -182.59268880 -182.60065606 -0.00796726 -182.60065514 -0.00796634 -182.60098902 -0.00830022 -182.66381680 -0.07112800 coulomb-14 -268.74668800 -268.75468726 -0.00799926 0.00000000 268.74668800 -268.75473216 -0.00804416 0.00000000 268.74668800 improper 0.00000000 0.00020012 0.00020012 0.00000000 0.00000000 0.00000000 0.00000000 0.00020920 0.00020920 proper 4.63503520 4.63495112 -0.00008408 4.63515110 0.00011590 4.63515963 0.00012443 4.63495152 -0.00008368 vdw (SR) 0.00000000 19.86203563 19.86203563 0.00000000 0.00000000 0.00000000 0.00000000 45.26359984 45.26359984 vdw total 45.26376720 45.26331430 -0.00045290 45.26331533 -0.00045187 45.26314876 -0.00061844 45.26359984 -0.00016736 vdw-14 25.40148240 25.40127868 -0.00020372 0.00000000 -25.40148240 25.40140470 -0.00007770 0.00000000 -25.40148240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 8.75836720 8.75854267 0.00017547 8.75854251 0.00017531 8.75902731 0.00066011 8.75857640 0.00020920 bond 6.50904880 6.50890739 -0.00014141 6.50890738 -0.00014142 6.50868705 -0.00036175 6.50892328 -0.00012552 bonded 19.90245120 19.90260130 0.00015010 19.90260099 0.00014979 19.90287399 0.00042279 19.90266040 0.00020920 dihedral 4.63503520 4.63515124 0.00011604 4.63515110 0.00011590 4.63515963 0.00012443 4.63516072 0.00012552 nonbonded -137.32892160 -137.33734176 -0.00842016 -137.33733981 -0.00841821 -137.33784026 -0.00891866 -137.40021696 -0.07129536 potential -117.42647040 -117.43474045 -0.00827005 -117.43473798 -0.00826758 -117.43510325 -0.00863285 -117.49755656 -0.07108616 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -117.42647040 Difference in potential energy from amber=>gromacs conversion: -0.00827005 Difference in potential energy from amber=>lammps conversion: -0.00826758 Difference in potential energy from amber=>desmond conversion: -0.00863285 Difference in potential energy from amber=>charmm conversion: -0.07108616 ======================================================================= INFO 2017-03-19 00:15:03 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7463408.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7463408.inpcrd') INFO 2017-03-19 00:15:04 Beginning InterMol conversion INFO 2017-03-19 00:15:04 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:15:04 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:15:04 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7463799.inpcrd INFO 2017-03-19 00:15:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7463799/mobley_7463799_converted.input INFO 2017-03-19 00:15:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7463799/mobley_7463799_converted.cms WARNING 2017-03-19 00:15:19 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:15:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7463799/mobley_7463799_converted.inp INFO 2017-03-19 00:15:20 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7463799/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7463799/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7463799/mobley_7463799_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7463799/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 15.81482729 15.81482729 0.00000000 0.00000000 0.00000000 0.00000000 -14.92780072 -14.92780072 coulomb total -14.90633680 -14.90671132 -0.00037452 -14.90671127 -0.00037447 -14.90667591 -0.00033911 -14.92780072 -0.02146392 coulomb-14 -30.72060160 -30.72153861 -0.00093701 0.00000000 30.72060160 -30.72143765 -0.00083605 0.00000000 30.72060160 improper 0.00000000 0.00007041 0.00007041 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 3.30912560 3.30891426 -0.00021134 3.30898460 -0.00014100 3.30897126 -0.00015434 3.30891640 -0.00020920 vdw (SR) 0.00000000 -4.65832026 -4.65832026 0.00000000 0.00000000 0.00000000 0.00000000 15.82259096 15.82259096 vdw total 15.82263280 15.82255462 -0.00007818 15.82255456 -0.00007824 15.82257556 -0.00005724 15.82259096 -0.00004184 vdw-14 20.48109840 20.48087488 -0.00022352 0.00000000 -20.48109840 20.48089631 -0.00020209 0.00000000 -20.48109840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.91208800 1.91218227 0.00009427 1.91218227 0.00009427 1.91210905 0.00002105 1.91212984 0.00004184 bond 2.16522000 2.16541788 0.00019788 2.16541786 0.00019786 2.16491385 -0.00030615 2.16542920 0.00020920 bonded 7.38643360 7.38658482 0.00015122 7.38658473 0.00015113 7.38599415 -0.00043945 7.38655912 0.00012552 dihedral 3.30912560 3.30898467 -0.00014093 3.30898460 -0.00014100 3.30897126 -0.00015434 3.30900008 -0.00012552 nonbonded 0.91629600 0.91584331 -0.00045269 0.91584346 -0.00045254 0.91589965 -0.00039635 0.89479024 -0.02150576 potential 8.30272960 8.30242813 -0.00030147 8.30242835 -0.00030125 8.30180937 -0.00092023 8.28134936 -0.02138024 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 8.30272960 Difference in potential energy from amber=>gromacs conversion: -0.00030147 Difference in potential energy from amber=>lammps conversion: -0.00030125 Difference in potential energy from amber=>desmond conversion: -0.00092023 Difference in potential energy from amber=>charmm conversion: -0.02138024 ======================================================================= INFO 2017-03-19 00:15:20 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7463799.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7463799.inpcrd') INFO 2017-03-19 00:15:20 Beginning InterMol conversion INFO 2017-03-19 00:15:20 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:15:20 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:15:20 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7497999.inpcrd INFO 2017-03-19 00:15:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7497999/mobley_7497999_converted.input INFO 2017-03-19 00:15:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7497999/mobley_7497999_converted.cms WARNING 2017-03-19 00:15:36 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:15:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7497999/mobley_7497999_converted.inp INFO 2017-03-19 00:15:36 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7497999/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7497999/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7497999/mobley_7497999_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7497999/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -21.62007803 -21.62007803 0.00000000 0.00000000 0.00000000 0.00000000 -12.90609192 -12.90609192 coulomb total -12.91558960 -12.91451562 0.00107398 -12.91451557 0.00107403 -12.91441946 0.00117014 -12.90609192 0.00949768 coulomb-14 8.70606720 8.70556241 -0.00050479 0.00000000 -8.70606720 8.70560135 -0.00046585 0.00000000 -8.70606720 improper 0.00000000 0.00131686 0.00131686 0.00000000 0.00000000 0.00000000 0.00000000 0.00129704 0.00129704 proper 19.40455520 19.40304143 -0.00151377 19.40437780 -0.00017740 19.40439805 -0.00015715 19.40304896 -0.00150624 vdw (SR) 0.00000000 0.98995343 0.98995343 0.00000000 0.00000000 0.00000000 0.00000000 22.18147600 22.18147600 vdw total 22.18147600 22.18143767 -0.00003833 22.18143793 -0.00003807 22.18163038 0.00015438 22.18147600 0.00000000 vdw-14 21.19154160 21.19148423 -0.00005737 0.00000000 -21.19154160 21.19164532 0.00010372 0.00000000 -21.19154160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 6.88770080 6.88760231 -0.00009849 6.88760248 -0.00009832 6.88779122 0.00009042 6.88757528 -0.00012552 bond 3.31205440 3.31218727 0.00013287 3.31218728 0.00013288 3.31222357 0.00016917 3.31217992 0.00012552 bonded 29.60431040 29.60414787 -0.00016253 29.60416756 -0.00014284 29.60441283 0.00010243 29.60410120 -0.00020920 dihedral 19.40455520 19.40435829 -0.00019691 19.40437780 -0.00017740 19.40439805 -0.00015715 19.40434600 -0.00020920 nonbonded 9.26588640 9.26692205 0.00103565 9.26692236 0.00103596 9.26721092 0.00132452 9.27538408 0.00949768 potential 38.87019680 38.87106992 0.00087312 38.87108967 0.00089287 38.87156342 0.00136662 38.87948528 0.00928848 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 38.87019680 Difference in potential energy from amber=>gromacs conversion: 0.00087312 Difference in potential energy from amber=>lammps conversion: 0.00089287 Difference in potential energy from amber=>desmond conversion: 0.00136662 Difference in potential energy from amber=>charmm conversion: 0.00928848 ======================================================================= INFO 2017-03-19 00:15:36 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7497999.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7497999.inpcrd') INFO 2017-03-19 00:15:36 Beginning InterMol conversion INFO 2017-03-19 00:15:36 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:15:36 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7532833.inpcrd INFO 2017-03-19 00:15:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7532833/mobley_7532833_converted.input INFO 2017-03-19 00:15:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7532833/mobley_7532833_converted.cms INFO 2017-03-19 00:15:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7532833/mobley_7532833_converted.rst7 WARNING 2017-03-19 00:15:52 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:15:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7532833/mobley_7532833_converted.inp INFO 2017-03-19 00:15:52 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7532833/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7532833/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7532833/mobley_7532833_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_7532833/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7532833/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -29.06817264 -29.06817264 coulomb total -29.05997200 -29.06662840 -0.00665640 -29.06662791 -0.00665591 -29.06664017 -0.00666817 -29.05997200 0.00000000 -29.06817264 -0.00820064 coulomb-14 -29.05997200 -29.06662840 -0.00665640 0.00000000 29.05997200 -29.06664017 -0.00666817 -29.05997200 0.00000000 0.00000000 29.05997200 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.29999280 -0.29999280 vdw total -0.29999280 -0.29999394 -0.00000114 -0.29999395 -0.00000115 -0.29999334 -0.00000054 -0.29999280 0.00000000 -0.29999280 0.00000000 vdw-14 -0.29999280 -0.29999394 -0.00000114 0.00000000 0.29999280 -0.29999334 -0.00000054 -0.29999280 0.00000000 0.00000000 0.29999280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.30459520 0.37976911 0.07517391 0.37976911 0.07517391 0.37988515 0.07528995 0.30459520 0.00000000 0.37978168 0.07518648 bond 2.37149120 2.37129105 -0.00020015 2.37129104 -0.00020016 2.37083318 -0.00065802 2.37149120 0.00000000 2.37128200 -0.00020920 bonded 2.67608640 2.75106016 0.07497376 2.75106014 0.07497374 2.75071833 0.07463193 2.67608640 0.00000000 2.75106368 0.07497728 nonbonded -29.35996480 -29.36662234 -0.00665754 -29.36662196 -0.00665716 -29.36663351 -0.00666871 -29.35996480 0.00000000 -29.36816544 -0.00820064 potential -26.68387840 -26.61556218 0.06831622 -26.61556205 0.06831635 -26.61592468 0.06795372 -26.68387840 0.00000000 -26.61705992 0.06681848 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -26.68387840 Difference in potential energy from amber=>gromacs conversion: 0.06831622 Difference in potential energy from amber=>lammps conversion: 0.06831635 Difference in potential energy from amber=>desmond conversion: 0.06795372 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.06681848 ======================================================================= INFO 2017-03-19 00:15:52 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7532833.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7532833.inpcrd') INFO 2017-03-19 00:15:52 Beginning InterMol conversion INFO 2017-03-19 00:15:52 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:15:52 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:15:52 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7542832.inpcrd INFO 2017-03-19 00:15:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7542832/mobley_7542832_converted.input INFO 2017-03-19 00:15:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7542832/mobley_7542832_converted.cms WARNING 2017-03-19 00:16:08 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:16:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7542832/mobley_7542832_converted.inp INFO 2017-03-19 00:16:08 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7542832/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7542832/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7542832/mobley_7542832_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7542832/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -12.53672832 -12.53672832 0.00000000 0.00000000 0.00000000 0.00000000 -8.62581808 -8.62581808 coulomb total -8.60523280 -8.62125374 -0.01602094 -8.62125375 -0.01602095 -8.62125111 -0.01601831 -8.62581808 -0.02058528 coulomb-14 3.92166320 3.91547459 -0.00618861 0.00000000 -3.92166320 3.91549394 -0.00616926 0.00000000 -3.92166320 proper 6.48645520 6.48648754 0.00003234 6.48648742 0.00003222 6.48649578 0.00004058 6.48649704 0.00004184 vdw (SR) 0.00000000 -2.79732204 -2.79732204 0.00000000 0.00000000 0.00000000 0.00000000 3.71112432 3.71112432 vdw total 3.71120800 3.71102745 -0.00018055 3.71102750 -0.00018050 3.71099011 -0.00021789 3.71112432 -0.00008368 vdw-14 6.50863040 6.50834949 -0.00028091 0.00000000 -6.50863040 6.50831903 -0.00031137 0.00000000 -6.50863040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.43636720 1.43628055 -0.00008665 1.43628055 -0.00008665 1.43626965 -0.00009755 1.43628352 -0.00008368 bond 2.19701840 2.19710313 0.00008473 2.19710313 0.00008473 2.19754426 0.00052586 2.19710208 0.00008368 bonded 10.11984080 10.11987123 0.00003043 10.11987109 0.00003029 10.12030969 0.00046889 10.11988264 0.00004184 dihedral 6.48645520 6.48648754 0.00003234 6.48648742 0.00003222 6.48649578 0.00004058 6.48649704 0.00004184 nonbonded -4.89402480 -4.91022628 -0.01620148 -4.91022608 -0.01620128 -4.91026100 -0.01623620 -4.91469376 -0.02066896 potential 5.22581600 5.20964495 -0.01617105 5.20964526 -0.01617074 5.20999320 -0.01582280 5.20523072 -0.02058528 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 5.22581600 Difference in potential energy from amber=>gromacs conversion: -0.01617105 Difference in potential energy from amber=>lammps conversion: -0.01617074 Difference in potential energy from amber=>desmond conversion: -0.01582280 Difference in potential energy from amber=>charmm conversion: -0.02058528 ======================================================================= INFO 2017-03-19 00:16:08 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7542832.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7542832.inpcrd') INFO 2017-03-19 00:16:08 Beginning InterMol conversion INFO 2017-03-19 00:16:08 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:16:08 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:16:08 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_755351.inpcrd INFO 2017-03-19 00:16:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_755351/mobley_755351_converted.input INFO 2017-03-19 00:16:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_755351/mobley_755351_converted.cms WARNING 2017-03-19 00:16:24 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:16:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_755351/mobley_755351_converted.inp INFO 2017-03-19 00:16:24 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_755351/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_755351/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_755351/mobley_755351_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_755351/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 176.68417434 176.68417434 0.00000000 0.00000000 0.00000000 0.00000000 -209.87241064 -209.87241064 coulomb total -209.85646960 -209.87077099 -0.01430139 -209.87077051 -0.01430091 -209.87136171 -0.01489211 -209.87241064 -0.01594104 coulomb-14 -386.54678960 -386.55494533 -0.00815573 0.00000000 386.54678960 -386.55502204 -0.00823244 0.00000000 386.54678960 improper 0.00000000 0.11309924 0.11309924 0.00000000 0.00000000 0.00000000 0.00000000 0.11309352 0.11309352 proper 0.21882320 0.10579125 -0.11303195 0.21888904 0.00006584 0.21883258 0.00000938 0.10577152 -0.11305168 vdw (SR) 0.00000000 13.25172725 13.25172725 0.00000000 0.00000000 0.00000000 0.00000000 39.70862856 39.70862856 vdw total 39.70867040 39.70856364 -0.00010676 39.70856413 -0.00010627 39.70848973 -0.00018067 39.70862856 -0.00004184 vdw-14 26.45668720 26.45683640 0.00014920 0.00000000 -26.45668720 26.45702811 0.00034091 0.00000000 -26.45668720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.69196160 3.69181653 -0.00014507 3.69181654 -0.00014506 3.69188315 -0.00007845 3.69191976 -0.00004184 bond 6.03039920 6.03053982 0.00014062 6.03053978 0.00014058 6.03111826 0.00071906 6.03052472 0.00012552 bonded 9.94118400 9.94124685 0.00006285 9.94124537 0.00006137 9.94183399 0.00064999 9.94130952 0.00012552 dihedral 0.21882320 0.21889049 0.00006729 0.21888904 0.00006584 0.21883258 0.00000938 0.21886504 0.00004184 nonbonded -170.14779920 -170.16220735 -0.01440815 -170.16220471 -0.01440551 -170.16287198 -0.01507278 -170.16378208 -0.01598288 potential -160.20661520 -160.22096050 -0.01434530 -160.22095795 -0.01434275 -160.22108305 -0.01446785 -160.22243072 -0.01581552 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -160.20661520 Difference in potential energy from amber=>gromacs conversion: -0.01434530 Difference in potential energy from amber=>lammps conversion: -0.01434275 Difference in potential energy from amber=>desmond conversion: -0.01446785 Difference in potential energy from amber=>charmm conversion: -0.01581552 ======================================================================= INFO 2017-03-19 00:16:24 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_755351.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_755351.inpcrd') INFO 2017-03-19 00:16:24 Beginning InterMol conversion INFO 2017-03-19 00:16:24 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:16:24 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:16:24 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7573149.inpcrd INFO 2017-03-19 00:16:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7573149/mobley_7573149_converted.input INFO 2017-03-19 00:16:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7573149/mobley_7573149_converted.cms WARNING 2017-03-19 00:16:40 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:16:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7573149/mobley_7573149_converted.inp INFO 2017-03-19 00:16:40 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7573149/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7573149/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7573149/mobley_7573149_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7573149/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -9.31093761 -9.31093761 0.00000000 0.00000000 0.00000000 0.00000000 -116.86041704 -116.86041704 coulomb total -116.80974880 -116.81163201 -0.00188321 -116.81163160 -0.00188280 -116.81158307 -0.00183427 -116.86041704 -0.05066824 coulomb-14 -107.49909360 -107.50069440 -0.00160080 0.00000000 107.49909360 -107.50066595 -0.00157235 0.00000000 107.49909360 improper 0.00000000 0.00000201 0.00000201 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 21.01748720 21.01755547 0.00006827 21.01755875 0.00007155 21.01758548 0.00009828 21.01757088 0.00008368 vdw (SR) 0.00000000 -2.35413414 -2.35413414 0.00000000 0.00000000 0.00000000 0.00000000 6.73603080 6.73603080 vdw total 6.73624000 6.73592591 -0.00031409 6.73592578 -0.00031422 6.73588644 -0.00035356 6.73603080 -0.00020920 vdw-14 9.09015840 9.09006004 -0.00009836 0.00000000 -9.09015840 9.09002573 -0.00013267 0.00000000 -9.09015840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.17191440 2.17204937 0.00013497 2.17204938 0.00013498 2.17207293 0.00015853 2.17208176 0.00016736 bond 2.66897360 2.66905729 0.00008369 2.66905728 0.00008368 2.66857504 -0.00039856 2.66905728 0.00008368 bonded 25.85837520 25.85866414 0.00028894 25.85866540 0.00029020 25.85823345 -0.00014175 25.85870992 0.00033472 dihedral 21.01748720 21.01755748 0.00007028 21.01755875 0.00007155 21.01758548 0.00009828 21.01757088 0.00008368 nonbonded -110.07350880 -110.07570610 -0.00219730 -110.07570540 -0.00219660 -110.07569663 -0.00218783 -110.12438624 -0.05087744 potential -84.21513360 -84.21704196 -0.00190836 -84.21703732 -0.00190372 -84.21751471 -0.00238111 -84.26567632 -0.05054272 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -84.21513360 Difference in potential energy from amber=>gromacs conversion: -0.00190836 Difference in potential energy from amber=>lammps conversion: -0.00190372 Difference in potential energy from amber=>desmond conversion: -0.00238111 Difference in potential energy from amber=>charmm conversion: -0.05054272 ======================================================================= INFO 2017-03-19 00:16:40 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7573149.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7573149.inpcrd') INFO 2017-03-19 00:16:40 Beginning InterMol conversion INFO 2017-03-19 00:16:40 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:16:40 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7599023.inpcrd INFO 2017-03-19 00:16:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7599023/mobley_7599023_converted.input INFO 2017-03-19 00:16:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7599023/mobley_7599023_converted.cms INFO 2017-03-19 00:16:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7599023/mobley_7599023_converted.rst7 WARNING 2017-03-19 00:16:56 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:16:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7599023/mobley_7599023_converted.inp INFO 2017-03-19 00:16:56 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7599023/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7599023/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7599023/mobley_7599023_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_7599023/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7599023/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 5.15696409 5.15696409 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 3.96379608 3.96379608 coulomb total 3.96224800 3.96249164 0.00024364 3.96249159 0.00024359 3.96248501 0.00023701 3.96224800 0.00000000 3.96379608 0.00154808 coulomb-14 -1.19453200 -1.19447245 0.00005955 0.00000000 1.19453200 -1.19448570 0.00004630 -1.19453200 0.00000000 0.00000000 1.19453200 improper 0.00000000 0.00001898 0.00001898 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00000000 0.00017344 0.00017344 0.00019240 0.00019240 0.00019402 0.00019402 0.00000000 0.00000000 0.00016736 0.00016736 vdw (SR) 0.00000000 -1.19536058 -1.19536058 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 14.10756936 14.10756936 vdw total 14.10761120 14.10758842 -0.00002278 14.10758861 -0.00002259 14.10766723 0.00005603 14.10761120 0.00000000 14.10756936 -0.00004184 vdw-14 15.30298000 15.30294901 -0.00003099 0.00000000 -15.30298000 15.30302883 0.00004883 15.30298000 0.00000000 0.00000000 -15.30298000 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.78408160 0.78400165 -0.00007995 0.78400164 -0.00007996 0.78392435 -0.00015725 0.78408160 0.00000000 0.78403976 -0.00004184 bond 0.79621520 0.79608179 -0.00013341 0.79608177 -0.00013343 0.79595387 -0.00026133 0.79621520 0.00000000 0.79608968 -0.00012552 bonded 1.58029680 1.58027586 -0.00002094 1.58027581 -0.00002099 1.58007225 -0.00022455 1.58029680 0.00000000 1.58029680 0.00000000 dihedral 0.00000000 0.00019242 0.00019242 0.00019240 0.00019240 0.00019402 0.00019402 0.00000000 0.00000000 0.00016736 0.00016736 nonbonded 18.06985920 18.07008007 0.00022087 18.07008012 0.00022092 18.07015224 0.00029304 18.06985920 0.00000000 18.07136544 0.00150624 potential 19.65015600 19.65035593 0.00019993 19.65035600 0.00020000 19.65017642 0.00002042 19.65015600 0.00000000 19.65166224 0.00150624 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 19.65015600 Difference in potential energy from amber=>gromacs conversion: 0.00019993 Difference in potential energy from amber=>lammps conversion: 0.00020000 Difference in potential energy from amber=>desmond conversion: 0.00002042 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00150624 ======================================================================= INFO 2017-03-19 00:16:56 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7599023.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7599023.inpcrd') INFO 2017-03-19 00:16:56 Beginning InterMol conversion INFO 2017-03-19 00:16:56 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:16:57 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:16:57 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7608435.inpcrd INFO 2017-03-19 00:16:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7608435/mobley_7608435_converted.input INFO 2017-03-19 00:16:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7608435/mobley_7608435_converted.cms WARNING 2017-03-19 00:17:12 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:17:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7608435/mobley_7608435_converted.inp INFO 2017-03-19 00:17:12 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7608435/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7608435/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7608435/mobley_7608435_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7608435/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -46.82362057 -46.82362057 0.00000000 0.00000000 0.00000000 0.00000000 -65.05655576 -65.05655576 coulomb total -65.05450560 -65.05391077 0.00059483 -65.05391147 0.00059413 -65.05397996 0.00052564 -65.05655576 -0.00205016 coulomb-14 -18.23219840 -18.23029020 0.00190820 0.00000000 18.23219840 -18.23031547 0.00188293 0.00000000 18.23219840 improper 0.00000000 0.00798610 0.00798610 0.00000000 0.00000000 0.00000000 0.00000000 0.00799144 0.00799144 proper 10.08887920 10.08098550 -0.00789370 10.08897250 0.00009330 10.08896874 0.00008954 10.08097144 -0.00790776 vdw (SR) 0.00000000 -4.60144086 -4.60144086 0.00000000 0.00000000 0.00000000 0.00000000 13.32825752 13.32825752 vdw total 13.32813200 13.32804669 -0.00008531 13.32804706 -0.00008494 13.32801631 -0.00011569 13.32825752 0.00012552 vdw-14 17.92969520 17.92948755 -0.00020765 0.00000000 -17.92969520 17.92944270 -0.00025250 0.00000000 -17.92969520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.56348880 4.56360190 0.00011310 4.56360177 0.00011297 4.56423322 0.00074442 4.56357248 0.00008368 bond 2.20664160 2.20684074 0.00019914 2.20684076 0.00019916 2.20669781 0.00005621 2.20685080 0.00020920 bonded 16.85900960 16.85941425 0.00040465 16.85941503 0.00040543 16.85989977 0.00089017 16.85938616 0.00037656 dihedral 10.08887920 10.08897160 0.00009240 10.08897250 0.00009330 10.08896874 0.00008954 10.08896288 0.00008368 nonbonded -51.72637360 -51.72586408 0.00050952 -51.72586315 0.00051045 -51.72596365 0.00040995 -51.72829824 -0.00192464 potential -34.86736400 -34.86644983 0.00091417 -34.86644770 0.00091630 -34.86619700 0.00116700 -34.86891208 -0.00154808 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -34.86736400 Difference in potential energy from amber=>gromacs conversion: 0.00091417 Difference in potential energy from amber=>lammps conversion: 0.00091630 Difference in potential energy from amber=>desmond conversion: 0.00116700 Difference in potential energy from amber=>charmm conversion: -0.00154808 ======================================================================= INFO 2017-03-19 00:17:12 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7608435.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7608435.inpcrd') INFO 2017-03-19 00:17:13 Beginning InterMol conversion INFO 2017-03-19 00:17:13 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:17:13 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7608462.inpcrd INFO 2017-03-19 00:17:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7608462/mobley_7608462_converted.input INFO 2017-03-19 00:17:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7608462/mobley_7608462_converted.cms INFO 2017-03-19 00:17:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7608462/mobley_7608462_converted.rst7 WARNING 2017-03-19 00:17:28 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:17:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7608462/mobley_7608462_converted.inp INFO 2017-03-19 00:17:28 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7608462/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7608462/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7608462/mobley_7608462_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_7608462/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7608462/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 5.87298258 5.87298258 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 2.42019296 2.42019296 coulomb total 2.41500480 2.42238582 0.00738102 2.42238579 0.00738099 2.42237243 0.00736763 2.41500480 0.00000000 2.42019296 0.00518816 coulomb-14 -3.45305520 -3.45059675 0.00245845 0.00000000 3.45305520 -3.45062678 0.00242842 -3.45305520 0.00000000 0.00000000 3.45305520 improper 0.00000000 0.00002707 0.00002707 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00024427 -0.00017413 0.00027131 -0.00014709 0.00027283 -0.00014557 0.00041840 0.00000000 0.00025104 -0.00016736 vdw (SR) 0.00000000 -1.10484511 -1.10484511 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 14.48417120 14.48417120 vdw total 14.48417120 14.48419846 0.00002726 14.48419840 0.00002720 14.48427165 0.00010045 14.48417120 0.00000000 14.48417120 0.00000000 vdw-14 15.58916560 15.58904358 -0.00012202 0.00000000 -15.58916560 15.58911460 -0.00005100 15.58916560 0.00000000 0.00000000 -15.58916560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.22886480 0.22887110 0.00000630 0.22887111 0.00000631 0.22881261 -0.00005219 0.22886480 0.00000000 0.22886480 0.00000000 bond 0.81211440 0.81218647 0.00007207 0.81218645 0.00007205 0.81192658 -0.00018782 0.81211440 0.00000000 0.81219808 0.00008368 bonded 1.04139760 1.04132892 -0.00006868 1.04132886 -0.00006874 1.04101201 -0.00038559 1.04139760 0.00000000 1.04135576 -0.00004184 dihedral 0.00041840 0.00027135 -0.00014705 0.00027131 -0.00014709 0.00027283 -0.00014557 0.00041840 0.00000000 0.00029288 -0.00012552 nonbonded 16.89917600 16.90658429 0.00740829 16.90658419 0.00740819 16.90664408 0.00746808 16.89917600 0.00000000 16.90436416 0.00518816 potential 17.94057360 17.94791320 0.00733960 17.94791317 0.00733957 17.94761695 0.00704335 17.94057360 0.00000000 17.94571992 0.00514632 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 17.94057360 Difference in potential energy from amber=>gromacs conversion: 0.00733960 Difference in potential energy from amber=>lammps conversion: 0.00733957 Difference in potential energy from amber=>desmond conversion: 0.00704335 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00514632 ======================================================================= INFO 2017-03-19 00:17:28 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7608462.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7608462.inpcrd') INFO 2017-03-19 00:17:29 Beginning InterMol conversion INFO 2017-03-19 00:17:29 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:17:29 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:17:29 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7610437.inpcrd INFO 2017-03-19 00:17:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7610437/mobley_7610437_converted.input INFO 2017-03-19 00:17:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7610437/mobley_7610437_converted.cms WARNING 2017-03-19 00:17:44 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:17:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7610437/mobley_7610437_converted.inp INFO 2017-03-19 00:17:44 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7610437/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7610437/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7610437/mobley_7610437_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7610437/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -40.74877350 -40.74877350 0.00000000 0.00000000 0.00000000 0.00000000 -19.76638752 -19.76638752 coulomb total -19.73843840 -19.76351573 -0.02507733 -19.76351562 -0.02507722 -19.76366177 -0.02522337 -19.76638752 -0.02794912 coulomb-14 20.98108640 20.98525777 0.00417137 0.00000000 -20.98108640 20.98520898 0.00412258 0.00000000 -20.98108640 proper 11.66038960 11.66035072 -0.00003888 11.66035320 -0.00003640 11.66035416 -0.00003544 11.66034776 -0.00004184 vdw (SR) 0.00000000 3.97241156 3.97241156 0.00000000 0.00000000 0.00000000 0.00000000 15.27549112 15.27549112 vdw total 15.27578400 15.27524694 -0.00053706 15.27524719 -0.00053681 15.27550478 -0.00027922 15.27549112 -0.00029288 vdw-14 11.30307600 11.30283538 -0.00024062 0.00000000 -11.30307600 11.30299153 -0.00008447 0.00000000 -11.30307600 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.31537760 4.31523637 -0.00014123 4.31523618 -0.00014142 4.31516459 -0.00021301 4.31521024 -0.00016736 bond 0.59831200 0.59822616 -0.00008584 0.59822614 -0.00008586 0.59784945 -0.00046255 0.59822832 -0.00008368 bonded 16.57407920 16.57381324 -0.00026596 16.57381552 -0.00026368 16.57336820 -0.00071100 16.57378632 -0.00029288 dihedral 11.66038960 11.66035072 -0.00003888 11.66035320 -0.00003640 11.66035416 -0.00003544 11.66034776 -0.00004184 nonbonded -4.46265440 -4.48826880 -0.02561440 -4.48826843 -0.02561403 -4.48815699 -0.02550259 -4.49089640 -0.02824200 potential 12.11142480 12.08554445 -0.02588035 12.08554718 -0.02587762 12.08516183 -0.02626297 12.08288992 -0.02853488 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 12.11142480 Difference in potential energy from amber=>gromacs conversion: -0.02588035 Difference in potential energy from amber=>lammps conversion: -0.02587762 Difference in potential energy from amber=>desmond conversion: -0.02626297 Difference in potential energy from amber=>charmm conversion: -0.02853488 ======================================================================= INFO 2017-03-19 00:17:44 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7610437.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7610437.inpcrd') INFO 2017-03-19 00:17:45 Beginning InterMol conversion INFO 2017-03-19 00:17:45 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:17:45 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_766666.inpcrd INFO 2017-03-19 00:17:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_766666/mobley_766666_converted.input INFO 2017-03-19 00:17:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_766666/mobley_766666_converted.cms INFO 2017-03-19 00:18:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_766666/mobley_766666_converted.rst7 WARNING 2017-03-19 00:18:00 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:18:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_766666/mobley_766666_converted.inp INFO 2017-03-19 00:18:00 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_766666/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_766666/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_766666/mobley_766666_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_766666/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_766666/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -4.24876832 -4.24876832 coulomb total -4.24801520 -4.24795896 0.00005624 -4.24795872 0.00005648 -4.24794901 0.00006619 -4.24801520 0.00000000 -4.24876832 -0.00075312 coulomb-14 -4.24801520 -4.24795896 0.00005624 0.00000000 4.24801520 -4.24794901 0.00006619 -4.24801520 0.00000000 0.00000000 4.24801520 improper 0.00000000 0.00004444 0.00004444 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00031830 -0.00010010 0.00036281 -0.00005559 0.00036360 -0.00005480 0.00041840 0.00000000 0.00033472 -0.00008368 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.94794488 1.94794488 vdw total 1.94807040 1.94793374 -0.00013666 1.94793375 -0.00013665 1.94793263 -0.00013777 1.94807040 0.00000000 1.94794488 -0.00012552 vdw-14 1.94807040 1.94793374 -0.00013666 0.00000000 -1.94807040 1.94793263 -0.00013777 1.94807040 0.00000000 0.00000000 -1.94807040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.33718240 2.33700567 -0.00017673 2.33700567 -0.00017673 2.33703631 -0.00014609 2.33718240 0.00000000 2.33701504 -0.00016736 bond 0.54099120 0.54109702 0.00010582 0.54109701 0.00010581 0.54129823 0.00030703 0.54099120 0.00000000 0.54111672 0.00012552 bonded 2.87859200 2.87846542 -0.00012658 2.87846549 -0.00012651 2.87869814 0.00010614 2.87859200 0.00000000 2.87850832 -0.00008368 dihedral 0.00041840 0.00036274 -0.00005566 0.00036281 -0.00005559 0.00036360 -0.00005480 0.00041840 0.00000000 0.00037656 -0.00004184 nonbonded -2.29994480 -2.30002522 -0.00008042 -2.30002517 -0.00008037 -2.30001638 -0.00007158 -2.29994480 0.00000000 -2.30082344 -0.00087864 potential 0.57864720 0.57844020 -0.00020700 0.57844030 -0.00020690 0.57865135 0.00000415 0.57864720 0.00000000 0.57764304 -0.00100416 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 0.57864720 Difference in potential energy from amber=>gromacs conversion: -0.00020700 Difference in potential energy from amber=>lammps conversion: -0.00020690 Difference in potential energy from amber=>desmond conversion: 0.00000415 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.00100416 ======================================================================= INFO 2017-03-19 00:18:00 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_766666.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_766666.inpcrd') INFO 2017-03-19 00:18:01 Beginning InterMol conversion INFO 2017-03-19 00:18:01 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:18:01 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:18:01 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7676709.inpcrd INFO 2017-03-19 00:18:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7676709/mobley_7676709_converted.input INFO 2017-03-19 00:18:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7676709/mobley_7676709_converted.cms WARNING 2017-03-19 00:18:17 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:18:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7676709/mobley_7676709_converted.inp INFO 2017-03-19 00:18:17 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7676709/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7676709/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7676709/mobley_7676709_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7676709/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 52.79254981 52.79254981 0.00000000 0.00000000 0.00000000 0.00000000 -40.27300832 -40.27300832 coulomb total -40.26305040 -40.27346188 -0.01041148 -40.27346145 -0.01041105 -40.27327359 -0.01022319 -40.27300832 -0.00995792 coulomb-14 -93.06680400 -93.06601169 0.00079231 0.00000000 93.06680400 -93.06600360 0.00080040 0.00000000 93.06680400 improper 0.00000000 0.34920069 0.34920069 0.00000000 0.00000000 0.00000000 0.00000000 0.34919664 0.34919664 proper 14.02602320 13.67678505 -0.34923815 14.02597257 -0.00005063 14.02606048 0.00003728 13.67711944 -0.34890376 vdw (SR) 0.00000000 25.74537121 25.74537121 0.00000000 0.00000000 0.00000000 0.00000000 55.40929776 55.40929776 vdw total 55.40954880 55.40884200 -0.00070680 55.40884170 -0.00070710 55.40963754 0.00008874 55.40929776 -0.00025104 vdw-14 29.66372320 29.66347080 -0.00025240 0.00000000 -29.66372320 29.66371814 -0.00000506 0.00000000 -29.66372320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.39236320 4.39238321 0.00002001 4.39238328 0.00002008 4.39220973 -0.00015347 4.39227952 -0.00008368 bond 2.14806560 2.14796157 -0.00010403 2.14796159 -0.00010401 2.14817689 0.00011129 2.14798192 -0.00008368 bonded 20.56645200 20.56633053 -0.00012147 20.56631744 -0.00013456 20.56644710 -0.00000490 20.56657752 0.00012552 dihedral 14.02602320 14.02598574 -0.00003746 14.02597257 -0.00005063 14.02606048 0.00003728 14.02631608 0.00029288 nonbonded 15.14649840 15.13538012 -0.01111828 15.13538151 -0.01111689 15.13636396 -0.01013444 15.13628944 -0.01020896 potential 35.71295040 35.70171065 -0.01123975 35.70169879 -0.01125161 35.70269889 -0.01025151 35.70286696 -0.01008344 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 35.71295040 Difference in potential energy from amber=>gromacs conversion: -0.01123975 Difference in potential energy from amber=>lammps conversion: -0.01125161 Difference in potential energy from amber=>desmond conversion: -0.01025151 Difference in potential energy from amber=>charmm conversion: -0.01008344 ======================================================================= INFO 2017-03-19 00:18:17 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7676709.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7676709.inpcrd') INFO 2017-03-19 00:18:17 Beginning InterMol conversion INFO 2017-03-19 00:18:17 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:18:17 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7688753.inpcrd INFO 2017-03-19 00:18:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7688753/mobley_7688753_converted.input INFO 2017-03-19 00:18:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7688753/mobley_7688753_converted.cms INFO 2017-03-19 00:18:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7688753/mobley_7688753_converted.rst7 WARNING 2017-03-19 00:18:33 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:18:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7688753/mobley_7688753_converted.inp INFO 2017-03-19 00:18:33 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7688753/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7688753/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7688753/mobley_7688753_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_7688753/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7688753/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -45.88356228 -45.88356228 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -14.26082928 -14.26082928 coulomb total -14.21346640 -14.21369341 -0.00022701 -14.21369317 -0.00022677 -14.21410086 -0.00063446 -14.21346640 0.00000000 -14.26082928 -0.04736288 coulomb-14 31.66869600 31.66986887 0.00117287 0.00000000 -31.66869600 31.66976401 0.00106801 31.66869600 0.00000000 0.00000000 -31.66869600 improper 0.00000000 0.00012008 0.00012008 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00083680 0.00079265 -0.00004415 0.00091285 0.00007605 0.00091101 0.00007421 0.00083680 0.00000000 0.00079496 -0.00004184 vdw (SR) 0.00000000 -1.28416610 -1.28416610 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 17.69007752 17.69007752 vdw total 17.68995200 17.69003906 0.00008706 17.69003903 0.00008703 17.69012105 0.00016905 17.68995200 0.00000000 17.69007752 0.00012552 vdw-14 18.97402160 18.97420516 0.00018356 0.00000000 -18.97402160 18.97427607 0.00025447 18.97402160 0.00000000 0.00000000 -18.97402160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.56442160 0.56443691 0.00001531 0.56443691 0.00001531 0.56447197 0.00005037 0.56442160 0.00000000 0.56442160 0.00000000 bond 3.37941680 3.37921466 -0.00020214 3.37921467 -0.00020213 3.37872293 -0.00069387 3.37941680 0.00000000 3.37920760 -0.00020920 bonded 3.94467520 3.94456430 -0.00011090 3.94456444 -0.00011076 3.94410590 -0.00056930 3.94467520 0.00000000 3.94454968 -0.00012552 dihedral 0.00083680 0.00091273 0.00007593 0.00091285 0.00007605 0.00091101 0.00007421 0.00083680 0.00000000 0.00092048 0.00008368 nonbonded 3.47648560 3.47634565 -0.00013995 3.47634581 -0.00013979 3.47602018 -0.00046542 3.47648560 0.00000000 3.42924824 -0.04723736 potential 7.42116080 7.42090995 -0.00025085 7.42091018 -0.00025062 7.42007158 -0.00108922 7.42116080 0.00000000 7.37379792 -0.04736288 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 7.42116080 Difference in potential energy from amber=>gromacs conversion: -0.00025085 Difference in potential energy from amber=>lammps conversion: -0.00025062 Difference in potential energy from amber=>desmond conversion: -0.00108922 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.04736288 ======================================================================= INFO 2017-03-19 00:18:33 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7688753.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7688753.inpcrd') INFO 2017-03-19 00:18:33 Beginning InterMol conversion INFO 2017-03-19 00:18:33 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:18:33 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:18:33 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7690440.inpcrd INFO 2017-03-19 00:18:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7690440/mobley_7690440_converted.input INFO 2017-03-19 00:18:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7690440/mobley_7690440_converted.cms WARNING 2017-03-19 00:18:49 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:18:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7690440/mobley_7690440_converted.inp INFO 2017-03-19 00:18:49 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7690440/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7690440/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7690440/mobley_7690440_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7690440/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 7.70783487 7.70783487 0.00000000 0.00000000 0.00000000 0.00000000 -15.50406304 -15.50406304 coulomb total -15.50590400 -15.50382382 0.00208018 -15.50382372 0.00208028 -15.50384413 0.00205987 -15.50406304 0.00184096 coulomb-14 -23.20864800 -23.21165869 -0.00301069 0.00000000 23.20864800 -23.21166148 -0.00301348 0.00000000 23.20864800 proper 2.50830800 2.50816861 -0.00013939 2.50816859 -0.00013941 2.50816348 -0.00014452 2.50818248 -0.00012552 vdw (SR) 0.00000000 -0.69294447 -0.69294447 0.00000000 0.00000000 0.00000000 0.00000000 -1.40335544 -1.40335544 vdw total -1.40331360 -1.40334984 -0.00003624 -1.40334988 -0.00003628 -1.40334830 -0.00003470 -1.40335544 -0.00004184 vdw-14 -0.71044320 -0.71040536 0.00003784 0.00000000 0.71044320 -0.71040309 0.00004011 0.00000000 0.71044320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.38911200 0.38920451 0.00009251 0.38920451 0.00009251 0.38926260 0.00015060 0.38919568 0.00008368 bond 0.30794240 0.30779764 -0.00014476 0.30779764 -0.00014476 0.30785483 -0.00008757 0.30781688 -0.00012552 bonded 3.20536240 3.20517076 -0.00019164 3.20517074 -0.00019166 3.20528092 -0.00008148 3.20519504 -0.00016736 dihedral 2.50830800 2.50816861 -0.00013939 2.50816859 -0.00013941 2.50816348 -0.00014452 2.50818248 -0.00012552 nonbonded -16.90921760 -16.90717366 0.00204394 -16.90717330 0.00204430 -16.90719244 0.00202516 -16.90741848 0.00179912 potential -13.70385520 -13.70200290 0.00185230 -13.70200294 0.00185226 -13.70193725 0.00191795 -13.70226528 0.00158992 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -13.70385520 Difference in potential energy from amber=>gromacs conversion: 0.00185230 Difference in potential energy from amber=>lammps conversion: 0.00185226 Difference in potential energy from amber=>desmond conversion: 0.00191795 Difference in potential energy from amber=>charmm conversion: 0.00158992 ======================================================================= INFO 2017-03-19 00:18:49 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7690440.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7690440.inpcrd') INFO 2017-03-19 00:18:49 Beginning InterMol conversion INFO 2017-03-19 00:18:49 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:18:49 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:18:49 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7708038.inpcrd INFO 2017-03-19 00:18:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7708038/mobley_7708038_converted.input INFO 2017-03-19 00:18:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7708038/mobley_7708038_converted.cms WARNING 2017-03-19 00:19:05 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:19:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7708038/mobley_7708038_converted.inp INFO 2017-03-19 00:19:05 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7708038/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7708038/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7708038/mobley_7708038_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7708038/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 1.21452545 1.21452545 0.00000000 0.00000000 0.00000000 0.00000000 4.27232424 4.27232424 coulomb total 4.26977200 4.27433338 0.00456138 4.27433340 0.00456140 4.27431741 0.00454541 4.27232424 0.00255224 coulomb-14 3.05683040 3.05980793 0.00297753 0.00000000 -3.05683040 3.05981127 0.00298087 0.00000000 -3.05683040 proper 7.02451760 7.02458884 0.00007124 7.02458873 0.00007113 7.02458906 0.00007146 7.02460128 0.00008368 vdw (SR) 0.00000000 -0.52642257 -0.52642257 0.00000000 0.00000000 0.00000000 0.00000000 0.87453968 0.87453968 vdw total 0.87445600 0.87450872 0.00005272 0.87450872 0.00005272 0.87453616 0.00008016 0.87453968 0.00008368 vdw-14 1.40080320 1.40093129 0.00012809 0.00000000 -1.40080320 1.40096069 0.00015749 0.00000000 -1.40080320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.25977840 2.25998707 0.00020867 2.25998706 0.00020866 2.25987755 0.00009915 2.26002944 0.00025104 bond 1.16608080 1.16620987 0.00012907 1.16620988 0.00012908 1.16629167 0.00021087 1.16620632 0.00012552 bonded 10.45037680 10.45078579 0.00040899 10.45078566 0.00040886 10.45075828 0.00038148 10.45083704 0.00046024 dihedral 7.02451760 7.02458884 0.00007124 7.02458873 0.00007113 7.02458906 0.00007146 7.02460128 0.00008368 nonbonded 5.14422800 5.14884210 0.00461410 5.14884212 0.00461412 5.14885357 0.00462557 5.14686392 0.00263592 potential 15.59460480 15.59962789 0.00502309 15.59962769 0.00502289 15.59958464 0.00497984 15.59770096 0.00309616 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 15.59460480 Difference in potential energy from amber=>gromacs conversion: 0.00502309 Difference in potential energy from amber=>lammps conversion: 0.00502289 Difference in potential energy from amber=>desmond conversion: 0.00497984 Difference in potential energy from amber=>charmm conversion: 0.00309616 ======================================================================= INFO 2017-03-19 00:19:05 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7708038.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7708038.inpcrd') INFO 2017-03-19 00:19:05 Beginning InterMol conversion INFO 2017-03-19 00:19:05 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:19:05 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7735340.inpcrd INFO 2017-03-19 00:19:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7735340/mobley_7735340_converted.input INFO 2017-03-19 00:19:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7735340/mobley_7735340_converted.cms INFO 2017-03-19 00:19:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7735340/mobley_7735340_converted.rst7 WARNING 2017-03-19 00:19:21 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:19:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7735340/mobley_7735340_converted.inp INFO 2017-03-19 00:19:21 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7735340/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7735340/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7735340/mobley_7735340_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_7735340/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7735340/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 8.40352539 8.40352539 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -11.78390128 -11.78390128 coulomb total -11.68716720 -11.69760550 -0.01043830 -11.69760544 -0.01043824 -11.69764515 -0.01047795 -11.68716720 0.00000000 -11.78390128 -0.09673408 coulomb-14 -20.09282320 -20.10113089 -0.00830769 0.00000000 20.09282320 -20.10117254 -0.00834934 -20.09282320 0.00000000 0.00000000 20.09282320 improper 0.00000000 0.00020453 0.00020453 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00020920 0.00020920 proper 0.00125520 0.00120761 -0.00004759 0.00141202 0.00015682 0.00141053 0.00015533 0.00125520 0.00000000 0.00121336 -0.00004184 vdw (SR) 0.00000000 -0.02148087 -0.02148087 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.64513096 -0.64513096 vdw total -0.64517280 -0.64513258 0.00004022 -0.64513259 0.00004021 -0.64513283 0.00003997 -0.64517280 0.00000000 -0.64513096 0.00004184 vdw-14 -0.62383440 -0.62365171 0.00018269 0.00000000 0.62383440 -0.62365191 0.00018249 -0.62383440 0.00000000 0.00000000 0.62383440 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.26558800 4.26578222 0.00019422 4.26578214 0.00019414 4.26611749 0.00052949 4.26558800 0.00000000 4.26575536 0.00016736 bond 0.98867920 0.98872417 0.00004497 0.98872418 0.00004498 0.98852876 -0.00015044 0.98867920 0.00000000 0.98872104 0.00004184 bonded 5.25552240 5.25591853 0.00039613 5.25591834 0.00039594 5.25605678 0.00053438 5.25552240 0.00000000 5.25589896 0.00037656 dihedral 0.00125520 0.00141214 0.00015694 0.00141202 0.00015682 0.00141053 0.00015533 0.00125520 0.00000000 0.00142256 0.00016736 nonbonded -12.33234000 -12.34273808 -0.01039808 -12.34273808 -0.01039808 -12.34277798 -0.01043798 -12.33234000 0.00000000 -12.42903224 -0.09669224 potential -7.07681760 -7.08681954 -0.01000194 -7.08681945 -0.01000185 -7.08674167 -0.00992407 -7.07681760 0.00000000 -7.17313328 -0.09631568 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -7.07681760 Difference in potential energy from amber=>gromacs conversion: -0.01000194 Difference in potential energy from amber=>lammps conversion: -0.01000185 Difference in potential energy from amber=>desmond conversion: -0.00992407 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.09631568 ======================================================================= INFO 2017-03-19 00:19:21 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7735340.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7735340.inpcrd') INFO 2017-03-19 00:19:21 Beginning InterMol conversion INFO 2017-03-19 00:19:21 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:19:21 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:19:21 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7754849.inpcrd INFO 2017-03-19 00:19:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7754849/mobley_7754849_converted.input INFO 2017-03-19 00:19:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7754849/mobley_7754849_converted.cms WARNING 2017-03-19 00:19:37 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:19:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7754849/mobley_7754849_converted.inp INFO 2017-03-19 00:19:37 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7754849/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7754849/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7754849/mobley_7754849_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7754849/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 30.34553876 30.34553876 0.00000000 0.00000000 0.00000000 0.00000000 -463.12118608 -463.12118608 coulomb total -462.97549920 -462.97283140 0.00266780 -462.97282144 0.00267776 -462.97247760 0.00302160 -463.12118608 -0.14568688 coulomb-14 -493.33125600 -493.31837016 0.01288584 0.00000000 493.33125600 -493.31811406 0.01314194 0.00000000 493.33125600 proper 142.65431680 142.65424377 -0.00007303 142.65424567 -0.00007113 142.65444860 0.00013180 142.65423312 -0.00008368 vdw (SR) 0.00000000 -22.97192186 -22.97192186 0.00000000 0.00000000 0.00000000 0.00000000 -22.94250376 -22.94250376 vdw total -22.94254560 -22.94269306 -0.00014746 -22.94269330 -0.00014770 -22.94253540 0.00001020 -22.94250376 0.00004184 vdw-14 0.02928800 0.02922880 -0.00005920 0.00000000 -0.02928800 0.02936967 0.00008167 0.00000000 -0.02928800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 28.13488960 28.13481181 -0.00007779 28.13481178 -0.00007782 28.13555440 0.00066480 28.13455488 -0.00033472 bond 14.92934880 14.92950546 0.00015666 14.92950528 0.00015648 14.93012334 0.00077454 14.92951616 0.00016736 bonded 185.71855520 185.71856104 0.00000584 185.71856273 0.00000753 185.72012633 0.00157113 185.71830416 -0.00025104 dihedral 142.65431680 142.65424377 -0.00007303 142.65424567 -0.00007113 142.65444860 0.00013180 142.65423312 -0.00008368 nonbonded -485.91804480 -485.91552445 0.00252035 -485.91553440 0.00251040 -485.91501300 0.00303180 -486.06368984 -0.14564504 potential -300.19948960 -300.19696341 0.00252619 -300.19695410 0.00253550 -300.19536752 0.00412208 -300.34542752 -0.14593792 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -300.19948960 Difference in potential energy from amber=>gromacs conversion: 0.00252619 Difference in potential energy from amber=>lammps conversion: 0.00253550 Difference in potential energy from amber=>desmond conversion: 0.00412208 Difference in potential energy from amber=>charmm conversion: -0.14593792 ======================================================================= INFO 2017-03-19 00:19:37 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7754849.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7754849.inpcrd') INFO 2017-03-19 00:19:37 Beginning InterMol conversion INFO 2017-03-19 00:19:37 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:19:37 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:19:37 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7758918.inpcrd INFO 2017-03-19 00:19:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7758918/mobley_7758918_converted.input INFO 2017-03-19 00:19:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7758918/mobley_7758918_converted.cms WARNING 2017-03-19 00:19:53 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:19:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7758918/mobley_7758918_converted.inp INFO 2017-03-19 00:19:53 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7758918/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7758918/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7758918/mobley_7758918_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7758918/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -20.75242559 -20.75242559 0.00000000 0.00000000 0.00000000 0.00000000 -114.67653640 -114.67653640 coulomb total -114.63992640 -114.64366586 -0.00373946 -114.64366271 -0.00373631 -114.64380271 -0.00387631 -114.67653640 -0.03661000 coulomb-14 -93.88812320 -93.89124027 -0.00311707 0.00000000 93.88812320 -93.89144237 -0.00331917 0.00000000 93.88812320 improper 0.00000000 0.00001095 0.00001095 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 3.26979600 3.26971513 -0.00008087 3.26972604 -0.00006996 3.26975933 -0.00003667 3.26971232 -0.00008368 vdw (SR) 0.00000000 -0.37084711 -0.37084711 0.00000000 0.00000000 0.00000000 0.00000000 3.92015696 3.92015696 vdw total 3.92040800 3.92008640 -0.00032160 3.92008646 -0.00032154 3.91993608 -0.00047192 3.92015696 -0.00025104 vdw-14 4.29111040 4.29093351 -0.00017689 0.00000000 -4.29111040 4.29079007 -0.00032033 0.00000000 -4.29111040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.24469200 3.24470868 0.00001668 3.24470869 0.00001669 3.24466244 -0.00002956 3.24477568 0.00008368 bond 5.78019600 5.78009570 -0.00010030 5.78009558 -0.00010042 5.78075908 0.00056308 5.78011232 -0.00008368 bonded 12.29468400 12.29453046 -0.00015354 12.29453032 -0.00015368 12.29518085 0.00049685 12.29460032 -0.00008368 dihedral 3.26979600 3.26972608 -0.00006992 3.26972604 -0.00006996 3.26975933 -0.00003667 3.26971232 -0.00008368 nonbonded -110.71951840 -110.72357946 -0.00406106 -110.72357688 -0.00405848 -110.72386662 -0.00434822 -110.75637944 -0.03686104 potential -98.42483440 -98.42904900 -0.00421460 -98.42904769 -0.00421329 -98.42870042 -0.00386602 -98.46182096 -0.03698656 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -98.42483440 Difference in potential energy from amber=>gromacs conversion: -0.00421460 Difference in potential energy from amber=>lammps conversion: -0.00421329 Difference in potential energy from amber=>desmond conversion: -0.00386602 Difference in potential energy from amber=>charmm conversion: -0.03698656 ======================================================================= INFO 2017-03-19 00:19:53 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7758918.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7758918.inpcrd') INFO 2017-03-19 00:19:53 Beginning InterMol conversion INFO 2017-03-19 00:19:53 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:19:53 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:19:53 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7768165.inpcrd INFO 2017-03-19 00:19:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7768165/mobley_7768165_converted.input INFO 2017-03-19 00:19:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7768165/mobley_7768165_converted.cms WARNING 2017-03-19 00:20:09 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:20:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7768165/mobley_7768165_converted.inp INFO 2017-03-19 00:20:09 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7768165/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7768165/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7768165/mobley_7768165_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7768165/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -3.19586472 -3.19586472 coulomb total -3.19699440 -3.19779331 -0.00079891 -3.19779329 -0.00079889 -3.19779325 -0.00079885 -3.19586472 0.00112968 coulomb-14 -3.19699440 -3.19779331 -0.00079891 0.00000000 3.19699440 -3.19779325 -0.00079885 0.00000000 3.19699440 proper 9.95875680 9.95889743 0.00014063 9.95889738 0.00014058 9.95889211 0.00013531 9.95888232 0.00012552 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.49751944 -0.49751944 vdw total -0.49747760 -0.49752781 -0.00005021 -0.49752781 -0.00005021 -0.49752785 -0.00005025 -0.49751944 -0.00004184 vdw-14 -0.49747760 -0.49752781 -0.00005021 0.00000000 0.49747760 -0.49752785 -0.00005025 0.00000000 0.49747760 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.58989600 2.58981967 -0.00007633 2.58981968 -0.00007632 2.58989173 -0.00000427 2.58989600 0.00000000 bond 1.05227600 1.05237432 0.00009832 1.05237432 0.00009832 1.05222358 -0.00005242 1.05235968 0.00008368 bonded 13.60092880 13.60109142 0.00016262 13.60109139 0.00016259 13.60100743 0.00007863 13.60113800 0.00020920 dihedral 9.95875680 9.95889743 0.00014063 9.95889738 0.00014058 9.95889211 0.00013531 9.95888232 0.00012552 nonbonded -3.69447200 -3.69532113 -0.00084913 -3.69532110 -0.00084910 -3.69532110 -0.00084910 -3.69338416 0.00108784 potential 9.90645680 9.90577029 -0.00068651 9.90577021 -0.00068659 9.90565833 -0.00079847 9.90779568 0.00133888 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 9.90645680 Difference in potential energy from amber=>gromacs conversion: -0.00068651 Difference in potential energy from amber=>lammps conversion: -0.00068659 Difference in potential energy from amber=>desmond conversion: -0.00079847 Difference in potential energy from amber=>charmm conversion: 0.00133888 ======================================================================= INFO 2017-03-19 00:20:09 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7768165.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7768165.inpcrd') INFO 2017-03-19 00:20:09 Beginning InterMol conversion INFO 2017-03-19 00:20:09 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:20:10 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:20:10 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7769613.inpcrd INFO 2017-03-19 00:20:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7769613/mobley_7769613_converted.input INFO 2017-03-19 00:20:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7769613/mobley_7769613_converted.cms WARNING 2017-03-19 00:20:25 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:20:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7769613/mobley_7769613_converted.inp INFO 2017-03-19 00:20:25 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7769613/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7769613/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7769613/mobley_7769613_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7769613/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 26.27462137 26.27462137 0.00000000 0.00000000 0.00000000 0.00000000 -37.51428792 -37.51428792 coulomb total -37.52043840 -37.51456030 0.00587810 -37.51455988 0.00587852 -37.51458264 0.00585576 -37.51428792 0.00615048 coulomb-14 -63.76332320 -63.78918167 -0.02585847 0.00000000 63.76332320 -63.78916609 -0.02584289 0.00000000 63.76332320 proper 20.86728160 20.86723757 -0.00004403 20.86723767 -0.00004393 20.86725700 -0.00002460 20.86723976 -0.00004184 vdw (SR) 0.00000000 -0.47684093 -0.47684093 0.00000000 0.00000000 0.00000000 0.00000000 4.41340872 4.41340872 vdw total 4.41328320 4.41333384 0.00005064 4.41333383 0.00005063 4.41327339 -0.00000981 4.41340872 0.00012552 vdw-14 4.89025920 4.89017477 -0.00008443 0.00000000 -4.89025920 4.89012309 -0.00013611 0.00000000 -4.89025920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.86857440 1.86851755 -0.00005685 1.86851754 -0.00005686 1.86825619 -0.00031821 1.86853256 -0.00004184 bond 0.54350160 0.54364217 0.00014057 0.54364218 0.00014058 0.54332347 -0.00017813 0.54362712 0.00012552 bonded 23.27935760 23.27939729 0.00003969 23.27939739 0.00003979 23.27883666 -0.00052094 23.27939944 0.00004184 dihedral 20.86728160 20.86723757 -0.00004403 20.86723767 -0.00004393 20.86725700 -0.00002460 20.86723976 -0.00004184 nonbonded -33.10715520 -33.10122647 0.00592873 -33.10122605 0.00592915 -33.10130925 0.00584595 -33.10087920 0.00627600 potential -9.82779760 -9.82182918 0.00596842 -9.82182871 0.00596889 -9.82251338 0.00528422 -9.82143792 0.00635968 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -9.82779760 Difference in potential energy from amber=>gromacs conversion: 0.00596842 Difference in potential energy from amber=>lammps conversion: 0.00596889 Difference in potential energy from amber=>desmond conversion: 0.00528422 Difference in potential energy from amber=>charmm conversion: 0.00635968 ======================================================================= INFO 2017-03-19 00:20:25 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7769613.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7769613.inpcrd') INFO 2017-03-19 00:20:26 Beginning InterMol conversion INFO 2017-03-19 00:20:26 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:20:26 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:20:26 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7774695.inpcrd INFO 2017-03-19 00:20:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7774695/mobley_7774695_converted.input INFO 2017-03-19 00:20:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7774695/mobley_7774695_converted.cms WARNING 2017-03-19 00:20:41 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:20:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7774695/mobley_7774695_converted.inp INFO 2017-03-19 00:20:41 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7774695/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7774695/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7774695/mobley_7774695_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7774695/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 39.35494094 39.35494094 0.00000000 0.00000000 0.00000000 0.00000000 -100.86255832 -100.86255832 coulomb total -100.81473520 -100.84092476 -0.02618956 -100.84092286 -0.02618766 -100.84129686 -0.02656166 -100.86255832 -0.04782312 coulomb-14 -140.18826720 -140.19586571 -0.00759851 0.00000000 140.18826720 -140.19572351 -0.00745631 0.00000000 140.18826720 improper 0.00000000 0.00005218 0.00005218 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00044074 0.00002234 0.00049289 0.00007449 0.00049029 0.00007189 0.00046024 0.00004184 vdw (SR) 0.00000000 0.89867031 0.89867031 0.00000000 0.00000000 0.00000000 0.00000000 20.03613000 20.03613000 vdw total 20.03633920 20.03615121 -0.00018799 20.03615134 -0.00018786 20.03619468 -0.00014452 20.03613000 -0.00020920 vdw-14 19.13761600 19.13748090 -0.00013510 0.00000000 -19.13761600 19.13754324 -0.00007276 0.00000000 -19.13761600 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.97689200 3.97682691 -0.00006509 3.97682690 -0.00006510 3.97683275 -0.00005925 3.97689200 0.00000000 bond 5.15887200 5.15874140 -0.00013060 5.15874146 -0.00013054 5.15767659 -0.00119541 5.15874648 -0.00012552 bonded 9.13618240 9.13606124 -0.00012116 9.13606125 -0.00012115 9.13499963 -0.00118277 9.13614056 -0.00004184 dihedral 0.00041840 0.00049293 0.00007453 0.00049289 0.00007449 0.00049029 0.00007189 0.00050208 0.00008368 nonbonded -80.77839600 -80.80477356 -0.02637756 -80.80477194 -0.02637594 -80.80510219 -0.02670619 -80.82642832 -0.04803232 potential -71.64221360 -71.66871232 -0.02649872 -71.66871087 -0.02649727 -71.67015477 -0.02794117 -71.69028776 -0.04807416 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -71.64221360 Difference in potential energy from amber=>gromacs conversion: -0.02649872 Difference in potential energy from amber=>lammps conversion: -0.02649727 Difference in potential energy from amber=>desmond conversion: -0.02794117 Difference in potential energy from amber=>charmm conversion: -0.04807416 ======================================================================= INFO 2017-03-19 00:20:41 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7774695.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7774695.inpcrd') INFO 2017-03-19 00:20:42 Beginning InterMol conversion INFO 2017-03-19 00:20:42 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:20:42 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:20:42 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_778352.inpcrd INFO 2017-03-19 00:20:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_778352/mobley_778352_converted.input INFO 2017-03-19 00:20:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_778352/mobley_778352_converted.cms WARNING 2017-03-19 00:20:57 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:20:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_778352/mobley_778352_converted.inp INFO 2017-03-19 00:20:57 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_778352/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_778352/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_778352/mobley_778352_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_778352/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 16.35005784 16.35005784 0.00000000 0.00000000 0.00000000 0.00000000 -7.97943192 -7.97943192 coulomb total -7.98432720 -7.97921127 0.00511593 -7.97921100 0.00511620 -7.97921619 0.00511101 -7.97943192 0.00489528 coulomb-14 -24.32661280 -24.32926911 -0.00265631 0.00000000 24.32661280 -24.32924793 -0.00263513 0.00000000 24.32661280 improper 0.00000000 0.00000425 0.00000425 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 73.54969920 73.54955678 -0.00014242 73.54954021 -0.00015899 73.54957577 -0.00012343 73.54953184 -0.00016736 vdw (SR) 0.00000000 0.56385387 0.56385387 0.00000000 0.00000000 0.00000000 0.00000000 5.82416984 5.82416984 vdw total 5.82412800 5.82410438 -0.00002362 5.82410457 -0.00002343 5.82395963 -0.00016837 5.82416984 0.00004184 vdw-14 5.26012480 5.26025051 0.00012571 0.00000000 -5.26012480 5.26014275 0.00001795 0.00000000 -5.26012480 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.42832160 5.42814088 -0.00018072 5.42814085 -0.00018075 5.42834260 0.00002100 5.42811240 -0.00020920 bond 3.08109760 3.08121183 0.00011423 3.08121182 0.00011422 3.08148469 0.00038709 3.08122312 0.00012552 bonded 82.05911840 82.05891375 -0.00020465 82.05889288 -0.00022552 82.05940307 0.00028467 82.05886736 -0.00025104 dihedral 73.54969920 73.54956103 -0.00013817 73.54954021 -0.00015899 73.54957577 -0.00012343 73.54953184 -0.00016736 nonbonded -2.16019920 -2.15510689 0.00509231 -2.15510669 0.00509251 -2.15525656 0.00494264 -2.15526208 0.00493712 potential 79.89891920 79.90380686 0.00488766 79.90378519 0.00486599 79.90411949 0.00520029 79.90360528 0.00468608 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 79.89891920 Difference in potential energy from amber=>gromacs conversion: 0.00488766 Difference in potential energy from amber=>lammps conversion: 0.00486599 Difference in potential energy from amber=>desmond conversion: 0.00520029 Difference in potential energy from amber=>charmm conversion: 0.00468608 ======================================================================= INFO 2017-03-19 00:20:57 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_778352.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_778352.inpcrd') INFO 2017-03-19 00:20:58 Beginning InterMol conversion INFO 2017-03-19 00:20:58 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:20:58 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:20:58 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7794077.inpcrd INFO 2017-03-19 00:20:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7794077/mobley_7794077_converted.input INFO 2017-03-19 00:20:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7794077/mobley_7794077_converted.cms WARNING 2017-03-19 00:21:13 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:21:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7794077/mobley_7794077_converted.inp INFO 2017-03-19 00:21:13 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7794077/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7794077/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7794077/mobley_7794077_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7794077/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 670.26644590 670.26644590 0.00000000 0.00000000 0.00000000 0.00000000 -916.27892928 -916.27892928 coulomb total -916.20855440 -916.24226002 -0.03370562 -916.24223560 -0.03368120 -916.24175862 -0.03320422 -916.27892928 -0.07037488 coulomb-14 -1586.46359760 -1586.50870592 -0.04510832 0.00000000 1586.46359760 -1586.50773880 -0.04414120 0.00000000 1586.46359760 improper 0.00000000 0.00006498 0.00006498 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 50.20841840 50.20823709 -0.00018131 50.20830125 -0.00011715 50.20829330 -0.00012510 50.20825104 -0.00016736 vdw (SR) 0.00000000 -0.72975394 -0.72975394 0.00000000 0.00000000 0.00000000 0.00000000 21.29317096 21.29317096 vdw total 21.29321280 21.29332492 0.00011212 21.29332493 0.00011213 21.29317733 -0.00003547 21.29317096 -0.00004184 vdw-14 22.02290240 22.02307886 0.00017646 0.00000000 -22.02290240 22.02288504 -0.00001736 0.00000000 -22.02290240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 14.24149920 14.24163535 0.00013615 14.24163518 0.00013598 14.24216462 0.00066542 14.24166656 0.00016736 bond 18.21922800 18.21933793 0.00010993 18.21933804 0.00011004 18.21993317 0.00070517 18.21935352 0.00012552 bonded 82.66914560 82.66927534 0.00012974 82.66927447 0.00012887 82.67039109 0.00124549 82.66935480 0.00020920 dihedral 50.20841840 50.20830207 -0.00011633 50.20830125 -0.00011715 50.20829330 -0.00012510 50.20833472 -0.00008368 nonbonded -894.91534160 -894.94893510 -0.03359350 -894.94893912 -0.03359752 -894.94858129 -0.03323969 -894.98575832 -0.07041672 potential -812.24619600 -812.27965976 -0.03346376 -812.27966800 -0.03347200 -812.27828728 -0.03209128 -812.31648720 -0.07029120 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -812.24619600 Difference in potential energy from amber=>gromacs conversion: -0.03346376 Difference in potential energy from amber=>lammps conversion: -0.03347200 Difference in potential energy from amber=>desmond conversion: -0.03209128 Difference in potential energy from amber=>charmm conversion: -0.07029120 ======================================================================= INFO 2017-03-19 00:21:13 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7794077.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7794077.inpcrd') INFO 2017-03-19 00:21:14 Beginning InterMol conversion INFO 2017-03-19 00:21:14 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:21:14 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7814642.inpcrd INFO 2017-03-19 00:21:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7814642/mobley_7814642_converted.input INFO 2017-03-19 00:21:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7814642/mobley_7814642_converted.cms INFO 2017-03-19 00:21:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7814642/mobley_7814642_converted.rst7 WARNING 2017-03-19 00:21:29 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:21:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7814642/mobley_7814642_converted.inp INFO 2017-03-19 00:21:30 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7814642/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7814642/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7814642/mobley_7814642_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_7814642/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7814642/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -6.38228130 -6.38228130 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -8.55899960 -8.55899960 coulomb total -8.56004560 -8.56045344 -0.00040784 -8.56045354 -0.00040794 -8.56043556 -0.00038996 -8.56004560 0.00000000 -8.55899960 0.00104600 coulomb-14 -2.17819040 -2.17817214 0.00001826 0.00000000 2.17819040 -2.17814945 0.00004095 -2.17819040 0.00000000 0.00000000 2.17819040 improper 0.00000000 0.00012621 0.00012621 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00167360 0.00155933 -0.00011427 0.00168554 0.00001194 0.00168186 0.00000826 0.00167360 0.00000000 0.00154808 -0.00012552 vdw (SR) 0.00000000 -2.19231455 -2.19231455 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 15.07896864 15.07896864 vdw total 15.07871760 15.07894862 0.00023102 15.07894856 0.00023096 15.07902090 0.00030330 15.07871760 0.00000000 15.07896864 0.00025104 vdw-14 17.27113360 17.27126317 0.00012957 0.00000000 -17.27113360 17.27134125 0.00020765 17.27113360 0.00000000 0.00000000 -17.27113360 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.77987360 1.77979189 -0.00008171 1.77979189 -0.00008171 1.77989092 0.00001732 1.77987360 0.00000000 1.77983176 -0.00004184 bond 0.80039920 0.80023491 -0.00016429 0.80023489 -0.00016431 0.80013856 -0.00026064 0.80039920 0.00000000 0.80023184 -0.00016736 bonded 2.58194640 2.58171235 -0.00023405 2.58171232 -0.00023408 2.58171134 -0.00023506 2.58194640 0.00000000 2.58173720 -0.00020920 dihedral 0.00167360 0.00168555 0.00001195 0.00168554 0.00001194 0.00168186 0.00000826 0.00167360 0.00000000 0.00167360 0.00000000 nonbonded 6.51867200 6.51849518 -0.00017682 6.51849544 -0.00017656 6.51858534 -0.00008666 6.51867200 0.00000000 6.51996904 0.00129704 potential 9.10061840 9.10020753 -0.00041087 9.10020753 -0.00041087 9.10022125 -0.00039715 9.10061840 0.00000000 9.10166440 0.00104600 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 9.10061840 Difference in potential energy from amber=>gromacs conversion: -0.00041087 Difference in potential energy from amber=>lammps conversion: -0.00041087 Difference in potential energy from amber=>desmond conversion: -0.00039715 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00104600 ======================================================================= INFO 2017-03-19 00:21:30 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7814642.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7814642.inpcrd') INFO 2017-03-19 00:21:30 Beginning InterMol conversion INFO 2017-03-19 00:21:30 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:21:30 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:21:30 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7829570.inpcrd INFO 2017-03-19 00:21:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7829570/mobley_7829570_converted.input INFO 2017-03-19 00:21:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7829570/mobley_7829570_converted.cms WARNING 2017-03-19 00:21:46 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:21:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7829570/mobley_7829570_converted.inp INFO 2017-03-19 00:21:46 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7829570/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7829570/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7829570/mobley_7829570_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7829570/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 219.93410173 219.93410173 0.00000000 0.00000000 0.00000000 0.00000000 -127.71086792 -127.71086792 coulomb total -127.74003040 -127.74437238 -0.00434198 -127.74436921 -0.00433881 -127.74429975 -0.00426935 -127.71086792 0.02916248 coulomb-14 -347.66655120 -347.67847411 -0.01192291 0.00000000 347.66655120 -347.67861911 -0.01206791 0.00000000 347.66655120 improper 0.00000000 0.00124612 0.00124612 0.00000000 0.00000000 0.00000000 0.00000000 0.00125520 0.00125520 proper 77.09563920 77.09435353 -0.00128567 77.09560154 -0.00003766 77.09559276 -0.00004644 77.09438400 -0.00125520 vdw (SR) 0.00000000 -12.31698675 -12.31698675 0.00000000 0.00000000 0.00000000 0.00000000 28.56450272 28.56450272 vdw total 28.56458640 28.56432372 -0.00026268 28.56432364 -0.00026276 28.56437682 -0.00020958 28.56450272 -0.00008368 vdw-14 40.88144560 40.88131047 -0.00013513 0.00000000 -40.88144560 40.88130159 -0.00014401 0.00000000 -40.88144560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 12.11477200 12.11472682 -0.00004518 12.11472681 -0.00004519 12.11438234 -0.00038966 12.11473016 -0.00004184 bond 32.22600480 32.22615827 0.00015347 32.22615835 0.00015355 32.22784476 0.00183996 32.22617216 0.00016736 bonded 121.43641600 121.43648474 0.00006874 121.43648671 0.00007071 121.43781986 0.00140386 121.43654152 0.00012552 dihedral 77.09563920 77.09559965 -0.00003955 77.09560154 -0.00003766 77.09559276 -0.00004644 77.09563920 -0.00000000 nonbonded -99.17544400 -99.18004866 -0.00460466 -99.18004640 -0.00460240 -99.17992293 -0.00447893 -99.14636520 0.02907880 potential 22.26097200 22.25643608 -0.00453592 22.25643780 -0.00453420 22.25749200 -0.00348000 22.29013448 0.02916248 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 22.26097200 Difference in potential energy from amber=>gromacs conversion: -0.00453592 Difference in potential energy from amber=>lammps conversion: -0.00453420 Difference in potential energy from amber=>desmond conversion: -0.00348000 Difference in potential energy from amber=>charmm conversion: 0.02916248 ======================================================================= INFO 2017-03-19 00:21:46 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7829570.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7829570.inpcrd') INFO 2017-03-19 00:21:46 Beginning InterMol conversion INFO 2017-03-19 00:21:46 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:21:46 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:21:46 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7859387.inpcrd INFO 2017-03-19 00:21:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7859387/mobley_7859387_converted.input INFO 2017-03-19 00:21:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7859387/mobley_7859387_converted.cms WARNING 2017-03-19 00:22:02 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:22:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7859387/mobley_7859387_converted.inp INFO 2017-03-19 00:22:02 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7859387/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7859387/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7859387/mobley_7859387_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7859387/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -8.54850574 -8.54850574 0.00000000 0.00000000 0.00000000 0.00000000 -6.76117664 -6.76117664 coulomb total -6.78435600 -6.77832693 0.00602907 -6.77832686 0.00602914 -6.77829894 0.00605706 -6.76117664 0.02317936 coulomb-14 1.76690320 1.77017881 0.00327561 0.00000000 -1.76690320 1.77020187 0.00329867 0.00000000 -1.76690320 improper 0.00000000 0.01593966 0.01593966 0.00000000 0.00000000 0.00000000 0.00000000 0.01594104 0.01594104 proper 8.35335600 8.33739315 -0.01596285 8.35333341 -0.00002259 8.35332173 -0.00003427 8.33741496 -0.01594104 vdw (SR) 0.00000000 -2.16153667 -2.16153667 0.00000000 0.00000000 0.00000000 0.00000000 8.89652288 8.89652288 vdw total 8.89643920 8.89639550 -0.00004370 8.89639569 -0.00004351 8.89646680 0.00002760 8.89652288 0.00008368 vdw-14 11.05789360 11.05793217 0.00003857 0.00000000 -11.05789360 11.05800891 0.00011531 0.00000000 -11.05789360 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.88907600 1.88897913 -0.00009687 1.88897914 -0.00009686 1.88878579 -0.00029021 1.88895048 -0.00012552 bond 1.38406720 1.38412880 0.00006160 1.38412879 0.00006159 1.38374905 -0.00031815 1.38410904 0.00004184 bonded 11.62649920 11.62644073 -0.00005847 11.62644134 -0.00005786 11.62585658 -0.00064262 11.62641552 -0.00008368 dihedral 8.35335600 8.35333280 -0.00002320 8.35333341 -0.00002259 8.35332173 -0.00003427 8.35335600 0.00000000 nonbonded 2.11208320 2.11806857 0.00598537 2.11806879 0.00598559 2.11816786 0.00608466 2.13534624 0.02326304 potential 13.73858240 13.74450931 0.00592691 13.74451029 0.00592789 13.74395545 0.00537305 13.76176176 0.02317936 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 13.73858240 Difference in potential energy from amber=>gromacs conversion: 0.00592691 Difference in potential energy from amber=>lammps conversion: 0.00592789 Difference in potential energy from amber=>desmond conversion: 0.00537305 Difference in potential energy from amber=>charmm conversion: 0.02317936 ======================================================================= INFO 2017-03-19 00:22:02 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7859387.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7859387.inpcrd') INFO 2017-03-19 00:22:02 Beginning InterMol conversion INFO 2017-03-19 00:22:02 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:22:02 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:22:02 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7860938.inpcrd INFO 2017-03-19 00:22:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7860938/mobley_7860938_converted.input INFO 2017-03-19 00:22:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7860938/mobley_7860938_converted.cms WARNING 2017-03-19 00:22:18 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:22:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7860938/mobley_7860938_converted.inp INFO 2017-03-19 00:22:18 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7860938/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7860938/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7860938/mobley_7860938_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7860938/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 23.47813415 23.47813415 0.00000000 0.00000000 0.00000000 0.00000000 -11.40675552 -11.40675552 coulomb total -11.40558400 -11.38911784 0.01646616 -11.38911787 0.01646613 -11.38914121 0.01644279 -11.40675552 -0.00117152 coulomb-14 -34.86903760 -34.86725198 0.00178562 0.00000000 34.86903760 -34.86720434 0.00183326 0.00000000 34.86903760 proper 3.60702640 3.60705632 0.00002992 3.60705632 0.00002992 3.60705928 0.00003288 3.60706824 0.00004184 vdw (SR) 0.00000000 -4.09511544 -4.09511544 0.00000000 0.00000000 0.00000000 0.00000000 5.69463320 5.69463320 vdw total 5.69442400 5.69449400 0.00007000 5.69449387 0.00006987 5.69456024 0.00013624 5.69463320 0.00020920 vdw-14 9.78972320 9.78960945 -0.00011375 0.00000000 -9.78972320 9.78966224 -0.00006096 0.00000000 -9.78972320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 6.27767360 6.27780405 0.00013045 6.27780414 0.00013054 6.27793531 0.00026171 6.27775728 0.00008368 bond 3.29657360 3.29643876 -0.00013484 3.29643875 -0.00013485 3.29677785 0.00020425 3.29644808 -0.00012552 bonded 13.18127360 13.18129913 0.00002553 13.18129921 0.00002561 13.18177244 0.00049884 13.18127360 0.00000000 dihedral 3.60702640 3.60705632 0.00002992 3.60705632 0.00002992 3.60705928 0.00003288 3.60706824 0.00004184 nonbonded -5.71116000 -5.69462383 0.01653617 -5.69462358 0.01653642 -5.69458098 0.01657902 -5.71212232 -0.00096232 potential 7.47011360 7.48667530 0.01656170 7.48667555 0.01656195 7.48709252 0.01697892 7.46915128 -0.00096232 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 7.47011360 Difference in potential energy from amber=>gromacs conversion: 0.01656170 Difference in potential energy from amber=>lammps conversion: 0.01656195 Difference in potential energy from amber=>desmond conversion: 0.01697892 Difference in potential energy from amber=>charmm conversion: -0.00096232 ======================================================================= INFO 2017-03-19 00:22:18 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7860938.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7860938.inpcrd') INFO 2017-03-19 00:22:18 Beginning InterMol conversion INFO 2017-03-19 00:22:18 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:22:18 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:22:18 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7869158.inpcrd INFO 2017-03-19 00:22:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7869158/mobley_7869158_converted.input INFO 2017-03-19 00:22:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7869158/mobley_7869158_converted.cms WARNING 2017-03-19 00:22:34 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:22:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7869158/mobley_7869158_converted.inp INFO 2017-03-19 00:22:34 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7869158/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7869158/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7869158/mobley_7869158_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7869158/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 13.33787667 13.33787667 0.00000000 0.00000000 0.00000000 0.00000000 -44.16735000 -44.16735000 coulomb total -44.17843760 -44.17992073 -0.00148313 -44.17991874 -0.00148114 -44.17984995 -0.00141235 -44.16735000 0.01108760 coulomb-14 -57.51577440 -57.51779740 -0.00202300 0.00000000 57.51577440 -57.51784339 -0.00206899 0.00000000 57.51577440 proper 8.62489760 8.62501925 0.00012165 8.62501935 0.00012175 8.62506567 0.00016807 8.62481392 -0.00008368 vdw (SR) 0.00000000 8.21005344 8.21005344 0.00000000 0.00000000 0.00000000 0.00000000 26.79441968 26.79441968 vdw total 26.79433600 26.79417865 -0.00015735 26.79417910 -0.00015690 26.79400873 -0.00032727 26.79441968 0.00008368 vdw-14 18.58407280 18.58412521 0.00005241 0.00000000 -18.58407280 18.58412431 0.00005151 0.00000000 -18.58407280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.46976720 4.46983141 0.00006421 4.46983122 0.00006402 4.46983456 0.00006736 4.46989272 0.00012552 bond 1.96187760 1.96202160 0.00014400 1.96202161 0.00014401 1.96112256 -0.00075504 1.96200312 0.00012552 bonded 15.05654240 15.05687226 0.00032986 15.05687218 0.00032978 15.05602279 -0.00051961 15.05670976 0.00016736 dihedral 8.62489760 8.62501925 0.00012165 8.62501935 0.00012175 8.62506567 0.00016807 8.62481392 -0.00008368 nonbonded -17.38410160 -17.38574208 -0.00164048 -17.38574131 -0.00163971 -17.38584122 -0.00173962 -17.37293032 0.01117128 potential -2.32755920 -2.32886982 -0.00131062 -2.32886908 -0.00130988 -2.32987543 -0.00231623 -2.31617872 0.01138048 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -2.32755920 Difference in potential energy from amber=>gromacs conversion: -0.00131062 Difference in potential energy from amber=>lammps conversion: -0.00130988 Difference in potential energy from amber=>desmond conversion: -0.00231623 Difference in potential energy from amber=>charmm conversion: 0.01138048 ======================================================================= INFO 2017-03-19 00:22:34 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7869158.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7869158.inpcrd') INFO 2017-03-19 00:22:34 Beginning InterMol conversion INFO 2017-03-19 00:22:34 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:22:35 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:22:35 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7893124.inpcrd INFO 2017-03-19 00:22:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7893124/mobley_7893124_converted.input INFO 2017-03-19 00:22:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7893124/mobley_7893124_converted.cms WARNING 2017-03-19 00:22:50 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:22:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7893124/mobley_7893124_converted.inp INFO 2017-03-19 00:22:50 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7893124/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7893124/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7893124/mobley_7893124_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7893124/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -8.00983403 -8.00983403 0.00000000 0.00000000 0.00000000 0.00000000 -18.23454144 -18.23454144 coulomb total -18.24224000 -18.23174010 0.01049990 -18.23173983 0.01050017 -18.23178218 0.01045782 -18.23454144 0.00769856 coulomb-14 -10.21607280 -10.22190607 -0.00583327 0.00000000 10.21607280 -10.22186902 -0.00579622 0.00000000 10.21607280 improper 0.00000000 0.00004528 0.00004528 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.12677520 0.12670828 -0.00006692 0.12675354 -0.00002166 0.12674149 -0.00003371 0.12669152 -0.00008368 vdw (SR) 0.00000000 6.40284186 6.40284186 0.00000000 0.00000000 0.00000000 0.00000000 35.20179112 35.20179112 vdw total 35.20166560 35.20163240 -0.00003320 35.20163255 -0.00003305 35.20133791 -0.00032769 35.20179112 0.00012552 vdw-14 28.79889040 28.79879054 -0.00009986 0.00000000 -28.79889040 28.79855263 -0.00033777 0.00000000 -28.79889040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.09820400 5.09811181 -0.00009219 5.09811195 -0.00009205 5.09837165 0.00016765 5.09803664 -0.00016736 bond 2.12379840 2.12369130 -0.00010710 2.12369129 -0.00010711 2.12367059 -0.00012781 2.12367288 -0.00012552 bonded 7.34877760 7.34855667 -0.00022093 7.34855679 -0.00022081 7.34878373 0.00000613 7.34844288 -0.00033472 dihedral 0.12677520 0.12675356 -0.00002164 0.12675354 -0.00002166 0.12674149 -0.00003371 0.12673336 -0.00004184 nonbonded 16.95942560 16.96989230 0.01046670 16.96989271 0.01046711 16.96955573 0.01013013 16.96724968 0.00782408 potential 24.30820320 24.31844897 0.01024577 24.31844940 0.01024620 24.31825082 0.01004762 24.31569256 0.00748936 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 24.30820320 Difference in potential energy from amber=>gromacs conversion: 0.01024577 Difference in potential energy from amber=>lammps conversion: 0.01024620 Difference in potential energy from amber=>desmond conversion: 0.01004762 Difference in potential energy from amber=>charmm conversion: 0.00748936 ======================================================================= INFO 2017-03-19 00:22:50 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7893124.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7893124.inpcrd') INFO 2017-03-19 00:22:51 Beginning InterMol conversion INFO 2017-03-19 00:22:51 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:22:51 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:22:51 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7912193.inpcrd INFO 2017-03-19 00:22:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7912193/mobley_7912193_converted.input INFO 2017-03-19 00:22:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7912193/mobley_7912193_converted.cms WARNING 2017-03-19 00:23:06 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:23:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7912193/mobley_7912193_converted.inp INFO 2017-03-19 00:23:06 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7912193/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7912193/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7912193/mobley_7912193_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7912193/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 9.42853862 9.42853862 0.00000000 0.00000000 0.00000000 0.00000000 -108.88588040 -108.88588040 coulomb total -108.72082160 -108.72464241 -0.00382081 -108.72464159 -0.00381999 -108.72510648 -0.00428488 -108.88588040 -0.16505880 coulomb-14 -118.14904720 -118.15318103 -0.00413383 0.00000000 118.14904720 -118.15325338 -0.00420618 0.00000000 118.14904720 improper 0.00000000 0.00009643 0.00009643 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 11.63821440 11.63794315 -0.00027125 11.63803951 -0.00017489 11.63801905 -0.00019535 11.63796336 -0.00025104 vdw (SR) 0.00000000 -0.68261310 -0.68261310 0.00000000 0.00000000 0.00000000 0.00000000 32.38298848 32.38298848 vdw total 32.38290480 32.38276448 -0.00014032 32.38276464 -0.00014016 32.38322259 0.00031779 32.38298848 0.00008368 vdw-14 33.06531520 33.06537758 0.00006238 0.00000000 -33.06531520 33.06557285 0.00025765 0.00000000 -33.06531520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.85848480 3.85836463 -0.00012017 3.85836464 -0.00012016 3.85792036 -0.00056444 3.85835928 -0.00012552 bond 2.61416320 2.61399900 -0.00016420 2.61399902 -0.00016418 2.61381392 -0.00034928 2.61399584 -0.00016736 bonded 18.11086240 18.11040322 -0.00045918 18.11040316 -0.00045924 18.10975333 -0.00110907 18.11040216 -0.00046024 dihedral 11.63821440 11.63803958 -0.00017482 11.63803951 -0.00017489 11.63801905 -0.00019535 11.63804704 -0.00016736 nonbonded -76.33791680 -76.34187793 -0.00396113 -76.34187486 -0.00395806 -76.34188389 -0.00396709 -76.50289192 -0.16497512 potential -58.22705440 -58.23147471 -0.00442031 -58.23147270 -0.00441830 -58.23229653 -0.00524213 -58.39248976 -0.16543536 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -58.22705440 Difference in potential energy from amber=>gromacs conversion: -0.00442031 Difference in potential energy from amber=>lammps conversion: -0.00441830 Difference in potential energy from amber=>desmond conversion: -0.00524213 Difference in potential energy from amber=>charmm conversion: -0.16543536 ======================================================================= INFO 2017-03-19 00:23:06 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7912193.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7912193.inpcrd') INFO 2017-03-19 00:23:07 Beginning InterMol conversion INFO 2017-03-19 00:23:07 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:23:07 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:23:07 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7913234.inpcrd INFO 2017-03-19 00:23:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7913234/mobley_7913234_converted.input INFO 2017-03-19 00:23:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7913234/mobley_7913234_converted.cms WARNING 2017-03-19 00:23:23 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:23:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7913234/mobley_7913234_converted.inp INFO 2017-03-19 00:23:23 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7913234/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7913234/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7913234/mobley_7913234_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7913234/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -70.26188287 -70.26188287 0.00000000 0.00000000 0.00000000 0.00000000 13.98263512 13.98263512 coulomb total 13.99004080 13.97479401 -0.01524679 13.97479389 -0.01524691 13.97518760 -0.01485320 13.98263512 -0.00740568 coulomb-14 84.22684880 84.23667688 0.00982808 0.00000000 -84.22684880 84.23668622 0.00983742 0.00000000 -84.22684880 proper 15.43937840 15.43931341 -0.00006499 15.43931355 -0.00006485 15.43932259 -0.00005581 15.43971312 0.00033472 vdw (SR) 0.00000000 -3.98952707 -3.98952707 0.00000000 0.00000000 0.00000000 0.00000000 5.20841056 5.20841056 vdw total 5.20866160 5.20823672 -0.00042488 5.20823692 -0.00042468 5.20821215 -0.00044945 5.20841056 -0.00025104 vdw-14 9.19810560 9.19776379 -0.00034181 0.00000000 -9.19810560 9.19774050 -0.00036510 0.00000000 -9.19810560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.29785280 2.29766325 -0.00018955 2.29766326 -0.00018954 2.29751372 -0.00033908 2.29764360 -0.00020920 bond 2.04011840 2.04010862 -0.00000978 2.04010861 -0.00000979 2.03952627 -0.00059213 2.04011840 0.00000000 bonded 19.77734960 19.77708528 -0.00026432 19.77708542 -0.00026418 19.77636258 -0.00098702 19.77747512 0.00012552 dihedral 15.43937840 15.43931341 -0.00006499 15.43931355 -0.00006485 15.43932259 -0.00005581 15.43971312 0.00033472 nonbonded 19.19870240 19.18303073 -0.01567167 19.18303081 -0.01567159 19.18339975 -0.01530265 19.19104568 -0.00765672 potential 38.97605200 38.96011600 -0.01593600 38.96011598 -0.01593602 38.95966582 -0.01638618 38.96847896 -0.00757304 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 38.97605200 Difference in potential energy from amber=>gromacs conversion: -0.01593600 Difference in potential energy from amber=>lammps conversion: -0.01593602 Difference in potential energy from amber=>desmond conversion: -0.01638618 Difference in potential energy from amber=>charmm conversion: -0.00757304 ======================================================================= INFO 2017-03-19 00:23:23 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7913234.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7913234.inpcrd') INFO 2017-03-19 00:23:23 Beginning InterMol conversion INFO 2017-03-19 00:23:23 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:23:23 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:23:23 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7943327.inpcrd INFO 2017-03-19 00:23:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7943327/mobley_7943327_converted.input INFO 2017-03-19 00:23:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7943327/mobley_7943327_converted.cms WARNING 2017-03-19 00:23:39 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:23:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7943327/mobley_7943327_converted.inp INFO 2017-03-19 00:23:39 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7943327/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7943327/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7943327/mobley_7943327_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7943327/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -48.01286440 -48.01286440 0.00000000 0.00000000 0.00000000 0.00000000 -78.03339912 -78.03339912 coulomb total -78.01821120 -78.02066006 -0.00244886 -78.02065884 -0.00244764 -78.02055575 -0.00234455 -78.03339912 -0.01518792 coulomb-14 -30.00681120 -30.00779566 -0.00098446 0.00000000 30.00681120 -30.00767963 -0.00086843 0.00000000 30.00681120 improper 0.00000000 0.00000317 0.00000317 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 13.13399440 13.13401552 0.00002112 13.13401867 0.00002427 13.13403126 0.00003686 13.13403624 0.00004184 vdw (SR) 0.00000000 -2.10481559 -2.10481559 0.00000000 0.00000000 0.00000000 0.00000000 8.55075712 8.55075712 vdw total 8.55042240 8.55064980 0.00022740 8.55065001 0.00022761 8.55053659 0.00011419 8.55075712 0.00033472 vdw-14 10.65539280 10.65546538 0.00007258 0.00000000 -10.65539280 10.65534192 -0.00005088 0.00000000 -10.65539280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.86687680 2.86670840 -0.00016840 2.86670839 -0.00016841 2.86675816 -0.00011864 2.86675128 -0.00012552 bond 2.47316240 2.47319041 0.00002801 2.47319043 0.00002803 2.47301545 -0.00014695 2.47320424 0.00004184 bonded 18.47403360 18.47391750 -0.00011610 18.47391749 -0.00011611 18.47380488 -0.00022872 18.47399176 -0.00004184 dihedral 13.13399440 13.13401868 0.00002428 13.13401867 0.00002427 13.13403126 0.00003686 13.13403624 0.00004184 nonbonded -69.46778880 -69.47001026 -0.00222146 -69.47001050 -0.00222170 -69.47001915 -0.00223035 -69.48264200 -0.01485320 potential -50.99375520 -50.99609277 -0.00233757 -50.99608987 -0.00233467 -50.99625723 -0.00250203 -51.00869208 -0.01493688 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -50.99375520 Difference in potential energy from amber=>gromacs conversion: -0.00233757 Difference in potential energy from amber=>lammps conversion: -0.00233467 Difference in potential energy from amber=>desmond conversion: -0.00250203 Difference in potential energy from amber=>charmm conversion: -0.01493688 ======================================================================= INFO 2017-03-19 00:23:39 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7943327.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7943327.inpcrd') INFO 2017-03-19 00:23:39 Beginning InterMol conversion INFO 2017-03-19 00:23:39 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:23:39 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:23:39 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7977115.inpcrd INFO 2017-03-19 00:23:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7977115/mobley_7977115_converted.input INFO 2017-03-19 00:23:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7977115/mobley_7977115_converted.cms WARNING 2017-03-19 00:23:55 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:23:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7977115/mobley_7977115_converted.inp INFO 2017-03-19 00:23:55 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7977115/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7977115/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7977115/mobley_7977115_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7977115/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -6.84489360 -6.84489360 0.00000000 0.00000000 0.00000000 0.00000000 -24.40719664 -24.40719664 coulomb total -24.44376480 -24.43177544 0.01198936 -24.43177513 0.01198967 -24.43192090 0.01184390 -24.40719664 0.03656816 coulomb-14 -17.58451520 -17.58688184 -0.00236664 0.00000000 17.58451520 -17.58684686 -0.00233166 0.00000000 17.58451520 proper 11.35328400 11.35311926 -0.00016474 11.35311915 -0.00016485 11.35311986 -0.00016414 11.35311664 -0.00016736 vdw (SR) 0.00000000 -0.12962950 -0.12962950 0.00000000 0.00000000 0.00000000 0.00000000 9.22990400 9.22990400 vdw total 9.22990400 9.22971646 -0.00018754 9.22971656 -0.00018744 9.22978927 -0.00011473 9.22990400 -0.00000000 vdw-14 9.35960800 9.35934596 -0.00026204 0.00000000 -9.35960800 9.35940985 -0.00019815 0.00000000 -9.35960800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.82208400 3.82214564 0.00006164 3.82214563 0.00006163 3.82256102 0.00047702 3.82212584 0.00004184 bond 0.88073200 0.88059835 -0.00013365 0.88059836 -0.00013364 0.88103745 0.00030545 0.88060648 -0.00012552 bonded 16.05610000 16.05586326 -0.00023674 16.05586314 -0.00023686 16.05671833 0.00061833 16.05584896 -0.00025104 dihedral 11.35328400 11.35311926 -0.00016474 11.35311915 -0.00016485 11.35311986 -0.00016414 11.35311664 -0.00016736 nonbonded -15.21386080 -15.20205898 0.01180182 -15.20205857 0.01180223 -15.20213163 0.01172917 -15.17729264 0.03656816 potential 0.84223920 0.85380428 0.01156508 0.85380465 0.01156545 0.85452819 0.01228899 0.87855632 0.03631712 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 0.84223920 Difference in potential energy from amber=>gromacs conversion: 0.01156508 Difference in potential energy from amber=>lammps conversion: 0.01156545 Difference in potential energy from amber=>desmond conversion: 0.01228899 Difference in potential energy from amber=>charmm conversion: 0.03631712 ======================================================================= INFO 2017-03-19 00:23:55 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7977115.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7977115.inpcrd') INFO 2017-03-19 00:23:55 Beginning InterMol conversion INFO 2017-03-19 00:23:55 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:23:55 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:23:55 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7983227.inpcrd INFO 2017-03-19 00:23:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7983227/mobley_7983227_converted.input INFO 2017-03-19 00:23:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7983227/mobley_7983227_converted.cms WARNING 2017-03-19 00:24:11 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:24:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7983227/mobley_7983227_converted.inp INFO 2017-03-19 00:24:11 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7983227/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7983227/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7983227/mobley_7983227_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7983227/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -30.56068372 -30.56068372 0.00000000 0.00000000 0.00000000 0.00000000 1.95543424 1.95543424 coulomb total 1.96731680 1.95840333 -0.00891347 1.95840329 -0.00891351 1.95838701 -0.00892979 1.95543424 -0.01188256 coulomb-14 32.52181360 32.51908705 -0.00272655 0.00000000 -32.52181360 32.51908128 -0.00273232 0.00000000 -32.52181360 proper 3.88944640 3.88935367 -0.00009273 3.88935130 -0.00009510 3.88935514 -0.00009126 3.88936272 -0.00008368 vdw (SR) 0.00000000 1.36553903 1.36553903 0.00000000 0.00000000 0.00000000 0.00000000 9.66688096 9.66688096 vdw total 9.66713200 9.66673109 -0.00040091 9.66673117 -0.00040083 9.66673086 -0.00040114 9.66688096 -0.00025104 vdw-14 8.30147440 8.30119206 -0.00028234 0.00000000 -8.30147440 8.30122173 -0.00025267 0.00000000 -8.30147440 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.10910640 4.10891497 -0.00019143 4.10891498 -0.00019142 4.10911741 0.00001101 4.10889720 -0.00020920 bond 0.51295840 0.51295095 -0.00000745 0.51295095 -0.00000745 0.51300169 0.00004329 0.51295840 0.00000000 bonded 8.51151120 8.51121959 -0.00029161 8.51121723 -0.00029397 8.51147424 -0.00003696 8.51121832 -0.00029288 dihedral 3.88944640 3.88935367 -0.00009273 3.88935130 -0.00009510 3.88935514 -0.00009126 3.88936272 -0.00008368 nonbonded 11.63444880 11.62513442 -0.00931438 11.62513480 -0.00931400 11.62511787 -0.00933093 11.62231520 -0.01213360 potential 20.14596000 20.13635400 -0.00960600 20.13635186 -0.00960814 20.13655303 -0.00940697 20.13353352 -0.01242648 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 20.14596000 Difference in potential energy from amber=>gromacs conversion: -0.00960600 Difference in potential energy from amber=>lammps conversion: -0.00960814 Difference in potential energy from amber=>desmond conversion: -0.00940697 Difference in potential energy from amber=>charmm conversion: -0.01242648 ======================================================================= INFO 2017-03-19 00:24:11 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7983227.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7983227.inpcrd') INFO 2017-03-19 00:24:11 Beginning InterMol conversion INFO 2017-03-19 00:24:11 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:24:11 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7988076.inpcrd INFO 2017-03-19 00:24:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7988076/mobley_7988076_converted.input INFO 2017-03-19 00:24:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7988076/mobley_7988076_converted.cms INFO 2017-03-19 00:24:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7988076/mobley_7988076_converted.rst7 WARNING 2017-03-19 00:24:27 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:24:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7988076/mobley_7988076_converted.inp INFO 2017-03-19 00:24:27 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7988076/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7988076/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7988076/mobley_7988076_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_7988076/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7988076/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 61.46253212 61.46253212 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -64.88137168 -64.88137168 coulomb total -64.82940640 -64.83172761 -0.00232121 -64.83172852 -0.00232212 -64.83208751 -0.00268111 -64.82940640 0.00000000 -64.88137168 -0.05196528 coulomb-14 -126.28985600 -126.29425973 -0.00440373 0.00000000 126.28985600 -126.29414083 -0.00428483 -126.28985600 0.00000000 0.00000000 126.28985600 improper 0.00000000 0.00016794 0.00016794 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00016736 0.00016736 proper 0.00041840 0.00009496 -0.00032344 0.00026302 -0.00015538 0.00026210 -0.00015630 0.00041840 0.00000000 0.00008368 -0.00033472 vdw (SR) 0.00000000 -1.21764588 -1.21764588 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 17.70375920 17.70375920 vdw total 17.70375920 17.70373447 -0.00002473 17.70373451 -0.00002469 17.70380398 0.00004478 17.70375920 0.00000000 17.70375920 -0.00000000 vdw-14 18.92130320 18.92138034 0.00007714 0.00000000 -18.92130320 18.92143721 0.00013401 18.92130320 0.00000000 0.00000000 -18.92130320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.61714000 0.61720269 0.00006269 0.61720268 0.00006268 0.61716571 0.00002571 0.61714000 0.00000000 0.61722368 0.00008368 bond 3.42125680 3.42143527 0.00017847 3.42143525 0.00017845 3.42065226 -0.00060454 3.42125680 0.00000000 3.42142416 0.00016736 bonded 4.03881520 4.03890086 0.00008566 4.03890095 0.00008575 4.03808007 -0.00073513 4.03881520 0.00000000 4.03889888 0.00008368 dihedral 0.00041840 0.00026290 -0.00015550 0.00026302 -0.00015538 0.00026210 -0.00015630 0.00041840 0.00000000 0.00025104 -0.00016736 nonbonded -47.12564720 -47.12799315 -0.00234595 -47.12799442 -0.00234722 -47.12828353 -0.00263633 -47.12564720 0.00000000 -47.17761248 -0.05196528 potential -43.08683200 -43.08909229 -0.00226029 -43.08909136 -0.00225936 -43.09027376 -0.00344176 -43.08683200 0.00000000 -43.13871360 -0.05188160 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -43.08683200 Difference in potential energy from amber=>gromacs conversion: -0.00226029 Difference in potential energy from amber=>lammps conversion: -0.00225936 Difference in potential energy from amber=>desmond conversion: -0.00344176 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.05188160 ======================================================================= INFO 2017-03-19 00:24:27 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7988076.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7988076.inpcrd') INFO 2017-03-19 00:24:27 Beginning InterMol conversion INFO 2017-03-19 00:24:27 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:24:27 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:24:27 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8006582.inpcrd INFO 2017-03-19 00:24:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8006582/mobley_8006582_converted.input INFO 2017-03-19 00:24:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8006582/mobley_8006582_converted.cms WARNING 2017-03-19 00:24:43 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:24:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8006582/mobley_8006582_converted.inp INFO 2017-03-19 00:24:43 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8006582/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8006582/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8006582/mobley_8006582_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8006582/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 12.18351442 12.18351442 0.00000000 0.00000000 0.00000000 0.00000000 2.39969136 2.39969136 coulomb total 2.43257760 2.39876385 -0.03381375 2.39876381 -0.03381379 2.39875536 -0.03382224 2.39969136 -0.03288624 coulomb-14 -9.77047680 -9.78475057 -0.01427377 0.00000000 9.77047680 -9.78475127 -0.01427447 0.00000000 9.77047680 proper 33.92638240 33.92644122 0.00005882 33.92644139 0.00005899 33.92639591 0.00001351 33.92642424 0.00004184 vdw (SR) 0.00000000 -0.56345781 -0.56345781 0.00000000 0.00000000 0.00000000 0.00000000 2.44722160 2.44722160 vdw total 2.44722160 2.44713920 -0.00008240 2.44713922 -0.00008238 2.44710212 -0.00011948 2.44722160 -0.00000000 vdw-14 3.01080640 3.01059700 -0.00020940 0.00000000 -3.01080640 3.01055953 -0.00024687 0.00000000 -3.01080640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 17.52091840 17.52074709 -0.00017131 17.52074727 -0.00017113 17.52079957 -0.00011883 17.52062552 -0.00029288 bond 1.18449040 1.18433311 -0.00015729 1.18433312 -0.00015728 1.18434312 -0.00014728 1.18432304 -0.00016736 bonded 52.63179120 52.63152142 -0.00026978 52.63152179 -0.00026941 52.63153861 -0.00025259 52.63137280 -0.00041840 dihedral 33.92638240 33.92644122 0.00005882 33.92644139 0.00005899 33.92639591 0.00001351 33.92642424 0.00004184 nonbonded 4.87979920 4.84590305 -0.03389615 4.84590294 -0.03389626 4.84585747 -0.03394173 4.84691296 -0.03288624 potential 57.51159040 57.47742447 -0.03416593 57.47742386 -0.03416654 57.47736905 -0.03422135 57.47828576 -0.03330464 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 57.51159040 Difference in potential energy from amber=>gromacs conversion: -0.03416593 Difference in potential energy from amber=>lammps conversion: -0.03416654 Difference in potential energy from amber=>desmond conversion: -0.03422135 Difference in potential energy from amber=>charmm conversion: -0.03330464 ======================================================================= INFO 2017-03-19 00:24:43 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8006582.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8006582.inpcrd') INFO 2017-03-19 00:24:43 Beginning InterMol conversion INFO 2017-03-19 00:24:43 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:24:43 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:24:43 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8011706.inpcrd INFO 2017-03-19 00:24:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8011706/mobley_8011706_converted.input INFO 2017-03-19 00:24:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8011706/mobley_8011706_converted.cms WARNING 2017-03-19 00:24:59 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:24:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8011706/mobley_8011706_converted.inp INFO 2017-03-19 00:24:59 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8011706/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8011706/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8011706/mobley_8011706_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8011706/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -49.33718132 -49.33718132 0.00000000 0.00000000 0.00000000 0.00000000 -10.94049056 -10.94049056 coulomb total -10.90183040 -10.91590465 -0.01407425 -10.91590454 -0.01407414 -10.91587019 -0.01403979 -10.94049056 -0.03866016 coulomb-14 38.44761280 38.42127667 -0.02633613 0.00000000 -38.44761280 38.42122854 -0.02638426 0.00000000 -38.44761280 improper 0.00000000 0.00002223 0.00002223 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00000000 0.00001457 0.00001457 0.00003678 0.00003678 0.00003043 0.00003043 0.00000000 0.00000000 vdw (SR) 0.00000000 -0.01894634 -0.01894634 0.00000000 0.00000000 0.00000000 0.00000000 4.97465048 4.97465048 vdw total 4.97477600 4.97460931 -0.00016669 4.97460948 -0.00016652 4.97453929 -0.00023671 4.97465048 -0.00012552 vdw-14 4.99360400 4.99355566 -0.00004834 0.00000000 -4.99360400 4.99349810 -0.00010590 0.00000000 -4.99360400 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.13376800 5.13387301 0.00010501 5.13387302 0.00010502 5.13356420 -0.00020380 5.13393536 0.00016736 bond 3.70786080 3.70797321 0.00011241 3.70797322 0.00011242 3.70837652 0.00051572 3.70798632 0.00012552 bonded 8.84162880 8.84188302 0.00025422 8.84188302 0.00025422 8.84197115 0.00034235 8.84196352 0.00033472 dihedral 0.00000000 0.00003680 0.00003680 0.00003678 0.00003678 0.00003043 0.00003043 0.00004184 0.00004184 nonbonded -5.92705440 -5.94129534 -0.01424094 -5.94129506 -0.01424066 -5.94133090 -0.01427650 -5.96584008 -0.03878568 potential 2.91457440 2.90058768 -0.01398672 2.90058787 -0.01398653 2.90062445 -0.01394995 2.87612344 -0.03845096 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 2.91457440 Difference in potential energy from amber=>gromacs conversion: -0.01398672 Difference in potential energy from amber=>lammps conversion: -0.01398653 Difference in potential energy from amber=>desmond conversion: -0.01394995 Difference in potential energy from amber=>charmm conversion: -0.03845096 ======================================================================= INFO 2017-03-19 00:24:59 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8011706.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8011706.inpcrd') INFO 2017-03-19 00:24:59 Beginning InterMol conversion INFO 2017-03-19 00:24:59 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:24:59 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:24:59 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8048190.inpcrd INFO 2017-03-19 00:25:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8048190/mobley_8048190_converted.input INFO 2017-03-19 00:25:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8048190/mobley_8048190_converted.cms WARNING 2017-03-19 00:25:15 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:25:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8048190/mobley_8048190_converted.inp INFO 2017-03-19 00:25:15 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8048190/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8048190/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8048190/mobley_8048190_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8048190/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 51.12494671 51.12494671 0.00000000 0.00000000 0.00000000 0.00000000 -245.81251040 -245.81251040 coulomb total -245.74514800 -245.75325065 -0.00810265 -245.75324822 -0.00810022 -245.75349466 -0.00834666 -245.81251040 -0.06736240 coulomb-14 -296.86818880 -296.87819737 -0.01000857 0.00000000 296.86818880 -296.87840404 -0.01021524 0.00000000 296.86818880 improper 0.00000000 0.01735195 0.01735195 0.00000000 0.00000000 0.00000000 0.00000000 0.01736360 0.01736360 proper 27.80393520 27.78649441 -0.01744079 27.80384775 -0.00008745 27.80390315 -0.00003205 27.78648792 -0.01744728 vdw (SR) 0.00000000 -0.08577778 -0.08577778 0.00000000 0.00000000 0.00000000 0.00000000 1.81443344 1.81443344 vdw total 1.81460080 1.81443732 -0.00016348 1.81443733 -0.00016347 1.81446988 -0.00013092 1.81443344 -0.00016736 vdw-14 1.90037280 1.90021511 -0.00015769 0.00000000 -1.90037280 1.90024773 -0.00012507 0.00000000 -1.90037280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.63257280 2.63242076 -0.00015204 2.63242075 -0.00015205 2.63256729 -0.00000551 2.63248912 -0.00008368 bond 2.50245040 2.50245814 0.00000774 2.50245814 0.00000774 2.50189941 -0.00055099 2.50245040 0.00000000 bonded 32.93895840 32.93872527 -0.00023313 32.93872665 -0.00023175 32.93836985 -0.00058855 32.93879104 -0.00016736 dihedral 27.80393520 27.80384636 -0.00008884 27.80384775 -0.00008745 27.80390315 -0.00003205 27.80385152 -0.00008368 nonbonded -243.93054720 -243.93881333 -0.00826613 -243.93881060 -0.00826340 -243.93902478 -0.00847758 -243.99807696 -0.06752976 potential -210.99158880 -211.00008806 -0.00849926 -211.00008232 -0.00849352 -211.00066892 -0.00908012 -211.05928592 -0.06769712 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -210.99158880 Difference in potential energy from amber=>gromacs conversion: -0.00849926 Difference in potential energy from amber=>lammps conversion: -0.00849352 Difference in potential energy from amber=>desmond conversion: -0.00908012 Difference in potential energy from amber=>charmm conversion: -0.06769712 ======================================================================= INFO 2017-03-19 00:25:15 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8048190.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8048190.inpcrd') INFO 2017-03-19 00:25:15 Beginning InterMol conversion INFO 2017-03-19 00:25:15 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:25:16 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8052240.inpcrd INFO 2017-03-19 00:25:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8052240/mobley_8052240_converted.input INFO 2017-03-19 00:25:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8052240/mobley_8052240_converted.cms INFO 2017-03-19 00:25:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8052240/mobley_8052240_converted.rst7 WARNING 2017-03-19 00:25:31 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:25:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8052240/mobley_8052240_converted.inp INFO 2017-03-19 00:25:31 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8052240/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8052240/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8052240/mobley_8052240_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_8052240/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8052240/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 63.48959096 63.48959096 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -52.73551256 -52.73551256 coulomb total -52.74643280 -52.74841623 -0.00198343 -52.74841602 -0.00198322 -52.74973439 -0.00330159 -52.74643280 0.00000000 -52.73551256 0.01092024 coulomb-14 -116.23403040 -116.23800720 -0.00397680 0.00000000 116.23403040 -116.23825373 -0.00422333 -116.23403040 0.00000000 0.00000000 116.23403040 improper 0.00000000 0.11320975 0.11320975 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.11321904 0.11321904 proper 0.21631280 0.10302144 -0.11329136 0.21622997 -0.00008283 0.21631004 -0.00000276 0.21631280 0.00000000 0.10301008 -0.11330272 vdw (SR) 0.00000000 10.67018321 10.67018321 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 62.92238104 62.92238104 vdw total 62.92275760 62.92233872 -0.00041888 62.92233920 -0.00041840 62.92185712 -0.00090048 62.92233920 -0.00041840 62.92238104 -0.00037656 vdw-14 52.25230240 52.25215551 -0.00014689 0.00000000 -52.25230240 52.25177020 -0.00053220 52.25230240 0.00000000 0.00000000 -52.25230240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 9.79641760 9.79658322 0.00016562 9.79658329 0.00016569 9.79579243 -0.00062517 9.79641760 0.00000000 9.79654312 0.00012552 bond 9.08471920 9.08473452 0.00001532 9.08473468 0.00001548 9.08514438 0.00042518 9.08471920 0.00000000 9.08471920 0.00000000 bonded 19.09744960 19.09754893 0.00009933 19.09754794 0.00009834 19.09724684 -0.00020276 19.09744960 0.00000000 19.09749144 0.00004184 dihedral 0.21631280 0.21623119 -0.00008161 0.21622997 -0.00008283 0.21631004 -0.00000276 0.21631280 0.00000000 0.21622912 -0.00008368 nonbonded 10.17632480 10.17392249 -0.00240231 10.17392318 -0.00240162 10.17212273 -0.00420207 10.17590640 -0.00041840 10.18686848 0.01054368 potential 29.27377440 29.27147142 -0.00230298 29.27147069 -0.00230371 29.26921669 -0.00455771 29.27335600 -0.00041840 29.28435992 0.01058552 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 29.27377440 Difference in potential energy from amber=>gromacs conversion: -0.00230298 Difference in potential energy from amber=>lammps conversion: -0.00230371 Difference in potential energy from amber=>desmond conversion: -0.00455771 Difference in potential energy from amber=>amber conversion: -0.00041840 Difference in potential energy from amber=>charmm conversion: 0.01058552 ======================================================================= INFO 2017-03-19 00:25:31 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8052240.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8052240.inpcrd') INFO 2017-03-19 00:25:32 Beginning InterMol conversion INFO 2017-03-19 00:25:32 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:25:32 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8057732.inpcrd INFO 2017-03-19 00:25:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8057732/mobley_8057732_converted.input INFO 2017-03-19 00:25:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8057732/mobley_8057732_converted.cms INFO 2017-03-19 00:25:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8057732/mobley_8057732_converted.rst7 WARNING 2017-03-19 00:25:47 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:25:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8057732/mobley_8057732_converted.inp INFO 2017-03-19 00:25:47 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8057732/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8057732/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8057732/mobley_8057732_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_8057732/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8057732/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 83.19899454 83.19899454 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -91.82721032 -91.82721032 coulomb total -91.79026560 -91.80897342 -0.01870782 -91.80897226 -0.01870666 -91.80945217 -0.01918657 -91.79026560 0.00000000 -91.82721032 -0.03694472 coulomb-14 -175.00542320 -175.00796796 -0.00254476 0.00000000 175.00542320 -175.00782189 -0.00239869 -175.00542320 0.00000000 0.00000000 175.00542320 improper 0.00000000 0.00002421 0.00002421 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00020922 -0.00020918 0.00023344 -0.00018496 0.00023592 -0.00018248 0.00041840 0.00000000 0.00020920 -0.00020920 vdw (SR) 0.00000000 -1.65157727 -1.65157727 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 14.27095456 14.27095456 vdw total 14.27120560 14.27096870 -0.00023690 14.27096879 -0.00023681 14.27100141 -0.00020419 14.27120560 0.00000000 14.27095456 -0.00025104 vdw-14 15.92263040 15.92254597 -0.00008443 0.00000000 -15.92263040 15.92257521 -0.00005519 15.92263040 0.00000000 0.00000000 -15.92263040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.21296560 0.21313282 0.00016722 0.21313281 0.00016721 0.21321428 0.00024868 0.21296560 0.00000000 0.21313296 0.00016736 bond 0.83052400 0.83043507 -0.00008893 0.83043509 -0.00008891 0.83020256 -0.00032144 0.83052400 0.00000000 0.83044032 -0.00008368 bonded 1.04390800 1.04380131 -0.00010669 1.04380134 -0.00010666 1.04365276 -0.00025524 1.04390800 0.00000000 1.04382432 -0.00008368 dihedral 0.00041840 0.00023343 -0.00018497 0.00023344 -0.00018496 0.00023592 -0.00018248 0.00041840 0.00000000 0.00025104 -0.00016736 nonbonded -77.51906000 -77.53800471 -0.01894471 -77.53800515 -0.01894515 -77.53845076 -0.01939076 -77.51906000 0.00000000 -77.55625576 -0.03719576 potential -76.47515200 -76.49420340 -0.01905140 -76.49420175 -0.01904975 -76.49484609 -0.01969409 -76.47515200 0.00000000 -76.51243144 -0.03727944 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -76.47515200 Difference in potential energy from amber=>gromacs conversion: -0.01905140 Difference in potential energy from amber=>lammps conversion: -0.01904975 Difference in potential energy from amber=>desmond conversion: -0.01969409 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.03727944 ======================================================================= INFO 2017-03-19 00:25:47 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8057732.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8057732.inpcrd') INFO 2017-03-19 00:25:48 Beginning InterMol conversion INFO 2017-03-19 00:25:48 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:25:48 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:25:48 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8117218.inpcrd INFO 2017-03-19 00:25:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8117218/mobley_8117218_converted.input INFO 2017-03-19 00:25:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8117218/mobley_8117218_converted.cms WARNING 2017-03-19 00:26:04 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:26:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8117218/mobley_8117218_converted.inp INFO 2017-03-19 00:26:04 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8117218/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8117218/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8117218/mobley_8117218_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8117218/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -10.11988074 -10.11988074 0.00000000 0.00000000 0.00000000 0.00000000 31.30899752 31.30899752 coulomb total 31.29841200 31.30330692 0.00489492 31.30330644 0.00489444 31.30322586 0.00481386 31.30899752 0.01058552 coulomb-14 41.42076320 41.42318766 0.00242446 0.00000000 -41.42076320 41.42318766 0.00242446 0.00000000 -41.42076320 improper 0.00000000 0.03890731 0.03890731 0.00000000 0.00000000 0.00000000 0.00000000 0.03891120 0.03891120 proper 92.09695280 92.05796110 -0.03899170 92.09686912 -0.00008368 92.09686494 -0.00008786 92.06235112 -0.03460168 vdw (SR) 0.00000000 22.42901466 22.42901466 0.00000000 0.00000000 0.00000000 0.00000000 65.06492376 65.06492376 vdw total 65.06496560 65.06436193 -0.00060367 65.06436310 -0.00060250 65.06295950 -0.00200610 65.06492376 -0.00004184 vdw-14 42.63537840 42.63534728 -0.00003112 0.00000000 -42.63537840 42.63517213 -0.00020627 0.00000000 -42.63537840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 365.55566160 365.55569309 0.00003149 365.55569507 0.00003347 365.55537081 -0.00029079 365.55499216 -0.00066944 bond 26.44120640 26.44113159 -0.00007481 26.44113151 -0.00007489 26.44103101 -0.00017539 26.44112272 -0.00008368 bonded 484.09382080 484.09369309 -0.00012771 484.09369570 -0.00012510 484.09326675 -0.00055405 484.09737720 0.00355640 dihedral 92.09695280 92.09686841 -0.00008439 92.09686912 -0.00008368 92.09686494 -0.00008786 92.10126232 0.00430952 nonbonded 96.36337760 96.36766885 0.00429125 96.36767038 0.00429278 96.36618536 0.00280776 96.37392128 0.01054368 potential 580.45719840 580.46136194 0.00416354 580.46138240 0.00418400 580.45908120 0.00188280 580.47125664 0.01405824 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 580.45719840 Difference in potential energy from amber=>gromacs conversion: 0.00416354 Difference in potential energy from amber=>lammps conversion: 0.00418400 Difference in potential energy from amber=>desmond conversion: 0.00188280 Difference in potential energy from amber=>charmm conversion: 0.01405824 ======================================================================= INFO 2017-03-19 00:26:04 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8117218.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8117218.inpcrd') INFO 2017-03-19 00:26:04 Beginning InterMol conversion INFO 2017-03-19 00:26:04 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:26:04 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:26:04 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8118832.inpcrd INFO 2017-03-19 00:26:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8118832/mobley_8118832_converted.input INFO 2017-03-19 00:26:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8118832/mobley_8118832_converted.cms WARNING 2017-03-19 00:26:20 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:26:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8118832/mobley_8118832_converted.inp INFO 2017-03-19 00:26:20 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8118832/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8118832/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8118832/mobley_8118832_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8118832/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -22.37429377 -22.37429377 0.00000000 0.00000000 0.00000000 0.00000000 -2.83951344 -2.83951344 coulomb total -2.84512000 -2.86350059 -0.01838059 -2.86350056 -0.01838056 -2.86352579 -0.01840579 -2.83951344 0.00560656 coulomb-14 19.51919680 19.51079318 -0.00840362 0.00000000 -19.51919680 19.51078960 -0.00840720 0.00000000 -19.51919680 improper 0.00000000 0.00083881 0.00083881 0.00000000 0.00000000 0.00000000 0.00000000 0.00083680 0.00083680 proper 0.01631760 0.01549385 -0.00082375 0.01633403 0.00001643 0.01632068 0.00000308 0.01548080 -0.00083680 vdw (SR) 0.00000000 -0.19043581 -0.19043581 0.00000000 0.00000000 0.00000000 0.00000000 0.48668288 0.48668288 vdw total 0.48659920 0.48666975 0.00007055 0.48666974 0.00007054 0.48664342 0.00004422 0.48668288 0.00008368 vdw-14 0.67697120 0.67710556 0.00013436 0.00000000 -0.67697120 0.67708018 0.00010898 0.00000000 -0.67697120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.14557920 1.14541156 -0.00016764 1.14541155 -0.00016765 1.14550662 -0.00007258 1.14537000 -0.00020920 bond 0.85437280 0.85445254 0.00007974 0.85445255 0.00007975 0.85429031 -0.00008249 0.85445648 0.00008368 bonded 2.01626960 2.01619676 -0.00007284 2.01619812 -0.00007148 2.01611762 -0.00015198 2.01614408 -0.00012552 dihedral 0.01631760 0.01633267 0.00001507 0.01633403 0.00001643 0.01632068 0.00000308 0.01631760 0.00000000 nonbonded -2.35852080 -2.37683085 -0.01831005 -2.37683082 -0.01831002 -2.37688237 -0.01836157 -2.35283056 0.00569024 potential -0.34225120 -0.36063409 -0.01838289 -0.36063269 -0.01838149 -0.36078416 -0.01853296 -0.33668648 0.00556472 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -0.34225120 Difference in potential energy from amber=>gromacs conversion: -0.01838289 Difference in potential energy from amber=>lammps conversion: -0.01838149 Difference in potential energy from amber=>desmond conversion: -0.01853296 Difference in potential energy from amber=>charmm conversion: 0.00556472 ======================================================================= INFO 2017-03-19 00:26:20 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8118832.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8118832.inpcrd') INFO 2017-03-19 00:26:20 Beginning InterMol conversion INFO 2017-03-19 00:26:20 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:26:20 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:26:20 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8124669.inpcrd INFO 2017-03-19 00:26:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8124669/mobley_8124669_converted.input INFO 2017-03-19 00:26:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8124669/mobley_8124669_converted.cms WARNING 2017-03-19 00:26:36 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:26:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8124669/mobley_8124669_converted.inp INFO 2017-03-19 00:26:36 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8124669/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8124669/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8124669/mobley_8124669_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8124669/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 65.35469491 65.35469491 0.00000000 0.00000000 0.00000000 0.00000000 -106.26606880 -106.26606880 coulomb total -106.28908080 -106.28726214 0.00181866 -106.28726076 0.00182004 -106.28726494 0.00181586 -106.26606880 0.02301200 coulomb-14 -171.63688480 -171.64195705 -0.00507225 0.00000000 171.63688480 -171.64202401 -0.00513921 0.00000000 171.63688480 improper 0.00000000 0.07165808 0.07165808 0.00000000 0.00000000 0.00000000 0.00000000 0.07167192 0.07167192 proper 18.72423680 18.65269255 -0.07154425 18.72435228 0.00011548 18.72437780 0.00014100 18.65269040 -0.07154640 vdw (SR) 0.00000000 -15.06586686 -15.06586686 0.00000000 0.00000000 0.00000000 0.00000000 28.03175400 28.03175400 vdw total 28.03154480 28.03154953 0.00000473 28.03154940 0.00000460 28.03168563 0.00014083 28.03175400 0.00020920 vdw-14 43.09729200 43.09741639 0.00012439 0.00000000 -43.09729200 43.09758279 0.00029079 0.00000000 -43.09729200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 8.15880000 8.15874614 -0.00005386 8.15874603 -0.00005397 8.15874720 -0.00005280 8.15875816 -0.00004184 bond 16.19333520 16.19328399 -0.00005121 16.19328416 -0.00005104 16.19350674 0.00017154 16.19329336 -0.00004184 bonded 43.07637200 43.07638076 0.00000876 43.07638246 0.00001046 43.07663174 0.00025974 43.07641384 0.00004184 dihedral 18.72423680 18.72435063 0.00011383 18.72435228 0.00011548 18.72437780 0.00014100 18.72436232 0.00012552 nonbonded -78.25753600 -78.25571261 0.00182339 -78.25571178 0.00182422 -78.25557931 0.00195669 -78.23431480 0.02322120 potential -35.18116400 -35.17933185 0.00183215 -35.17932890 0.00183510 -35.17923296 0.00193104 -35.15790096 0.02326304 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -35.18116400 Difference in potential energy from amber=>gromacs conversion: 0.00183215 Difference in potential energy from amber=>lammps conversion: 0.00183510 Difference in potential energy from amber=>desmond conversion: 0.00193104 Difference in potential energy from amber=>charmm conversion: 0.02326304 ======================================================================= INFO 2017-03-19 00:26:36 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8124669.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8124669.inpcrd') INFO 2017-03-19 00:26:36 Beginning InterMol conversion INFO 2017-03-19 00:26:36 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:26:37 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:26:37 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8127829.inpcrd INFO 2017-03-19 00:26:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8127829/mobley_8127829_converted.input INFO 2017-03-19 00:26:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8127829/mobley_8127829_converted.cms WARNING 2017-03-19 00:26:52 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:26:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8127829/mobley_8127829_converted.inp INFO 2017-03-19 00:26:52 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8127829/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8127829/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8127829/mobley_8127829_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8127829/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 1.30740660 1.30740660 0.00000000 0.00000000 0.00000000 0.00000000 -3.43309752 -3.43309752 coulomb total -3.44008480 -3.44044069 -0.00035589 -3.44044065 -0.00035585 -3.44047421 -0.00038941 -3.43309752 0.00698728 coulomb-14 -4.74758480 -4.74784728 -0.00026248 0.00000000 4.74758480 -4.74788094 -0.00029614 0.00000000 4.74758480 improper 0.00000000 0.00001306 0.00001306 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.01966480 0.01960941 -0.00005539 0.01962246 -0.00004234 0.01962193 -0.00004287 0.01962296 -0.00004184 vdw (SR) 0.00000000 -3.12438072 -3.12438072 0.00000000 0.00000000 0.00000000 0.00000000 15.91861376 15.91861376 vdw total 15.91886480 15.91861678 -0.00024802 15.91861669 -0.00024811 15.91870859 -0.00015621 15.91861376 -0.00025104 vdw-14 19.04305760 19.04299750 -0.00006010 0.00000000 -19.04305760 19.04309178 0.00003418 0.00000000 -19.04305760 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.64935680 0.64923081 -0.00012599 0.64923082 -0.00012598 0.64907932 -0.00027748 0.64918944 -0.00016736 bond 1.70456160 1.70438646 -0.00017514 1.70438646 -0.00017514 1.70417943 -0.00038217 1.70439424 -0.00016736 bonded 2.37358320 2.37323974 -0.00034346 2.37323974 -0.00034346 2.37288067 -0.00070253 2.37320664 -0.00037656 dihedral 0.01966480 0.01962247 -0.00004233 0.01962246 -0.00004234 0.01962193 -0.00004287 0.01962296 -0.00004184 nonbonded 12.47878000 12.47817609 -0.00060391 12.47817625 -0.00060375 12.47823438 -0.00054562 12.48551624 0.00673624 potential 14.85236320 14.85141583 -0.00094737 14.85141594 -0.00094726 14.85105947 -0.00130373 14.85876472 0.00640152 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 14.85236320 Difference in potential energy from amber=>gromacs conversion: -0.00094737 Difference in potential energy from amber=>lammps conversion: -0.00094726 Difference in potential energy from amber=>desmond conversion: -0.00130373 Difference in potential energy from amber=>charmm conversion: 0.00640152 ======================================================================= INFO 2017-03-19 00:26:52 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8127829.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8127829.inpcrd') INFO 2017-03-19 00:26:52 Beginning InterMol conversion INFO 2017-03-19 00:26:52 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:26:53 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:26:53 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_819018.inpcrd INFO 2017-03-19 00:26:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_819018/mobley_819018_converted.input INFO 2017-03-19 00:26:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_819018/mobley_819018_converted.cms WARNING 2017-03-19 00:27:08 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:27:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_819018/mobley_819018_converted.inp INFO 2017-03-19 00:27:08 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_819018/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_819018/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_819018/mobley_819018_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_819018/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 48.03965482 48.03965482 0.00000000 0.00000000 0.00000000 0.00000000 -38.80438248 -38.80438248 coulomb total -38.78777200 -38.78939613 -0.00162413 -38.78939581 -0.00162381 -38.78958953 -0.00181753 -38.80438248 -0.01661048 coulomb-14 -86.82594960 -86.82905094 -0.00310134 0.00000000 86.82594960 -86.82910726 -0.00315766 0.00000000 86.82594960 improper 0.00000000 0.01305487 0.01305487 0.00000000 0.00000000 0.00000000 0.00000000 0.01305408 0.01305408 proper 114.64745760 114.63443556 -0.01302204 114.64749526 0.00003766 114.64739902 -0.00005858 114.63444536 -0.01301224 vdw (SR) 0.00000000 3.62960175 3.62960175 0.00000000 0.00000000 0.00000000 0.00000000 15.92091496 15.92091496 vdw total 15.92095680 15.92071812 -0.00023868 15.92071831 -0.00023849 15.92084950 -0.00010730 15.92091496 -0.00004184 vdw-14 12.29133680 12.29111637 -0.00022043 0.00000000 -12.29133680 12.29115082 -0.00018598 0.00000000 -12.29133680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 14.78583760 14.78574887 -0.00008873 14.78574890 -0.00008870 14.78548439 -0.00035321 14.78562840 -0.00020920 bond 3.13507120 3.13506621 -0.00000499 3.13506622 -0.00000498 3.13445521 -0.00061599 3.13507120 0.00000000 bonded 132.56836640 132.56830552 -0.00006088 132.56831038 -0.00005602 132.56733862 -0.00102778 132.56819904 -0.00016736 dihedral 114.64745760 114.64749044 0.00003284 114.64749526 0.00003766 114.64739902 -0.00005858 114.64749944 0.00004184 nonbonded -22.86681520 -22.86867801 -0.00186281 -22.86867750 -0.00186230 -22.86874003 -0.00192483 -22.88346752 -0.01665232 potential 109.70155120 109.69962751 -0.00192369 109.69963074 -0.00192046 109.69847638 -0.00307482 109.68477336 -0.01677784 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 109.70155120 Difference in potential energy from amber=>gromacs conversion: -0.00192369 Difference in potential energy from amber=>lammps conversion: -0.00192046 Difference in potential energy from amber=>desmond conversion: -0.00307482 Difference in potential energy from amber=>charmm conversion: -0.01677784 ======================================================================= INFO 2017-03-19 00:27:08 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_819018.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_819018.inpcrd') INFO 2017-03-19 00:27:09 Beginning InterMol conversion INFO 2017-03-19 00:27:09 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:27:09 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:27:09 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8191186.inpcrd INFO 2017-03-19 00:27:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8191186/mobley_8191186_converted.input INFO 2017-03-19 00:27:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8191186/mobley_8191186_converted.cms WARNING 2017-03-19 00:27:24 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:27:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8191186/mobley_8191186_converted.inp INFO 2017-03-19 00:27:24 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8191186/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8191186/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8191186/mobley_8191186_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8191186/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -30.86264840 -30.86264840 coulomb total -30.84361120 -30.85309615 -0.00948495 -30.85309591 -0.00948471 -30.85308465 -0.00947345 -30.86264840 -0.01903720 coulomb-14 -30.84361120 -30.85309615 -0.00948495 0.00000000 30.84361120 -30.85308465 -0.00947345 0.00000000 30.84361120 proper 4.78440400 4.78448690 0.00008290 4.78448684 0.00008284 4.78448454 0.00008054 4.78448768 0.00008368 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 2.36019440 2.36019440 vdw total 2.36019440 2.36021852 0.00002412 2.36021854 0.00002414 2.36026691 0.00007251 2.36019440 0.00000000 vdw-14 2.36019440 2.36021852 0.00002412 0.00000000 -2.36019440 2.36026691 0.00007251 0.00000000 -2.36019440 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.47946240 1.47944595 -0.00001645 1.47944596 -0.00001644 1.47954980 0.00008740 1.47954608 0.00008368 bond 1.22674880 1.22674106 -0.00000774 1.22674106 -0.00000774 1.22689766 0.00014886 1.22674880 0.00000000 bonded 7.49061520 7.49067391 0.00005871 7.49067386 0.00005866 7.49093200 0.00031680 7.49078256 0.00016736 dihedral 4.78440400 4.78448690 0.00008290 4.78448684 0.00008284 4.78448454 0.00008054 4.78448768 0.00008368 nonbonded -28.48341680 -28.49287763 -0.00946083 -28.49287724 -0.00946044 -28.49281775 -0.00940095 -28.50245400 -0.01903720 potential -20.99280160 -21.00220372 -0.00940212 -21.00220347 -0.00940187 -21.00190640 -0.00910480 -21.01171328 -0.01891168 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -20.99280160 Difference in potential energy from amber=>gromacs conversion: -0.00940212 Difference in potential energy from amber=>lammps conversion: -0.00940187 Difference in potential energy from amber=>desmond conversion: -0.00910480 Difference in potential energy from amber=>charmm conversion: -0.01891168 ======================================================================= INFO 2017-03-19 00:27:24 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8191186.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8191186.inpcrd') INFO 2017-03-19 00:27:25 Beginning InterMol conversion INFO 2017-03-19 00:27:25 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:27:25 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:27:25 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8207196.inpcrd INFO 2017-03-19 00:27:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8207196/mobley_8207196_converted.input INFO 2017-03-19 00:27:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8207196/mobley_8207196_converted.cms WARNING 2017-03-19 00:27:40 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:27:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8207196/mobley_8207196_converted.inp INFO 2017-03-19 00:27:40 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8207196/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8207196/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8207196/mobley_8207196_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8207196/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 1012.27123963 1012.27123963 0.00000000 0.00000000 0.00000000 0.00000000 -1853.38610344 -1853.38610344 coulomb total -1853.38271440 -1853.45184602 -0.06913162 -1853.45183408 -0.06911968 -1853.45249934 -0.06978494 -1853.38610344 -0.00338904 coulomb-14 -2865.62076320 -2865.72308565 -0.10232245 0.00000000 2865.62076320 -2865.72419586 -0.10343266 0.00000000 2865.62076320 improper 0.00000000 0.00008243 0.00008243 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.01631760 0.01618721 -0.00013039 0.01626974 -0.00004786 0.01626762 -0.00004998 0.01619208 -0.00012552 vdw (SR) 0.00000000 -8.19146053 -8.19146053 0.00000000 0.00000000 0.00000000 0.00000000 33.07933160 33.07933160 vdw total 33.07954080 33.07946322 -0.00007758 33.07946340 -0.00007740 33.07965209 0.00011129 33.07933160 -0.00020920 vdw-14 41.27097600 41.27092375 -0.00005225 0.00000000 -41.27097600 41.27109215 0.00011615 0.00000000 -41.27097600 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 11.15245200 11.15265365 0.00020165 11.15265367 0.00020167 11.15257622 0.00012422 11.15270304 0.00025104 bond 12.81726560 12.81707263 -0.00019297 12.81707272 -0.00019288 12.81770320 0.00043760 12.81705640 -0.00020920 bonded 23.98603520 23.98599592 -0.00003928 23.98599612 -0.00003908 23.98654705 0.00051185 23.98603520 -0.00000000 dihedral 0.01631760 0.01626964 -0.00004796 0.01626974 -0.00004786 0.01626762 -0.00004998 0.01627576 -0.00004184 nonbonded -1820.30317360 -1820.37238280 -0.06920920 -1820.37237696 -0.06920336 -1820.37284724 -0.06967364 -1820.30677184 -0.00359824 potential -1796.31713840 -1796.38638688 -0.06924848 -1796.38638360 -0.06924520 -1796.38657606 -0.06943766 -1796.32069480 -0.00355640 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -1796.31713840 Difference in potential energy from amber=>gromacs conversion: -0.06924848 Difference in potential energy from amber=>lammps conversion: -0.06924520 Difference in potential energy from amber=>desmond conversion: -0.06943766 Difference in potential energy from amber=>charmm conversion: -0.00355640 ======================================================================= INFO 2017-03-19 00:27:40 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8207196.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8207196.inpcrd') INFO 2017-03-19 00:27:41 Beginning InterMol conversion INFO 2017-03-19 00:27:41 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:27:41 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:27:41 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_820789.inpcrd INFO 2017-03-19 00:27:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_820789/mobley_820789_converted.input INFO 2017-03-19 00:27:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_820789/mobley_820789_converted.cms WARNING 2017-03-19 00:27:57 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:27:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_820789/mobley_820789_converted.inp INFO 2017-03-19 00:27:57 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_820789/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_820789/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_820789/mobley_820789_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_820789/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 33.76669962 33.76669962 0.00000000 0.00000000 0.00000000 0.00000000 -119.29793176 -119.29793176 coulomb total -119.30508640 -119.30415674 0.00092966 -119.30415337 0.00093303 -119.30458516 0.00050124 -119.29793176 0.00715464 coulomb-14 -153.06452720 -153.07085635 -0.00632915 0.00000000 153.06452720 -153.07101407 -0.00648687 0.00000000 153.06452720 improper 0.00000000 0.00551595 0.00551595 0.00000000 0.00000000 0.00000000 0.00000000 0.00552288 0.00552288 proper 3.24050800 3.23486327 -0.00564473 3.24038001 -0.00012799 3.24038034 -0.00012766 3.23485960 -0.00564840 vdw (SR) 0.00000000 -0.74579862 -0.74579862 0.00000000 0.00000000 0.00000000 0.00000000 5.42568568 5.42568568 vdw total 5.42581120 5.42558385 -0.00022735 5.42558401 -0.00022719 5.42561007 -0.00020113 5.42568568 -0.00012552 vdw-14 6.17140000 6.17138247 -0.00001753 0.00000000 -6.17140000 6.17140770 0.00000770 0.00000000 -6.17140000 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 6.37055840 6.37060829 0.00004989 6.37060819 0.00004979 6.37107968 0.00052128 6.37068392 0.00012552 bond 5.63710320 5.63693231 -0.00017089 5.63693249 -0.00017071 5.63660631 -0.00049689 5.63693584 -0.00016736 bonded 15.24816960 15.24791981 -0.00024979 15.24792069 -0.00024891 15.24806633 -0.00010327 15.24800224 -0.00016736 dihedral 3.24050800 3.24037922 -0.00012878 3.24038001 -0.00012799 3.24038034 -0.00012766 3.24038248 -0.00012552 nonbonded -113.87927520 -113.87857289 0.00070231 -113.87857229 0.00070291 -113.87897509 0.00030011 -113.87224608 0.00702912 potential -98.63110560 -98.63065307 0.00045253 -98.63064954 0.00045606 -98.63094201 0.00016359 -98.62428568 0.00681992 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -98.63110560 Difference in potential energy from amber=>gromacs conversion: 0.00045253 Difference in potential energy from amber=>lammps conversion: 0.00045606 Difference in potential energy from amber=>desmond conversion: 0.00016359 Difference in potential energy from amber=>charmm conversion: 0.00681992 ======================================================================= INFO 2017-03-19 00:27:57 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_820789.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_820789.inpcrd') INFO 2017-03-19 00:27:57 Beginning InterMol conversion INFO 2017-03-19 00:27:57 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:27:57 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8208692.inpcrd INFO 2017-03-19 00:27:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8208692/mobley_8208692_converted.input INFO 2017-03-19 00:27:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8208692/mobley_8208692_converted.cms INFO 2017-03-19 00:28:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8208692/mobley_8208692_converted.rst7 WARNING 2017-03-19 00:28:13 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:28:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8208692/mobley_8208692_converted.inp INFO 2017-03-19 00:28:13 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8208692/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8208692/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8208692/mobley_8208692_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_8208692/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8208692/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 2.62035752 2.62035752 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -8.52238960 -8.52238960 coulomb total -8.52322640 -8.52222374 0.00100266 -8.52222350 0.00100290 -8.52222473 0.00100167 -8.52322640 0.00000000 -8.52238960 0.00083680 coulomb-14 -11.14241040 -11.14258126 -0.00017086 0.00000000 11.14241040 -11.14258136 -0.00017096 -11.14241040 0.00000000 0.00000000 11.14241040 improper 0.00000000 0.00015373 0.00015373 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00016736 0.00016736 proper 33.47409200 33.47394880 -0.00014320 33.47410246 0.00001046 33.47409857 0.00000657 33.47409200 0.00000000 33.47396648 -0.00012552 vdw (SR) 0.00000000 -20.53133456 -20.53133456 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 31.94450528 31.94450528 vdw total 31.94442160 31.94441029 -0.00001131 31.94441030 -0.00001130 31.94466720 0.00024560 31.94442160 0.00000000 31.94450528 0.00008368 vdw-14 52.47572800 52.47574485 0.00001685 0.00000000 -52.47572800 52.47602130 0.00029330 52.47572800 0.00000000 0.00000000 -52.47572800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.54170800 5.54167212 -0.00003588 5.54167202 -0.00003598 5.54185720 0.00014920 5.54170800 0.00000000 5.54174984 0.00004184 bond 4.31746960 4.31727935 -0.00019025 4.31727923 -0.00019037 4.31735040 -0.00011920 4.31746960 0.00000000 4.31726040 -0.00020920 bonded 43.33326960 43.33305400 -0.00021560 43.33305371 -0.00021589 43.33330617 0.00003657 43.33326960 0.00000000 43.33314408 -0.00012552 dihedral 33.47409200 33.47410254 0.00001054 33.47410246 0.00001046 33.47409857 0.00000657 33.47409200 0.00000000 33.47413384 0.00004184 nonbonded 23.42119520 23.42218655 0.00099135 23.42218681 0.00099161 23.42244248 0.00124728 23.42119520 0.00000000 23.42211568 0.00092048 potential 66.75446480 66.75524056 0.00077576 66.75523884 0.00077404 66.75536562 0.00090082 66.75446480 0.00000000 66.75525976 0.00079496 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 66.75446480 Difference in potential energy from amber=>gromacs conversion: 0.00077576 Difference in potential energy from amber=>lammps conversion: 0.00077404 Difference in potential energy from amber=>desmond conversion: 0.00090082 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00079496 ======================================================================= INFO 2017-03-19 00:28:13 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8208692.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8208692.inpcrd') INFO 2017-03-19 00:28:13 Beginning InterMol conversion INFO 2017-03-19 00:28:13 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:28:13 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:28:13 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8221999.inpcrd INFO 2017-03-19 00:28:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8221999/mobley_8221999_converted.input INFO 2017-03-19 00:28:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8221999/mobley_8221999_converted.cms WARNING 2017-03-19 00:28:29 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:28:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8221999/mobley_8221999_converted.inp INFO 2017-03-19 00:28:29 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8221999/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8221999/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8221999/mobley_8221999_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8221999/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -0.80879297 -0.80879297 0.00000000 0.00000000 0.00000000 0.00000000 -3.17004944 -3.17004944 coulomb total -3.17021680 -3.17427066 -0.00405386 -3.17427064 -0.00405384 -3.17424034 -0.00402354 -3.17004944 0.00016736 coulomb-14 -2.35977600 -2.36547770 -0.00570170 0.00000000 2.35977600 -2.36543732 -0.00566132 0.00000000 2.35977600 proper 0.03640080 0.03647260 0.00007180 0.03647260 0.00007180 0.03647025 0.00006945 0.03648448 0.00008368 vdw (SR) 0.00000000 -0.99453854 -0.99453854 0.00000000 0.00000000 0.00000000 0.00000000 1.89016384 1.89016384 vdw total 1.89033120 1.89012051 -0.00021069 1.89012054 -0.00021066 1.89018703 -0.00014417 1.89016384 -0.00016736 vdw-14 2.88486800 2.88465905 -0.00020895 0.00000000 -2.88486800 2.88472309 -0.00014491 0.00000000 -2.88486800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.62048720 0.68842396 0.06793676 0.68842394 0.06793674 0.68839577 0.06790857 0.68843536 0.06794816 bond 2.61207120 2.61197704 -0.00009416 2.61197706 -0.00009414 2.61293187 0.00086067 2.61198752 -0.00008368 bonded 3.26895920 3.33687360 0.06791440 3.33687360 0.06791440 3.33779789 0.06883869 3.33690736 0.06794816 dihedral 0.03640080 0.03647260 0.00007180 0.03647260 0.00007180 0.03647025 0.00006945 0.03648448 0.00008368 nonbonded -1.27988560 -1.28415015 -0.00426455 -1.28415010 -0.00426450 -1.28405332 -0.00416772 -1.27988560 -0.00000000 potential 1.98907360 2.05272345 0.06364985 2.05272349 0.06364989 2.05371566 0.06464206 2.05702176 0.06794816 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 1.98907360 Difference in potential energy from amber=>gromacs conversion: 0.06364985 Difference in potential energy from amber=>lammps conversion: 0.06364989 Difference in potential energy from amber=>desmond conversion: 0.06464206 Difference in potential energy from amber=>charmm conversion: 0.06794816 ======================================================================= INFO 2017-03-19 00:28:29 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8221999.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8221999.inpcrd') INFO 2017-03-19 00:28:29 Beginning InterMol conversion INFO 2017-03-19 00:28:29 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:28:29 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8260524.inpcrd INFO 2017-03-19 00:28:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8260524/mobley_8260524_converted.input INFO 2017-03-19 00:28:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8260524/mobley_8260524_converted.cms INFO 2017-03-19 00:28:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8260524/mobley_8260524_converted.rst7 WARNING 2017-03-19 00:28:45 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:28:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8260524/mobley_8260524_converted.inp INFO 2017-03-19 00:28:45 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8260524/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8260524/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8260524/mobley_8260524_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_8260524/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8260524/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 8.64760134 8.64760134 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -1.98530800 -1.98530800 coulomb total -1.98363440 -1.98145465 0.00217975 -1.98145462 0.00217978 -1.98145039 0.00218401 -1.98363440 0.00000000 -1.98530800 -0.00167360 coulomb-14 -10.62777840 -10.62905598 -0.00127758 0.00000000 10.62777840 -10.62905728 -0.00127888 -10.62777840 0.00000000 0.00000000 10.62777840 vdw (SR) 0.00000000 -0.04077492 -0.04077492 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.41731216 -0.41731216 vdw total -0.41714480 -0.41729920 -0.00015440 -0.41729920 -0.00015440 -0.41729963 -0.00015483 -0.41714480 0.00000000 -0.41731216 -0.00016736 vdw-14 -0.37656000 -0.37652428 0.00003572 0.00000000 0.37656000 -0.37652452 0.00003548 -0.37656000 0.00000000 0.00000000 0.37656000 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.35312960 0.53112006 0.17799046 0.53112006 0.17799046 0.53134602 0.17821642 0.35312960 0.00000000 0.53115880 0.17802920 bond 1.61711600 1.61729663 0.00018063 1.61729662 0.00018062 1.61838686 0.00127086 1.61711600 0.00000000 1.61728336 0.00016736 bonded 1.97024560 2.14841668 0.17817108 2.14841668 0.17817108 2.14973288 0.17948728 1.97024560 0.00000000 2.14844216 0.17819656 nonbonded -2.40077920 -2.39875385 0.00202535 -2.39875381 0.00202539 -2.39875002 0.00202918 -2.40077920 0.00000000 -2.40262016 -0.00184096 potential -0.43053360 -0.25033716 0.18019644 -0.25033714 0.18019646 -0.24902974 0.18150386 -0.43053360 0.00000000 -0.25417800 0.17635560 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -0.43053360 Difference in potential energy from amber=>gromacs conversion: 0.18019644 Difference in potential energy from amber=>lammps conversion: 0.18019646 Difference in potential energy from amber=>desmond conversion: 0.18150386 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.17635560 ======================================================================= INFO 2017-03-19 00:28:45 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8260524.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8260524.inpcrd') INFO 2017-03-19 00:28:45 Beginning InterMol conversion INFO 2017-03-19 00:28:45 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:28:45 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8311303.inpcrd INFO 2017-03-19 00:28:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8311303/mobley_8311303_converted.input INFO 2017-03-19 00:28:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8311303/mobley_8311303_converted.cms INFO 2017-03-19 00:29:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8311303/mobley_8311303_converted.rst7 WARNING 2017-03-19 00:29:01 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:29:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8311303/mobley_8311303_converted.inp INFO 2017-03-19 00:29:01 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8311303/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8311303/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8311303/mobley_8311303_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_8311303/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8311303/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -3.95747159 -3.95747159 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -2.42266152 -2.42266152 coulomb total -2.42211760 -2.41916076 0.00295684 -2.41916073 0.00295687 -2.41914055 0.00297705 -2.42211760 0.00000000 -2.42266152 -0.00054392 coulomb-14 1.53803840 1.53831083 0.00027243 0.00000000 -1.53803840 1.53833819 0.00029979 1.53803840 0.00000000 0.00000000 -1.53803840 improper 0.00000000 0.00028256 0.00028256 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00029288 0.00029288 proper 33.47576560 33.47536911 -0.00039649 33.47565180 -0.00011380 33.47565000 -0.00011560 33.47576560 0.00000000 33.47538904 -0.00037656 vdw (SR) 0.00000000 -15.09317803 -15.09317803 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 29.34599024 29.34599024 vdw total 29.34573920 29.34598082 0.00024162 29.34598104 0.00024184 29.34595459 0.00021539 29.34573920 0.00000000 29.34599024 0.00025104 vdw-14 44.43910080 44.43915885 0.00005805 0.00000000 -44.43910080 44.43912214 0.00002134 44.43910080 0.00000000 0.00000000 -44.43910080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.19443600 5.19436416 -0.00007184 5.19436404 -0.00007196 5.19441023 -0.00002577 5.19443600 0.00000000 5.19443600 0.00000000 bond 4.22249280 4.22244082 -0.00005198 4.22244092 -0.00005188 4.22164064 -0.00085216 4.22249280 0.00000000 4.22245096 -0.00004184 bonded 42.89269440 42.89245665 -0.00023775 42.89245675 -0.00023765 42.89170087 -0.00099353 42.89269440 0.00000000 42.89256888 -0.00012552 dihedral 33.47576560 33.47565167 -0.00011393 33.47565180 -0.00011380 33.47565000 -0.00011560 33.47576560 0.00000000 33.47568192 -0.00008368 nonbonded 26.92362160 26.92682006 0.00319846 26.92682027 0.00319867 26.92681404 0.00319244 26.92362160 0.00000000 26.92332872 -0.00029288 potential 69.81631600 69.81927671 0.00296071 69.81927827 0.00296227 69.81822265 0.00190665 69.81631600 0.00000000 69.81585576 -0.00046024 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 69.81631600 Difference in potential energy from amber=>gromacs conversion: 0.00296071 Difference in potential energy from amber=>lammps conversion: 0.00296227 Difference in potential energy from amber=>desmond conversion: 0.00190665 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.00046024 ======================================================================= INFO 2017-03-19 00:29:01 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8311303.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8311303.inpcrd') INFO 2017-03-19 00:29:01 Beginning InterMol conversion INFO 2017-03-19 00:29:01 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:29:01 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:29:01 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8320545.inpcrd INFO 2017-03-19 00:29:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8320545/mobley_8320545_converted.input INFO 2017-03-19 00:29:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8320545/mobley_8320545_converted.cms WARNING 2017-03-19 00:29:17 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:29:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8320545/mobley_8320545_converted.inp INFO 2017-03-19 00:29:17 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8320545/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8320545/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8320545/mobley_8320545_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8320545/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -32.45353900 -32.45353900 0.00000000 0.00000000 0.00000000 0.00000000 -15.12700096 -15.12700096 coulomb total -15.12892560 -15.12940307 -0.00047747 -15.12940299 -0.00047739 -15.12937789 -0.00045229 -15.12700096 0.00192464 coulomb-14 17.32343360 17.32413593 0.00070233 0.00000000 -17.32343360 17.32414333 0.00070973 0.00000000 -17.32343360 proper 0.01046000 0.01065560 0.00019560 0.01065559 0.00019559 0.01065619 0.00019619 0.01066920 0.00020920 vdw (SR) 0.00000000 -0.90188367 -0.90188367 0.00000000 0.00000000 0.00000000 0.00000000 1.75527168 1.75527168 vdw total 1.75518800 1.75522905 0.00004105 1.75522905 0.00004105 1.75523551 0.00004751 1.75527168 0.00008368 vdw-14 2.65725840 2.65711272 -0.00014568 0.00000000 -2.65725840 2.65712238 -0.00013602 0.00000000 -2.65725840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.62632080 1.62611479 -0.00020601 1.62611478 -0.00020602 1.62613148 -0.00018932 1.62619528 -0.00012552 bond 11.17295360 11.17277080 -0.00018280 11.17277076 -0.00018284 11.17237085 -0.00058275 11.17278624 -0.00016736 bonded 12.80973440 12.80954120 -0.00019320 12.80954113 -0.00019327 12.80915853 -0.00057587 12.80965072 -0.00008368 dihedral 0.01046000 0.01065560 0.00019560 0.01065559 0.00019559 0.01065619 0.00019619 0.01066920 0.00020920 nonbonded -13.37373760 -13.37417402 -0.00043642 -13.37417399 -0.00043639 -13.37414239 -0.00040479 -13.37172928 0.00200832 potential -0.56400320 -0.56463282 -0.00062962 -0.56463264 -0.00062944 -0.56500551 -0.00100231 -0.56212040 0.00188280 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -0.56400320 Difference in potential energy from amber=>gromacs conversion: -0.00062962 Difference in potential energy from amber=>lammps conversion: -0.00062944 Difference in potential energy from amber=>desmond conversion: -0.00100231 Difference in potential energy from amber=>charmm conversion: 0.00188280 ======================================================================= INFO 2017-03-19 00:29:17 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8320545.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8320545.inpcrd') INFO 2017-03-19 00:29:17 Beginning InterMol conversion INFO 2017-03-19 00:29:17 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:29:18 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:29:18 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8337722.inpcrd INFO 2017-03-19 00:29:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8337722/mobley_8337722_converted.input INFO 2017-03-19 00:29:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8337722/mobley_8337722_converted.cms WARNING 2017-03-19 00:29:33 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:29:33 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8337722/mobley_8337722_converted.inp INFO 2017-03-19 00:29:33 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8337722/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8337722/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8337722/mobley_8337722_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8337722/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 14.33417316 14.33417316 0.00000000 0.00000000 0.00000000 0.00000000 -26.91228296 -26.91228296 coulomb total -26.89935440 -26.90026764 -0.00091324 -26.90026735 -0.00091295 -26.90033007 -0.00097567 -26.91228296 -0.01292856 coulomb-14 -41.23290160 -41.23444081 -0.00153921 0.00000000 41.23290160 -41.23442930 -0.00152770 0.00000000 41.23290160 proper 32.66239600 32.66219259 -0.00020341 32.66219015 -0.00020585 32.66216617 -0.00022983 32.66227048 -0.00012552 vdw (SR) 0.00000000 28.35153990 28.35153990 0.00000000 0.00000000 0.00000000 0.00000000 57.74129200 57.74129200 vdw total 57.74129200 57.74066625 -0.00062575 57.74066858 -0.00062342 57.74044825 -0.00084375 57.74129200 0.00000000 vdw-14 29.38925280 29.38912635 -0.00012645 0.00000000 -29.38925280 29.38918050 -0.00007230 0.00000000 -29.38925280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.27604800 4.27615874 0.00011074 4.27615888 0.00011088 4.27577575 -0.00027225 4.27604800 0.00000000 bond 1.00081280 1.00062233 -0.00019047 1.00062234 -0.00019046 1.00043297 -0.00037983 1.00060360 -0.00020920 bonded 37.93925680 37.93897365 -0.00028315 37.93897137 -0.00028543 37.93837489 -0.00088191 37.93892208 -0.00033472 dihedral 32.66239600 32.66219259 -0.00020341 32.66219015 -0.00020585 32.66216617 -0.00022983 32.66227048 -0.00012552 nonbonded 30.84193760 30.84039861 -0.00153899 30.84039998 -0.00153762 30.84011819 -0.00181941 30.82900904 -0.01292856 potential 68.78119440 68.77937226 -0.00182214 68.77937018 -0.00182422 68.77836643 -0.00282797 68.76793112 -0.01326328 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 68.78119440 Difference in potential energy from amber=>gromacs conversion: -0.00182214 Difference in potential energy from amber=>lammps conversion: -0.00182422 Difference in potential energy from amber=>desmond conversion: -0.00282797 Difference in potential energy from amber=>charmm conversion: -0.01326328 ======================================================================= INFO 2017-03-19 00:29:33 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8337722.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8337722.inpcrd') INFO 2017-03-19 00:29:34 Beginning InterMol conversion INFO 2017-03-19 00:29:34 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:29:34 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:29:34 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8337977.inpcrd INFO 2017-03-19 00:29:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8337977/mobley_8337977_converted.input INFO 2017-03-19 00:29:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8337977/mobley_8337977_converted.cms WARNING 2017-03-19 00:29:49 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:29:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8337977/mobley_8337977_converted.inp INFO 2017-03-19 00:29:49 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8337977/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8337977/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8337977/mobley_8337977_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8337977/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 57.32764775 57.32764775 0.00000000 0.00000000 0.00000000 0.00000000 -74.60741440 -74.60741440 coulomb total -74.58565760 -74.58818015 -0.00252255 -74.58818055 -0.00252295 -74.58826172 -0.00260412 -74.60741440 -0.02175680 coulomb-14 -131.91147840 -131.91582790 -0.00434950 0.00000000 131.91147840 -131.91585277 -0.00437437 0.00000000 131.91147840 improper 0.00000000 0.00928956 0.00928956 0.00000000 0.00000000 0.00000000 0.00000000 0.00928848 0.00928848 proper 19.66982080 19.66053254 -0.00928826 19.66982373 0.00000293 19.66979193 -0.00002887 19.66053232 -0.00928848 vdw (SR) 0.00000000 -1.93250722 -1.93250722 0.00000000 0.00000000 0.00000000 0.00000000 6.94686256 6.94686256 vdw total 6.94669520 6.94675758 0.00006238 6.94675754 0.00006234 6.94674233 0.00004713 6.94686256 0.00016736 vdw-14 8.87928480 8.87926480 -0.00002000 0.00000000 -8.87928480 8.87927961 -0.00000519 0.00000000 -8.87928480 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.35180240 3.35174388 -0.00005852 3.35174387 -0.00005853 3.35189612 0.00009372 3.35171872 -0.00008368 bond 1.15562080 1.15582217 0.00020137 1.15582218 0.00020138 1.15580845 0.00018765 1.15583000 0.00020920 bonded 24.17724400 24.17738816 0.00014416 24.17738977 0.00014577 24.17749650 0.00025250 24.17736952 0.00012552 dihedral 19.66982080 19.66982211 0.00000131 19.66982373 0.00000293 19.66979193 -0.00002887 19.66982080 -0.00000000 nonbonded -67.63896240 -67.64142258 -0.00246018 -67.64142259 -0.00246019 -67.64151939 -0.00255699 -67.66055184 -0.02158944 potential -43.46171840 -43.46403442 -0.00231602 -43.46403215 -0.00231375 -43.46407985 -0.00236145 -43.48314048 -0.02142208 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -43.46171840 Difference in potential energy from amber=>gromacs conversion: -0.00231602 Difference in potential energy from amber=>lammps conversion: -0.00231375 Difference in potential energy from amber=>desmond conversion: -0.00236145 Difference in potential energy from amber=>charmm conversion: -0.02142208 ======================================================================= INFO 2017-03-19 00:29:49 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8337977.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8337977.inpcrd') INFO 2017-03-19 00:29:50 Beginning InterMol conversion INFO 2017-03-19 00:29:50 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:29:50 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:29:50 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8426916.inpcrd INFO 2017-03-19 00:29:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8426916/mobley_8426916_converted.input INFO 2017-03-19 00:29:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8426916/mobley_8426916_converted.cms WARNING 2017-03-19 00:30:05 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:30:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8426916/mobley_8426916_converted.inp INFO 2017-03-19 00:30:06 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8426916/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8426916/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8426916/mobley_8426916_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8426916/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 53.90093610 53.90093610 0.00000000 0.00000000 0.00000000 0.00000000 -36.01336160 -36.01336160 coulomb total -36.00834080 -36.00025659 0.00808421 -36.00025606 0.00808474 -36.00040082 0.00793998 -36.01336160 -0.00502080 coulomb-14 -89.89616880 -89.90119269 -0.00502389 0.00000000 89.89616880 -89.90123353 -0.00506473 0.00000000 89.89616880 proper 0.08744560 0.08731328 -0.00013232 0.08731326 -0.00013234 0.08731721 -0.00012839 0.08732008 -0.00012552 vdw (SR) 0.00000000 -1.29822818 -1.29822818 0.00000000 0.00000000 0.00000000 0.00000000 3.61271664 3.61271664 vdw total 3.61246560 3.61267225 0.00020665 3.61267229 0.00020669 3.61271138 0.00024578 3.61271664 0.00025104 vdw-14 4.91076080 4.91090043 0.00013963 0.00000000 -4.91076080 4.91093791 0.00017711 0.00000000 -4.91076080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.33381120 3.33373383 -0.00007737 3.33373384 -0.00007736 3.33401895 0.00020775 3.33372752 -0.00008368 bond 7.93286400 7.93296739 0.00010339 7.93296734 0.00010334 7.93419798 0.00133398 7.93294768 0.00008368 bonded 11.35412080 11.35401450 -0.00010630 11.35401444 -0.00010636 11.35553415 0.00141335 11.35399528 -0.00012552 dihedral 0.08744560 0.08731328 -0.00013232 0.08731326 -0.00013234 0.08731721 -0.00012839 0.08732008 -0.00012552 nonbonded -32.39587520 -32.38758433 0.00829087 -32.38758377 0.00829143 -32.38768945 0.00818575 -32.40064496 -0.00476976 potential -21.04175440 -21.03356984 0.00818456 -21.03356924 0.00818516 -21.03218254 0.00957186 -21.04664968 -0.00489528 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -21.04175440 Difference in potential energy from amber=>gromacs conversion: 0.00818456 Difference in potential energy from amber=>lammps conversion: 0.00818516 Difference in potential energy from amber=>desmond conversion: 0.00957186 Difference in potential energy from amber=>charmm conversion: -0.00489528 ======================================================================= INFO 2017-03-19 00:30:06 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8426916.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8426916.inpcrd') INFO 2017-03-19 00:30:06 Beginning InterMol conversion INFO 2017-03-19 00:30:06 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:30:06 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:30:06 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8427539.inpcrd INFO 2017-03-19 00:30:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8427539/mobley_8427539_converted.input INFO 2017-03-19 00:30:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8427539/mobley_8427539_converted.cms WARNING 2017-03-19 00:30:21 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:30:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8427539/mobley_8427539_converted.inp INFO 2017-03-19 00:30:22 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8427539/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8427539/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8427539/mobley_8427539_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8427539/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -27.79588406 -27.79588406 0.00000000 0.00000000 0.00000000 0.00000000 -196.44842320 -196.44842320 coulomb total -196.46139360 -196.47559246 -0.01419886 -196.47558991 -0.01419631 -196.47596442 -0.01457082 -196.44842320 0.01297040 coulomb-14 -168.66540800 -168.67970840 -0.01430040 0.00000000 168.66540800 -168.68002815 -0.01462015 0.00000000 168.66540800 improper 0.00000000 0.00030680 0.00030680 0.00000000 0.00000000 0.00000000 0.00000000 0.00029288 0.00029288 proper 21.36266720 21.36248179 -0.00018541 21.36278812 0.00012092 21.36282184 0.00015464 21.36249984 -0.00016736 vdw (SR) 0.00000000 -0.38085624 -0.38085624 0.00000000 0.00000000 0.00000000 0.00000000 4.16379128 4.16379128 vdw total 4.16391680 4.16376638 -0.00015042 4.16376643 -0.00015037 4.16382879 -0.00008801 4.16379128 -0.00012552 vdw-14 4.54466080 4.54462262 -0.00003818 0.00000000 -4.54466080 4.54467423 0.00001343 0.00000000 -4.54466080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.08570000 3.08553798 -0.00016202 3.08553800 -0.00016200 3.08553227 -0.00016773 3.08557448 -0.00012552 bond 3.39950000 3.39969274 0.00019274 3.39969272 0.00019272 3.39871990 -0.00078010 3.39970920 0.00020920 bonded 27.84786720 27.84801930 0.00015210 27.84801883 0.00015163 27.84707401 -0.00079319 27.84807640 0.00020920 dihedral 21.36266720 21.36278858 0.00012138 21.36278812 0.00012092 21.36282184 0.00015464 21.36279272 0.00012552 nonbonded -192.29747680 -192.31182607 -0.01434927 -192.31182374 -0.01434694 -192.31213563 -0.01465883 -192.28463192 0.01284488 potential -164.44960960 -164.46380678 -0.01419718 -164.46380591 -0.01419631 -164.46507492 -0.01546532 -164.43655552 0.01305408 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -164.44960960 Difference in potential energy from amber=>gromacs conversion: -0.01419718 Difference in potential energy from amber=>lammps conversion: -0.01419631 Difference in potential energy from amber=>desmond conversion: -0.01546532 Difference in potential energy from amber=>charmm conversion: 0.01305408 ======================================================================= INFO 2017-03-19 00:30:22 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8427539.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8427539.inpcrd') INFO 2017-03-19 00:30:22 Beginning InterMol conversion INFO 2017-03-19 00:30:22 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:30:22 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:30:22 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8436428.inpcrd INFO 2017-03-19 00:30:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8436428/mobley_8436428_converted.input INFO 2017-03-19 00:30:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8436428/mobley_8436428_converted.cms WARNING 2017-03-19 00:30:38 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:30:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8436428/mobley_8436428_converted.inp INFO 2017-03-19 00:30:38 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8436428/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8436428/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8436428/mobley_8436428_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8436428/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 12.81745811 12.81745811 0.00000000 0.00000000 0.00000000 0.00000000 -6.43984544 -6.43984544 coulomb total -6.46135120 -6.44127777 0.02007343 -6.44127762 0.02007358 -6.44132858 0.02002262 -6.43984544 0.02150576 coulomb-14 -19.25309440 -19.25873588 -0.00564148 0.00000000 19.25309440 -19.25873539 -0.00564099 0.00000000 19.25309440 proper 7.59312320 7.59299602 -0.00012718 7.59300061 -0.00012259 7.59297203 -0.00015117 7.59299768 -0.00012552 vdw (SR) 0.00000000 1.72612300 1.72612300 0.00000000 0.00000000 0.00000000 0.00000000 13.04700904 13.04700904 vdw total 13.04696720 13.04683927 -0.00012793 13.04683959 -0.00012761 13.04687588 -0.00009132 13.04700904 0.00004184 vdw-14 11.32064880 11.32071627 0.00006747 0.00000000 -11.32064880 11.32073344 0.00008464 0.00000000 -11.32064880 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 6.22495520 6.22488159 -0.00007361 6.22488156 -0.00007364 6.22464797 -0.00030723 6.22487152 -0.00008368 bond 0.56986080 0.56973990 -0.00012090 0.56973988 -0.00012092 0.56952205 -0.00033875 0.56973528 -0.00012552 bonded 14.38793920 14.38761751 -0.00032169 14.38762205 -0.00031715 14.38714205 -0.00079715 14.38760448 -0.00033472 dihedral 7.59312320 7.59299602 -0.00012718 7.59300061 -0.00012259 7.59297203 -0.00015117 7.59299768 -0.00012552 nonbonded 6.58561600 6.60556150 0.01994550 6.60556196 0.01994596 6.60554729 0.01993129 6.60716360 0.02154760 potential 20.97355520 20.99317901 0.01962381 20.99318402 0.01962882 20.99262688 0.01907168 20.99476808 0.02121288 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 20.97355520 Difference in potential energy from amber=>gromacs conversion: 0.01962381 Difference in potential energy from amber=>lammps conversion: 0.01962882 Difference in potential energy from amber=>desmond conversion: 0.01907168 Difference in potential energy from amber=>charmm conversion: 0.02121288 ======================================================================= INFO 2017-03-19 00:30:38 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8436428.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8436428.inpcrd') INFO 2017-03-19 00:30:38 Beginning InterMol conversion INFO 2017-03-19 00:30:38 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:30:38 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:30:38 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8449031.inpcrd INFO 2017-03-19 00:30:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8449031/mobley_8449031_converted.input INFO 2017-03-19 00:30:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8449031/mobley_8449031_converted.cms WARNING 2017-03-19 00:30:54 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:30:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8449031/mobley_8449031_converted.inp INFO 2017-03-19 00:30:54 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8449031/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8449031/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8449031/mobley_8449031_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8449031/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 50.01816675 50.01816675 0.00000000 0.00000000 0.00000000 0.00000000 -47.84445840 -47.84445840 coulomb total -47.80638400 -47.81555930 -0.00917530 -47.81555951 -0.00917551 -47.81588879 -0.00950479 -47.84445840 -0.03807440 coulomb-14 -97.83405360 -97.83372605 0.00032755 0.00000000 97.83405360 -97.83374064 0.00031296 0.00000000 97.83405360 proper 9.10773120 9.10765746 -0.00007374 9.10764961 -0.00008159 9.10770530 -0.00002590 9.10768936 -0.00004184 vdw (SR) 0.00000000 95.33538820 95.33538820 0.00000000 0.00000000 0.00000000 0.00000000 120.51522472 120.51522472 vdw total 120.51509920 120.51402013 -0.00107907 120.51401973 -0.00107947 120.51433918 -0.00076002 120.51522472 0.00012552 vdw-14 25.17847520 25.17863193 0.00015673 0.00000000 -25.17847520 25.17842269 -0.00005251 0.00000000 -25.17847520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.23000000 5.22993691 -0.00006309 5.22993682 -0.00006318 5.23040263 0.00040263 5.22987448 -0.00012552 bond 10.28510880 10.28513859 0.00002979 10.28513851 0.00002971 10.28660215 0.00149335 10.28515064 0.00004184 bonded 24.62284000 24.62273296 -0.00010704 24.62272494 -0.00011506 24.62471008 0.00187008 24.62271448 -0.00012552 dihedral 9.10773120 9.10765746 -0.00007374 9.10764961 -0.00008159 9.10770530 -0.00002590 9.10768936 -0.00004184 nonbonded 72.70871520 72.69846083 -0.01025437 72.69846440 -0.01025080 72.69845038 -0.01026482 72.67076632 -0.03794888 potential 97.33155520 97.32119379 -0.01036141 97.32118725 -0.01036795 97.32309264 -0.00846256 97.29348080 -0.03807440 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 97.33155520 Difference in potential energy from amber=>gromacs conversion: -0.01036141 Difference in potential energy from amber=>lammps conversion: -0.01036795 Difference in potential energy from amber=>desmond conversion: -0.00846256 Difference in potential energy from amber=>charmm conversion: -0.03807440 ======================================================================= INFO 2017-03-19 00:30:54 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8449031.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8449031.inpcrd') INFO 2017-03-19 00:30:54 Beginning InterMol conversion INFO 2017-03-19 00:30:54 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:30:54 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:30:54 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8467917.inpcrd INFO 2017-03-19 00:30:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8467917/mobley_8467917_converted.input INFO 2017-03-19 00:30:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8467917/mobley_8467917_converted.cms WARNING 2017-03-19 00:31:10 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:31:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8467917/mobley_8467917_converted.inp INFO 2017-03-19 00:31:10 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8467917/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8467917/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8467917/mobley_8467917_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8467917/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 11.37454351 11.37454351 0.00000000 0.00000000 0.00000000 0.00000000 6.84899880 6.84899880 coulomb total 6.86301520 6.85058445 -0.01243075 6.85058454 -0.01243066 6.85052554 -0.01248966 6.84899880 -0.01401640 coulomb-14 -4.52164880 -4.52395906 -0.00231026 0.00000000 4.52164880 -4.52396674 -0.00231794 0.00000000 4.52164880 improper 0.00000000 0.00076348 0.00076348 0.00000000 0.00000000 0.00000000 0.00000000 0.00075312 0.00075312 proper 48.90844960 48.90778452 -0.00066508 48.90854165 0.00009205 48.90854458 0.00009498 48.90778016 -0.00066944 vdw (SR) 0.00000000 -2.26038855 -2.26038855 0.00000000 0.00000000 0.00000000 0.00000000 3.83216744 3.83216744 vdw total 3.83212560 3.83206664 -0.00005896 3.83206665 -0.00005895 3.83210184 -0.00002376 3.83216744 0.00004184 vdw-14 6.09232240 6.09245518 0.00013278 0.00000000 -6.09232240 6.09249486 0.00017246 0.00000000 -6.09232240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.70537440 2.70533634 -0.00003806 2.70533633 -0.00003807 2.70523553 -0.00013887 2.70529072 -0.00008368 bond 1.64556720 1.64577514 0.00020794 1.64577514 0.00020794 1.64567043 0.00010323 1.64577640 0.00020920 bonded 53.25939120 53.25965948 0.00026828 53.25965312 0.00026192 53.25945054 0.00005934 53.25960040 0.00020920 dihedral 48.90844960 48.90854800 0.00009840 48.90854165 0.00009205 48.90854458 0.00009498 48.90853328 0.00008368 nonbonded 10.69514080 10.68265108 -0.01248972 10.68265114 -0.01248966 10.68262738 -0.01251342 10.68116624 -0.01397456 potential 63.95453200 63.94231057 -0.01222143 63.94230217 -0.01222983 63.94201807 -0.01251393 63.94072480 -0.01380720 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 63.95453200 Difference in potential energy from amber=>gromacs conversion: -0.01222143 Difference in potential energy from amber=>lammps conversion: -0.01222983 Difference in potential energy from amber=>desmond conversion: -0.01251393 Difference in potential energy from amber=>charmm conversion: -0.01380720 ======================================================================= INFO 2017-03-19 00:31:10 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8467917.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8467917.inpcrd') INFO 2017-03-19 00:31:10 Beginning InterMol conversion INFO 2017-03-19 00:31:10 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:31:10 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:31:10 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8492526.inpcrd INFO 2017-03-19 00:31:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8492526/mobley_8492526_converted.input INFO 2017-03-19 00:31:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8492526/mobley_8492526_converted.cms WARNING 2017-03-19 00:31:26 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:31:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8492526/mobley_8492526_converted.inp INFO 2017-03-19 00:31:26 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8492526/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8492526/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8492526/mobley_8492526_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8492526/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -9.62978203 -9.62978203 0.00000000 0.00000000 0.00000000 0.00000000 -7.12765320 -7.12765320 coulomb total -7.13330160 -7.13209673 0.00120487 -7.13209661 0.00120499 -7.13198696 0.00131464 -7.12765320 0.00564840 coulomb-14 2.49575600 2.49768530 0.00192930 0.00000000 -2.49575600 2.49772845 0.00197245 0.00000000 -2.49575600 improper 0.00000000 0.00000360 0.00000360 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 4.88021760 4.88017794 -0.00003966 4.88018162 -0.00003598 4.88018517 -0.00003243 4.88017576 -0.00004184 vdw (SR) 0.00000000 -1.25815199 -1.25815199 0.00000000 0.00000000 0.00000000 0.00000000 5.25974824 5.25974824 vdw total 5.25970640 5.25967066 -0.00003574 5.25967084 -0.00003556 5.25969618 -0.00001022 5.25974824 0.00004184 vdw-14 6.51783520 6.51782265 -0.00001255 0.00000000 -6.51783520 6.51784030 0.00000510 0.00000000 -6.51783520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.80623280 1.80634517 0.00011237 1.80634518 0.00011238 1.80629923 0.00006643 1.80635832 0.00012552 bond 1.14850800 1.14854747 0.00003947 1.14854746 0.00003946 1.14878832 0.00028032 1.14854984 0.00004184 bonded 7.83495840 7.83507418 0.00011578 7.83507425 0.00011585 7.83527271 0.00031431 7.83508392 0.00012552 dihedral 4.88021760 4.88018154 -0.00003606 4.88018162 -0.00003598 4.88018517 -0.00003243 4.88017576 -0.00004184 nonbonded -1.87359520 -1.87242606 0.00116914 -1.87242590 0.00116930 -1.87229078 0.00130442 -1.86790496 0.00569024 potential 5.96136320 5.96264811 0.00128491 5.96264811 0.00128491 5.96294534 0.00158214 5.96717896 0.00581576 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 5.96136320 Difference in potential energy from amber=>gromacs conversion: 0.00128491 Difference in potential energy from amber=>lammps conversion: 0.00128491 Difference in potential energy from amber=>desmond conversion: 0.00158214 Difference in potential energy from amber=>charmm conversion: 0.00581576 ======================================================================= INFO 2017-03-19 00:31:26 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8492526.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8492526.inpcrd') INFO 2017-03-19 00:31:26 Beginning InterMol conversion INFO 2017-03-19 00:31:26 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:31:26 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:31:26 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8514745.inpcrd INFO 2017-03-19 00:31:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8514745/mobley_8514745_converted.input INFO 2017-03-19 00:31:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8514745/mobley_8514745_converted.cms WARNING 2017-03-19 00:31:42 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:31:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8514745/mobley_8514745_converted.inp INFO 2017-03-19 00:31:42 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8514745/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8514745/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8514745/mobley_8514745_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8514745/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 1.03787275 1.03787275 0.00000000 0.00000000 0.00000000 0.00000000 -116.70230368 -116.70230368 coulomb total -116.65284880 -116.65979260 -0.00694380 -116.65979006 -0.00694126 -116.65986521 -0.00701641 -116.70230368 -0.04945488 coulomb-14 -117.69926720 -117.69766534 0.00160186 0.00000000 117.69926720 -117.69772707 0.00154013 0.00000000 117.69926720 improper 0.00000000 0.00000352 0.00000352 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 24.41238480 24.41246395 0.00007915 24.41246890 0.00008410 24.41250195 0.00011715 24.41246848 0.00008368 vdw (SR) 0.00000000 -3.68751392 -3.68751392 0.00000000 0.00000000 0.00000000 0.00000000 8.79041664 8.79041664 vdw total 8.79058400 8.79028394 -0.00030006 8.79028401 -0.00029999 8.79022824 -0.00035576 8.79041664 -0.00016736 vdw-14 12.47794320 12.47779786 -0.00014534 0.00000000 -12.47794320 12.47775015 -0.00019305 0.00000000 -12.47794320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.61290800 2.61301913 0.00011113 2.61301913 0.00011113 2.61341021 0.00050221 2.61303352 0.00012552 bond 2.72462080 2.72456726 -0.00005354 2.72456724 -0.00005356 2.72504419 0.00042339 2.72457896 -0.00004184 bonded 29.74991360 29.75005386 0.00014026 29.75005527 0.00014167 29.75095636 0.00104276 29.75008096 0.00016736 dihedral 24.41238480 24.41246747 0.00008267 24.41246890 0.00008410 24.41250195 0.00011715 24.41246848 0.00008368 nonbonded -107.86226480 -107.86950865 -0.00724385 -107.86950730 -0.00724250 -107.86963697 -0.00737217 -107.91188704 -0.04962224 potential -78.11235120 -78.11945479 -0.00710359 -78.11945145 -0.00710025 -78.11876192 -0.00641072 -78.16180608 -0.04945488 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -78.11235120 Difference in potential energy from amber=>gromacs conversion: -0.00710359 Difference in potential energy from amber=>lammps conversion: -0.00710025 Difference in potential energy from amber=>desmond conversion: -0.00641072 Difference in potential energy from amber=>charmm conversion: -0.04945488 ======================================================================= INFO 2017-03-19 00:31:42 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8514745.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8514745.inpcrd') INFO 2017-03-19 00:31:42 Beginning InterMol conversion INFO 2017-03-19 00:31:42 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:31:43 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:31:43 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8522124.inpcrd INFO 2017-03-19 00:31:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8522124/mobley_8522124_converted.input INFO 2017-03-19 00:31:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8522124/mobley_8522124_converted.cms WARNING 2017-03-19 00:31:58 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:31:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8522124/mobley_8522124_converted.inp INFO 2017-03-19 00:31:58 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8522124/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8522124/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8522124/mobley_8522124_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8522124/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 7.96625144 7.96625144 0.00000000 0.00000000 0.00000000 0.00000000 2.13120408 2.13120408 coulomb total 2.12003280 2.11511618 -0.00491662 2.11511614 -0.00491666 2.11508848 -0.00494432 2.13120408 0.01117128 coulomb-14 -5.85006880 -5.85113525 -0.00106645 0.00000000 5.85006880 -5.85113325 -0.00106445 0.00000000 5.85006880 proper 5.11452160 5.11461660 0.00009500 5.11461658 0.00009498 5.11458804 0.00006644 5.11460528 0.00008368 vdw (SR) 0.00000000 -3.27351996 -3.27351996 0.00000000 0.00000000 0.00000000 0.00000000 4.64164592 4.64164592 vdw total 4.64172960 4.64153464 -0.00019496 4.64153463 -0.00019497 4.64148520 -0.00024440 4.64164592 -0.00008368 vdw-14 7.91529120 7.91505460 -0.00023660 0.00000000 -7.91529120 7.91500510 -0.00028610 0.00000000 -7.91529120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.13511920 1.26897615 0.13385695 1.26897615 0.13385695 1.26867821 0.13355901 1.26896536 0.13384616 bond 2.33718240 2.33735737 0.00017497 2.33735737 0.00017497 2.33737675 0.00019435 2.33734976 0.00016736 bonded 8.58682320 8.72095012 0.13412692 8.72095011 0.13412691 8.72064300 0.13381980 8.72092040 0.13409720 dihedral 5.11452160 5.11461660 0.00009500 5.11461658 0.00009498 5.11458804 0.00006644 5.11460528 0.00008368 nonbonded 6.76176240 6.75665083 -0.00511157 6.75665081 -0.00511159 6.75657368 -0.00518872 6.77285000 0.01108760 potential 15.34858560 15.47760094 0.12901534 15.47760091 0.12901531 15.47713486 0.12854926 15.49377040 0.14518480 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 15.34858560 Difference in potential energy from amber=>gromacs conversion: 0.12901534 Difference in potential energy from amber=>lammps conversion: 0.12901531 Difference in potential energy from amber=>desmond conversion: 0.12854926 Difference in potential energy from amber=>charmm conversion: 0.14518480 ======================================================================= INFO 2017-03-19 00:31:58 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8522124.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8522124.inpcrd') INFO 2017-03-19 00:31:59 Beginning InterMol conversion INFO 2017-03-19 00:31:59 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:31:59 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:31:59 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8525830.inpcrd INFO 2017-03-19 00:31:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8525830/mobley_8525830_converted.input INFO 2017-03-19 00:31:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8525830/mobley_8525830_converted.cms WARNING 2017-03-19 00:32:14 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:32:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8525830/mobley_8525830_converted.inp INFO 2017-03-19 00:32:14 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8525830/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8525830/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8525830/mobley_8525830_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8525830/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 6.85574587 6.85574587 0.00000000 0.00000000 0.00000000 0.00000000 4.22466848 4.22466848 coulomb total 4.21496160 4.23215912 0.01719752 4.23215910 0.01719750 4.23214835 0.01718675 4.22466848 0.00970688 coulomb-14 -2.62964400 -2.62358674 0.00605726 0.00000000 2.62964400 -2.62358551 0.00605849 0.00000000 2.62964400 proper 3.49154800 3.49135654 -0.00019146 3.49135654 -0.00019146 3.49135828 -0.00018972 3.49138064 -0.00016736 vdw (SR) 0.00000000 -1.92704672 -1.92704672 0.00000000 0.00000000 0.00000000 0.00000000 2.09957304 2.09957304 vdw total 2.09953120 2.09947953 -0.00005167 2.09947957 -0.00005163 2.09946650 -0.00006470 2.09957304 0.00004184 vdw-14 4.02668160 4.02652624 -0.00015536 0.00000000 -4.02668160 4.02649298 -0.00018862 0.00000000 -4.02668160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.62373840 4.62380250 0.00006410 4.62380242 0.00006402 4.62379664 0.00005824 4.62382208 0.00008368 bond 1.13009840 1.13000220 -0.00009620 1.13000221 -0.00009619 1.12970995 -0.00038845 1.13001472 -0.00008368 bonded 9.24538480 9.24516124 -0.00022356 9.24516117 -0.00022363 9.24486487 -0.00051993 9.24521744 -0.00016736 dihedral 3.49154800 3.49135654 -0.00019146 3.49135654 -0.00019146 3.49135828 -0.00018972 3.49138064 -0.00016736 nonbonded 6.31449280 6.33163865 0.01714585 6.33163883 0.01714603 6.33161486 0.01712206 6.32424152 0.00974872 potential 15.55987760 15.57679989 0.01692229 15.57679979 0.01692219 15.57641302 0.01653542 15.56941712 0.00953952 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 15.55987760 Difference in potential energy from amber=>gromacs conversion: 0.01692229 Difference in potential energy from amber=>lammps conversion: 0.01692219 Difference in potential energy from amber=>desmond conversion: 0.01653542 Difference in potential energy from amber=>charmm conversion: 0.00953952 ======================================================================= INFO 2017-03-19 00:32:14 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8525830.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8525830.inpcrd') INFO 2017-03-19 00:32:15 Beginning InterMol conversion INFO 2017-03-19 00:32:15 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:32:15 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_852937.inpcrd INFO 2017-03-19 00:32:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_852937/mobley_852937_converted.input INFO 2017-03-19 00:32:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_852937/mobley_852937_converted.cms INFO 2017-03-19 00:32:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_852937/mobley_852937_converted.rst7 WARNING 2017-03-19 00:32:30 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:32:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_852937/mobley_852937_converted.inp INFO 2017-03-19 00:32:30 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_852937/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_852937/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_852937/mobley_852937_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_852937/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_852937/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -5.80735258 -5.80735258 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -58.38407992 -58.38407992 coulomb total -58.41198720 -58.39869627 0.01329093 -58.39869463 0.01329257 -58.39918157 0.01280563 -58.41198720 0.00000000 -58.38407992 0.02790728 coulomb-14 -52.58660400 -52.59134369 -0.00473969 0.00000000 52.58660400 -52.59122690 -0.00462290 -52.58660400 0.00000000 0.00000000 52.58660400 improper 0.00000000 0.00004882 0.00004882 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00041760 -0.00000080 0.00046643 0.00004803 0.00045264 0.00003424 0.00041840 0.00000000 0.00041840 0.00000000 vdw (SR) 0.00000000 -1.27645129 -1.27645129 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 14.87767640 14.87767640 vdw total 14.87746720 14.87770515 0.00023795 14.87770527 0.00023807 14.87774352 0.00027632 14.87746720 0.00000000 14.87767640 0.00020920 vdw-14 16.15400560 16.15415644 0.00015084 0.00000000 -16.15400560 16.15419225 0.00018665 16.15400560 0.00000000 0.00000000 -16.15400560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.25480560 0.25489058 0.00008498 0.25489059 0.00008499 0.25493371 0.00012811 0.25480560 0.00000000 0.25493112 0.00012552 bond 0.77613200 0.77614500 0.00001300 0.77614501 0.00001301 0.77600187 -0.00013013 0.77613200 0.00000000 0.77613200 0.00000000 bonded 1.03135600 1.03150201 0.00014601 1.03150203 0.00014603 1.03138821 0.00003221 1.03135600 0.00000000 1.03152336 0.00016736 dihedral 0.00041840 0.00046642 0.00004802 0.00046643 0.00004803 0.00045264 0.00003424 0.00041840 0.00000000 0.00046024 0.00004184 nonbonded -43.53452000 -43.52099112 0.01352888 -43.52098894 0.01353106 -43.52143804 0.01308196 -43.53452000 0.00000000 -43.50640352 0.02811648 potential -42.50316400 -42.48948911 0.01367489 -42.48948650 0.01367750 -42.49009109 0.01307291 -42.50316400 0.00000000 -42.47483832 0.02832568 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -42.50316400 Difference in potential energy from amber=>gromacs conversion: 0.01367489 Difference in potential energy from amber=>lammps conversion: 0.01367750 Difference in potential energy from amber=>desmond conversion: 0.01307291 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.02832568 ======================================================================= INFO 2017-03-19 00:32:30 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_852937.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_852937.inpcrd') INFO 2017-03-19 00:32:31 Beginning InterMol conversion INFO 2017-03-19 00:32:31 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:32:31 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:32:31 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8558116.inpcrd INFO 2017-03-19 00:32:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8558116/mobley_8558116_converted.input INFO 2017-03-19 00:32:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8558116/mobley_8558116_converted.cms WARNING 2017-03-19 00:32:46 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:32:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8558116/mobley_8558116_converted.inp INFO 2017-03-19 00:32:47 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8558116/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8558116/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8558116/mobley_8558116_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8558116/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 32.05947384 32.05947384 0.00000000 0.00000000 0.00000000 0.00000000 139.98973640 139.98973640 coulomb total 139.94182960 139.98885928 0.04702968 139.98885776 0.04702816 139.98892822 0.04709862 139.98973640 0.04790680 coulomb-14 107.92753520 107.92938544 0.00185024 0.00000000 -107.92753520 107.92950001 0.00196481 0.00000000 -107.92753520 proper 10.28301680 10.28286112 -0.00015568 10.28286116 -0.00015564 10.28283785 -0.00017895 10.28289128 -0.00012552 vdw (SR) 0.00000000 -2.80036951 -2.80036951 0.00000000 0.00000000 0.00000000 0.00000000 15.10976288 15.10976288 vdw total 15.10967920 15.10971457 0.00003537 15.10971518 0.00003598 15.10979442 0.00011522 15.10976288 0.00008368 vdw-14 17.91003040 17.91008408 0.00005368 0.00000000 -17.91003040 17.91016973 0.00013933 0.00000000 -17.91003040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.43299600 2.43294956 -0.00004644 2.43294956 -0.00004644 2.43292275 -0.00007325 2.43291232 -0.00008368 bond 0.75981440 0.76001041 0.00019601 0.76001042 0.00019602 0.76010223 0.00028783 0.76002360 0.00020920 bonded 13.47582720 13.47582109 -0.00000611 13.47582113 -0.00000607 13.47586284 0.00003564 13.47582720 -0.00000000 dihedral 10.28301680 10.28286112 -0.00015568 10.28286116 -0.00015564 10.28283785 -0.00017895 10.28289128 -0.00012552 nonbonded 155.05150880 155.09857385 0.04706505 155.09857462 0.04706582 155.09872264 0.04721384 155.09949928 0.04799048 potential 168.52733600 168.57439495 0.04705895 168.57439345 0.04705745 168.57453780 0.04720180 168.57532648 0.04799048 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 168.52733600 Difference in potential energy from amber=>gromacs conversion: 0.04705895 Difference in potential energy from amber=>lammps conversion: 0.04705745 Difference in potential energy from amber=>desmond conversion: 0.04720180 Difference in potential energy from amber=>charmm conversion: 0.04799048 ======================================================================= INFO 2017-03-19 00:32:47 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8558116.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8558116.inpcrd') INFO 2017-03-19 00:32:47 Beginning InterMol conversion INFO 2017-03-19 00:32:47 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:32:47 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:32:47 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8573194.inpcrd INFO 2017-03-19 00:32:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8573194/mobley_8573194_converted.input INFO 2017-03-19 00:32:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8573194/mobley_8573194_converted.cms WARNING 2017-03-19 00:33:03 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:33:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8573194/mobley_8573194_converted.inp INFO 2017-03-19 00:33:03 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8573194/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8573194/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8573194/mobley_8573194_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8573194/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -3.47843153 -3.47843153 0.00000000 0.00000000 0.00000000 0.00000000 -6.39135288 -6.39135288 coulomb total -6.38854960 -6.38829146 0.00025814 -6.38829145 0.00025815 -6.38821927 0.00033033 -6.39135288 -0.00280328 coulomb-14 -2.91206400 -2.90985994 0.00220406 0.00000000 2.91206400 -2.90983176 0.00223224 0.00000000 2.91206400 improper 0.00000000 0.00000688 0.00000688 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 3.18778960 3.18787008 0.00008048 3.18787696 0.00008736 3.18785927 0.00006967 3.18787328 0.00008368 vdw (SR) 0.00000000 -0.60360552 -0.60360552 0.00000000 0.00000000 0.00000000 0.00000000 4.27872576 4.27872576 vdw total 4.27855840 4.27867808 0.00011968 4.27867806 0.00011966 4.27867609 0.00011769 4.27872576 0.00016736 vdw-14 4.88230960 4.88228360 -0.00002600 0.00000000 -4.88230960 4.88227709 -0.00003251 0.00000000 -4.88230960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.65602720 1.65604891 0.00002171 1.65604891 0.00002171 1.65603897 0.00001177 1.65606904 0.00004184 bond 1.13972160 1.13959928 -0.00012232 1.13959930 -0.00012230 1.13949232 -0.00022928 1.13959608 -0.00012552 bonded 5.98353840 5.98352515 -0.00001325 5.98352518 -0.00001322 5.98339056 -0.00014784 5.98353840 0.00000000 dihedral 3.18778960 3.18787696 0.00008736 3.18787696 0.00008736 3.18785927 0.00006967 3.18787328 0.00008368 nonbonded -2.10999120 -2.10961339 0.00037781 -2.10961322 0.00037798 -2.10954318 0.00044802 -2.11262712 -0.00263592 potential 3.87354720 3.87391176 0.00036456 3.87391192 0.00036472 3.87382302 0.00027582 3.87095312 -0.00259408 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 3.87354720 Difference in potential energy from amber=>gromacs conversion: 0.00036456 Difference in potential energy from amber=>lammps conversion: 0.00036472 Difference in potential energy from amber=>desmond conversion: 0.00027582 Difference in potential energy from amber=>charmm conversion: -0.00259408 ======================================================================= INFO 2017-03-19 00:33:03 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8573194.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8573194.inpcrd') INFO 2017-03-19 00:33:03 Beginning InterMol conversion INFO 2017-03-19 00:33:03 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:33:03 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:33:03 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8578590.inpcrd INFO 2017-03-19 00:33:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8578590/mobley_8578590_converted.input INFO 2017-03-19 00:33:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8578590/mobley_8578590_converted.cms WARNING 2017-03-19 00:33:19 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:33:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8578590/mobley_8578590_converted.inp INFO 2017-03-19 00:33:19 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8578590/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8578590/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8578590/mobley_8578590_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8578590/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 25.69976897 25.69976897 0.00000000 0.00000000 0.00000000 0.00000000 -92.56405456 -92.56405456 coulomb total -92.54589600 -92.56211201 -0.01621601 -92.56210900 -0.01621300 -92.56214724 -0.01625124 -92.56405456 -0.01815856 coulomb-14 -118.22603280 -118.26188098 -0.03584818 0.00000000 118.22603280 -118.26188299 -0.03585019 0.00000000 118.22603280 proper 0.95980960 0.95996169 0.00015209 0.95996169 0.00015209 0.95995060 0.00014100 0.95997696 0.00016736 vdw (SR) 0.00000000 -0.19891806 -0.19891806 0.00000000 0.00000000 0.00000000 0.00000000 -0.40614088 -0.40614088 vdw total -0.40584800 -0.40615579 -0.00030779 -0.40615579 -0.00030779 -0.40617384 -0.00032584 -0.40614088 -0.00029288 vdw-14 -0.20710800 -0.20723774 -0.00012974 0.00000000 0.20710800 -0.20725560 -0.00014760 0.00000000 0.20710800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.92299040 0.92292427 -0.00006613 0.92292425 -0.00006615 0.92278892 -0.00020148 0.92294856 -0.00004184 bond 6.16805280 6.16796443 -0.00008837 6.16796452 -0.00008828 6.16784737 -0.00020543 6.16796912 -0.00008368 bonded 8.05085280 8.05085039 -0.00000241 8.05085046 -0.00000234 8.05058689 -0.00026591 8.05089464 0.00004184 dihedral 0.95980960 0.95996169 0.00015209 0.95996169 0.00015209 0.95995060 0.00014100 0.95997696 0.00016736 nonbonded -92.95174400 -92.96826780 -0.01652380 -92.96826662 -0.01652262 -92.96832108 -0.01657708 -92.97019544 -0.01845144 potential -84.90089120 -84.91741741 -0.01652621 -84.91741800 -0.01652680 -84.91775398 -0.01686278 -84.91934264 -0.01845144 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -84.90089120 Difference in potential energy from amber=>gromacs conversion: -0.01652621 Difference in potential energy from amber=>lammps conversion: -0.01652680 Difference in potential energy from amber=>desmond conversion: -0.01686278 Difference in potential energy from amber=>charmm conversion: -0.01845144 ======================================================================= INFO 2017-03-19 00:33:19 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8578590.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8578590.inpcrd') INFO 2017-03-19 00:33:19 Beginning InterMol conversion INFO 2017-03-19 00:33:19 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:33:19 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:33:19 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_859464.inpcrd INFO 2017-03-19 00:33:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_859464/mobley_859464_converted.input INFO 2017-03-19 00:33:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_859464/mobley_859464_converted.cms WARNING 2017-03-19 00:33:35 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:33:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_859464/mobley_859464_converted.inp INFO 2017-03-19 00:33:35 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_859464/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_859464/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_859464/mobley_859464_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_859464/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -24.53068871 -24.53068871 0.00000000 0.00000000 0.00000000 0.00000000 -112.64750560 -112.64750560 coulomb total -112.59897120 -112.59967735 -0.00070615 -112.59967411 -0.00070291 -112.59958775 -0.00061655 -112.64750560 -0.04853440 coulomb-14 -88.07487360 -88.06898864 0.00588496 0.00000000 88.07487360 -88.06891433 0.00595927 0.00000000 88.07487360 improper 0.00000000 0.00001015 0.00001015 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 19.48154080 19.48171008 0.00016928 19.48172155 0.00018075 19.48175577 0.00021497 19.48170816 0.00016736 vdw (SR) 0.00000000 -2.77060043 -2.77060043 0.00000000 0.00000000 0.00000000 0.00000000 9.86114408 9.86114408 vdw total 9.86126960 9.86100617 -0.00026343 9.86100643 -0.00026317 9.86092006 -0.00034954 9.86114408 -0.00012552 vdw-14 12.63191440 12.63160661 -0.00030779 0.00000000 -12.63191440 12.63150445 -0.00040995 0.00000000 -12.63191440 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.03130800 3.03123375 -0.00007425 3.03123373 -0.00007427 3.03111426 -0.00019374 3.03126616 -0.00004184 bond 2.03928160 2.03916363 -0.00011797 2.03916361 -0.00011799 2.03990797 0.00062637 2.03915608 -0.00012552 bonded 24.55213040 24.55211761 -0.00001279 24.55211889 -0.00001151 24.55277800 0.00064760 24.55213040 0.00000000 dihedral 19.48154080 19.48172024 0.00017944 19.48172155 0.00018075 19.48175577 0.00021497 19.48170816 0.00016736 nonbonded -102.73770160 -102.73867118 -0.00096958 -102.73866810 -0.00096650 -102.73866769 -0.00096609 -102.78636152 -0.04865992 potential -78.18557120 -78.18655357 -0.00098237 -78.18655026 -0.00097906 -78.18594902 -0.00037782 -78.23418928 -0.04861808 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -78.18557120 Difference in potential energy from amber=>gromacs conversion: -0.00098237 Difference in potential energy from amber=>lammps conversion: -0.00097906 Difference in potential energy from amber=>desmond conversion: -0.00037782 Difference in potential energy from amber=>charmm conversion: -0.04861808 ======================================================================= INFO 2017-03-19 00:33:35 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_859464.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_859464.inpcrd') INFO 2017-03-19 00:33:35 Beginning InterMol conversion INFO 2017-03-19 00:33:35 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:33:35 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:33:35 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8614858.inpcrd INFO 2017-03-19 00:33:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8614858/mobley_8614858_converted.input INFO 2017-03-19 00:33:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8614858/mobley_8614858_converted.cms WARNING 2017-03-19 00:33:51 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:33:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8614858/mobley_8614858_converted.inp INFO 2017-03-19 00:33:51 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8614858/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8614858/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8614858/mobley_8614858_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8614858/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 6.31513103 6.31513103 0.00000000 0.00000000 0.00000000 0.00000000 3.59008120 3.59008120 coulomb total 3.56518640 3.59877020 0.03358380 3.59877015 0.03358375 3.59873453 0.03354813 3.59008120 0.02489480 coulomb-14 -2.72378400 -2.71636083 0.00742317 0.00000000 2.72378400 -2.71636035 0.00742365 0.00000000 2.72378400 proper 6.85715760 6.85728467 0.00012707 6.85728479 0.00012719 6.85727099 0.00011339 6.85728312 0.00012552 vdw (SR) 0.00000000 -2.55179337 -2.55179337 0.00000000 0.00000000 0.00000000 0.00000000 5.45873928 5.45873928 vdw total 5.45886480 5.45861255 -0.00025225 5.45861250 -0.00025230 5.45862530 -0.00023950 5.45873928 -0.00012552 vdw-14 8.01068640 8.01040592 -0.00028048 0.00000000 -8.01068640 8.01041632 -0.00027008 0.00000000 -8.01068640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.04678880 3.04683962 0.00005082 3.04683964 0.00005084 3.04648371 -0.00030509 3.04678880 0.00000000 bond 0.98784240 0.98787978 0.00003738 0.98787976 0.00003736 0.98778127 -0.00006113 0.98788424 0.00004184 bonded 10.89178880 10.89200407 0.00021527 10.89200419 0.00021539 10.89153597 -0.00025283 10.89195616 0.00016736 dihedral 6.85715760 6.85728467 0.00012707 6.85728479 0.00012719 6.85727099 0.00011339 6.85728312 0.00012552 nonbonded 9.02405120 9.05738275 0.03333155 9.05738262 0.03333142 9.05735983 0.03330863 9.04882048 0.02476928 potential 19.91584000 19.94938683 0.03354683 19.94938689 0.03354689 19.94883469 0.03299469 19.94077664 0.02493664 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 19.91584000 Difference in potential energy from amber=>gromacs conversion: 0.03354683 Difference in potential energy from amber=>lammps conversion: 0.03354689 Difference in potential energy from amber=>desmond conversion: 0.03299469 Difference in potential energy from amber=>charmm conversion: 0.02493664 ======================================================================= INFO 2017-03-19 00:33:51 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8614858.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8614858.inpcrd') INFO 2017-03-19 00:33:51 Beginning InterMol conversion INFO 2017-03-19 00:33:51 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:33:51 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:33:51 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8668219.inpcrd INFO 2017-03-19 00:33:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8668219/mobley_8668219_converted.input INFO 2017-03-19 00:33:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8668219/mobley_8668219_converted.cms WARNING 2017-03-19 00:34:07 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:34:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8668219/mobley_8668219_converted.inp INFO 2017-03-19 00:34:07 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8668219/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8668219/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8668219/mobley_8668219_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8668219/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -2.04676194 -2.04676194 0.00000000 0.00000000 0.00000000 0.00000000 -6.23026888 -6.23026888 coulomb total -6.24336480 -6.22952586 0.01383894 -6.22952580 0.01383900 -6.22954168 0.01382312 -6.23026888 0.01309592 coulomb-14 -4.17981600 -4.18276392 -0.00294792 0.00000000 4.17981600 -4.18274815 -0.00293215 0.00000000 4.17981600 proper 12.04322560 12.04338116 0.00015556 12.04337622 0.00015062 12.04335756 0.00013196 12.04339296 0.00016736 vdw (SR) 0.00000000 10.44475473 10.44475473 0.00000000 0.00000000 0.00000000 0.00000000 22.07377984 22.07377984 vdw total 22.07394720 22.07352875 -0.00041845 22.07352922 -0.00041798 22.07383415 -0.00011305 22.07377984 -0.00016736 vdw-14 11.62900960 11.62877402 -0.00023558 0.00000000 -11.62900960 11.62889889 -0.00011071 0.00000000 -11.62900960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 9.47717840 9.47738608 0.00020768 9.47738593 0.00020753 9.47687083 -0.00030757 9.47738760 0.00020920 bond 1.25436320 1.25437800 0.00001480 1.25437801 0.00001481 1.25421574 -0.00014746 1.25436320 0.00000000 bonded 22.77476720 22.77514524 0.00037804 22.77514016 0.00037296 22.77444414 -0.00032306 22.77514376 0.00037656 dihedral 12.04322560 12.04338116 0.00015556 12.04337622 0.00015062 12.04335756 0.00013196 12.04339296 0.00016736 nonbonded 15.83058240 15.84400289 0.01342049 15.84400342 0.01342102 15.84429247 0.01371007 15.84351096 0.01292856 potential 38.60534960 38.61914813 0.01379853 38.61914341 0.01379381 38.61867497 0.01332537 38.61865472 0.01330512 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 38.60534960 Difference in potential energy from amber=>gromacs conversion: 0.01379853 Difference in potential energy from amber=>lammps conversion: 0.01379381 Difference in potential energy from amber=>desmond conversion: 0.01332537 Difference in potential energy from amber=>charmm conversion: 0.01330512 ======================================================================= INFO 2017-03-19 00:34:07 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8668219.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8668219.inpcrd') INFO 2017-03-19 00:34:07 Beginning InterMol conversion INFO 2017-03-19 00:34:07 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:34:07 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:34:07 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8685905.inpcrd INFO 2017-03-19 00:34:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8685905/mobley_8685905_converted.input INFO 2017-03-19 00:34:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8685905/mobley_8685905_converted.cms WARNING 2017-03-19 00:34:23 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:34:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8685905/mobley_8685905_converted.inp INFO 2017-03-19 00:34:23 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8685905/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8685905/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8685905/mobley_8685905_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8685905/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 36.81802848 36.81802848 coulomb total 36.81417920 36.81550096 0.00132176 36.81550051 0.00132131 36.81542858 0.00124938 36.81802848 0.00384928 coulomb-14 36.81417920 36.81550096 0.00132176 0.00000000 -36.81417920 36.81542858 0.00124938 0.00000000 -36.81417920 proper 15.00382400 15.00366763 -0.00015637 15.00366752 -0.00015648 15.00364756 -0.00017644 15.00365664 -0.00016736 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 4.49918072 4.49918072 vdw total 4.49905520 4.49928837 0.00023317 4.49928825 0.00023305 4.49922151 0.00016631 4.49918072 0.00012552 vdw-14 4.49905520 4.49928837 0.00023317 0.00000000 -4.49905520 4.49922151 0.00016631 0.00000000 -4.49905520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.22172800 1.22162371 -0.00010429 1.22162369 -0.00010431 1.22161735 -0.00011065 1.22168616 -0.00004184 bond 2.36814400 2.36806627 -0.00007773 2.36806626 -0.00007774 2.36825134 0.00010734 2.36806032 -0.00008368 bonded 18.59369600 18.59335761 -0.00033839 18.59335747 -0.00033853 18.59351624 -0.00017976 18.59340312 -0.00029288 dihedral 15.00382400 15.00366763 -0.00015637 15.00366752 -0.00015648 15.00364756 -0.00017644 15.00365664 -0.00016736 nonbonded 41.31323440 41.31478933 0.00155493 41.31478876 0.00155436 41.31465010 0.00141570 41.31720920 0.00397480 potential 59.90693040 59.90814695 0.00121655 59.90814794 0.00121754 59.90813790 0.00120750 59.91065416 0.00372376 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 59.90693040 Difference in potential energy from amber=>gromacs conversion: 0.00121655 Difference in potential energy from amber=>lammps conversion: 0.00121754 Difference in potential energy from amber=>desmond conversion: 0.00120750 Difference in potential energy from amber=>charmm conversion: 0.00372376 ======================================================================= INFO 2017-03-19 00:34:23 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8685905.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8685905.inpcrd') INFO 2017-03-19 00:34:23 Beginning InterMol conversion INFO 2017-03-19 00:34:23 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:34:23 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:34:23 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8691603.inpcrd INFO 2017-03-19 00:34:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8691603/mobley_8691603_converted.input INFO 2017-03-19 00:34:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8691603/mobley_8691603_converted.cms WARNING 2017-03-19 00:34:39 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:34:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8691603/mobley_8691603_converted.inp INFO 2017-03-19 00:34:39 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8691603/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8691603/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8691603/mobley_8691603_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8691603/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 72.57986808 72.57986808 0.00000000 0.00000000 0.00000000 0.00000000 -92.22280752 -92.22280752 coulomb total -92.21912560 -92.22226722 -0.00314162 -92.22226778 -0.00314218 -92.22279120 -0.00366560 -92.22280752 -0.00368192 coulomb-14 -164.79646320 -164.80213530 -0.00567210 0.00000000 164.79646320 -164.80208357 -0.00562037 0.00000000 164.79646320 improper 0.00000000 0.00001019 0.00001019 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00000000 0.00011589 0.00011589 0.00012604 0.00012604 0.00013093 0.00013093 0.00012552 0.00012552 vdw (SR) 0.00000000 -1.91694963 -1.91694963 0.00000000 0.00000000 0.00000000 0.00000000 16.08296128 16.08296128 vdw total 16.08287760 16.08295991 0.00008231 16.08296002 0.00008242 16.08304618 0.00016858 16.08296128 0.00008368 vdw-14 17.99998640 17.99990955 -0.00007685 0.00000000 -17.99998640 17.99999188 0.00000548 0.00000000 -17.99998640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.31672880 0.31688335 0.00015455 0.31688335 0.00015455 0.31685249 0.00012369 0.31689616 0.00016736 bond 1.38323040 1.38312174 -0.00010866 1.38312174 -0.00010866 1.38323740 0.00000700 1.38310488 -0.00012552 bonded 1.69995920 1.70013116 0.00017196 1.70013113 0.00017193 1.70022081 0.00026161 1.70012656 0.00016736 dihedral 0.00000000 0.00012607 0.00012607 0.00012604 0.00012604 0.00013093 0.00013093 0.00012552 0.00012552 nonbonded -76.13624800 -76.13930731 -0.00305931 -76.13930650 -0.00305850 -76.13974502 -0.00349702 -76.13984624 -0.00359824 potential -74.43628880 -74.43917615 -0.00288735 -74.43917576 -0.00288696 -74.43956822 -0.00327942 -74.43971968 -0.00343088 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -74.43628880 Difference in potential energy from amber=>gromacs conversion: -0.00288735 Difference in potential energy from amber=>lammps conversion: -0.00288696 Difference in potential energy from amber=>desmond conversion: -0.00327942 Difference in potential energy from amber=>charmm conversion: -0.00343088 ======================================================================= INFO 2017-03-19 00:34:39 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8691603.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8691603.inpcrd') INFO 2017-03-19 00:34:39 Beginning InterMol conversion INFO 2017-03-19 00:34:39 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:34:39 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:34:39 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8705848.inpcrd INFO 2017-03-19 00:34:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8705848/mobley_8705848_converted.input INFO 2017-03-19 00:34:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8705848/mobley_8705848_converted.cms WARNING 2017-03-19 00:34:55 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:34:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8705848/mobley_8705848_converted.inp INFO 2017-03-19 00:34:55 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8705848/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8705848/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8705848/mobley_8705848_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8705848/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 112.46324289 112.46324289 0.00000000 0.00000000 0.00000000 0.00000000 -112.55026944 -112.55026944 coulomb total -112.56006000 -112.57639504 -0.01633504 -112.57639434 -0.01633434 -112.57654245 -0.01648245 -112.55026944 0.00979056 coulomb-14 -225.05526800 -225.03963793 0.01563007 0.00000000 225.05526800 -225.03960436 0.01566364 0.00000000 225.05526800 proper 16.99624480 16.99622861 -0.00001619 16.99622262 -0.00002218 16.99619752 -0.00004728 16.99624480 0.00000000 vdw (SR) 0.00000000 5.53655072 5.53655072 0.00000000 0.00000000 0.00000000 0.00000000 17.09866912 17.09866912 vdw total 17.09875280 17.09848328 -0.00026952 17.09848335 -0.00026945 17.09885719 0.00010439 17.09866912 -0.00008368 vdw-14 11.56206560 11.56193256 -0.00013304 0.00000000 -11.56206560 11.56212531 0.00005971 0.00000000 -11.56206560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.65976880 2.65983889 0.00007009 2.65983888 0.00007008 2.65970623 -0.00006257 2.65981064 0.00004184 bond 1.88656560 1.88654327 -0.00002233 1.88654326 -0.00002234 1.88678969 0.00022409 1.88652376 -0.00004184 bonded 21.54257920 21.54261078 0.00003158 21.54260476 0.00002556 21.54269344 0.00011424 21.54257920 0.00000000 dihedral 16.99624480 16.99622861 -0.00001619 16.99622262 -0.00002218 16.99619752 -0.00004728 16.99624480 0.00000000 nonbonded -95.46130720 -95.47791177 -0.01660457 -95.47790931 -0.01660211 -95.47768526 -0.01637806 -95.45160032 0.00970688 potential -73.91872800 -73.93530099 -0.01657299 -73.93530501 -0.01657701 -73.93505397 -0.01632597 -73.90902112 0.00970688 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -73.91872800 Difference in potential energy from amber=>gromacs conversion: -0.01657299 Difference in potential energy from amber=>lammps conversion: -0.01657701 Difference in potential energy from amber=>desmond conversion: -0.01632597 Difference in potential energy from amber=>charmm conversion: 0.00970688 ======================================================================= INFO 2017-03-19 00:34:55 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8705848.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8705848.inpcrd') INFO 2017-03-19 00:34:55 Beginning InterMol conversion INFO 2017-03-19 00:34:55 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:34:56 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:34:56 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8713762.inpcrd INFO 2017-03-19 00:34:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8713762/mobley_8713762_converted.input INFO 2017-03-19 00:34:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8713762/mobley_8713762_converted.cms WARNING 2017-03-19 00:35:11 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:35:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8713762/mobley_8713762_converted.inp INFO 2017-03-19 00:35:11 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8713762/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8713762/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8713762/mobley_8713762_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8713762/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -74.06275129 -74.06275129 0.00000000 0.00000000 0.00000000 0.00000000 -77.72754872 -77.72754872 coulomb total -77.72867840 -77.71120403 0.01747437 -77.71120183 0.01747657 -77.71121899 0.01745941 -77.72754872 0.00112968 coulomb-14 -3.68275680 -3.64845274 0.03430406 0.00000000 3.68275680 -3.64855637 0.03420043 0.00000000 3.68275680 improper 0.00000000 0.00257643 0.00257643 0.00000000 0.00000000 0.00000000 0.00000000 0.00259408 0.00259408 proper 5.85048720 5.84781247 -0.00267473 5.85039222 -0.00009498 5.85034649 -0.00014071 5.84785128 -0.00263592 vdw (SR) 0.00000000 -1.33047285 -1.33047285 0.00000000 0.00000000 0.00000000 0.00000000 18.60218952 18.60218952 vdw total 18.60248240 18.60176129 -0.00072111 18.60176150 -0.00072090 18.60185181 -0.00063059 18.60218952 -0.00029288 vdw-14 19.93257600 19.93223414 -0.00034186 0.00000000 -19.93257600 19.93238036 -0.00019564 0.00000000 -19.93257600 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 11.46583360 11.46583199 -0.00000161 11.46583193 -0.00000167 11.46589343 0.00005983 11.46583360 0.00000000 bond 9.63114960 9.63094090 -0.00020870 9.63094082 -0.00020878 9.62973666 -0.00141294 9.63094040 -0.00020920 bonded 26.94747040 26.94716179 -0.00030861 26.94716497 -0.00030543 26.94597659 -0.00149381 26.94721936 -0.00025104 dihedral 5.85048720 5.85038890 -0.00009830 5.85039222 -0.00009498 5.85034649 -0.00014071 5.85044536 -0.00004184 nonbonded -59.12619600 -59.10944274 0.01675326 -59.10944326 0.01675274 -59.10936718 0.01682882 -59.12535920 0.00083680 potential -32.17872560 -32.16228096 0.01644464 -32.16227662 0.01644898 -32.16358124 0.01514436 -32.17818168 0.00054392 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -32.17872560 Difference in potential energy from amber=>gromacs conversion: 0.01644464 Difference in potential energy from amber=>lammps conversion: 0.01644898 Difference in potential energy from amber=>desmond conversion: 0.01514436 Difference in potential energy from amber=>charmm conversion: 0.00054392 ======================================================================= INFO 2017-03-19 00:35:11 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8713762.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8713762.inpcrd') INFO 2017-03-19 00:35:12 Beginning InterMol conversion INFO 2017-03-19 00:35:12 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:35:12 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8723116.inpcrd INFO 2017-03-19 00:35:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8723116/mobley_8723116_converted.input INFO 2017-03-19 00:35:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8723116/mobley_8723116_converted.cms INFO 2017-03-19 00:35:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8723116/mobley_8723116_converted.rst7 WARNING 2017-03-19 00:35:27 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:35:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8723116/mobley_8723116_converted.inp INFO 2017-03-19 00:35:28 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8723116/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8723116/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8723116/mobley_8723116_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_8723116/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8723116/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 36.08137304 36.08137304 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -119.75223048 -119.75223048 coulomb total -119.74105920 -119.74533402 -0.00427482 -119.74533106 -0.00427186 -119.74569541 -0.00463621 -119.74105920 0.00000000 -119.75223048 -0.01117128 coulomb-14 -155.82136480 -155.82670706 -0.00534226 0.00000000 155.82136480 -155.82670317 -0.00533837 -155.82136480 0.00000000 0.00000000 155.82136480 improper 0.00000000 0.11350276 0.11350276 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.11351192 0.11351192 proper 0.21798640 0.10450615 -0.11348025 0.21800753 0.00002113 0.21804102 0.00005462 0.21798640 0.00000000 0.10451632 -0.11347008 vdw (SR) 0.00000000 -1.71181750 -1.71181750 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 14.31300376 14.31300376 vdw total 14.31304560 14.31301345 -0.00003215 14.31301338 -0.00003222 14.31304378 -0.00000182 14.31304560 0.00000000 14.31300376 -0.00004184 vdw-14 16.02472000 16.02483095 0.00011095 0.00000000 -16.02472000 16.02485682 0.00013682 16.02472000 0.00000000 0.00000000 -16.02472000 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.59572960 3.59569994 -0.00002966 3.59569994 -0.00002966 3.59581850 0.00008890 3.59572960 0.00000000 3.59577144 0.00004184 bond 5.50321520 5.50318063 -0.00003457 5.50318047 -0.00003473 5.50478186 0.00156666 5.50321520 0.00000000 5.50317336 -0.00004184 bonded 9.31693120 9.31688948 -0.00004172 9.31688793 -0.00004327 9.31864138 0.00171018 9.31693120 0.00000000 9.31697304 0.00004184 dihedral 0.21798640 0.21800891 0.00002251 0.21800753 0.00002113 0.21804102 0.00005462 0.21798640 0.00000000 0.21802824 0.00004184 nonbonded -105.42801360 -105.43232057 -0.00430697 -105.43231894 -0.00430534 -105.43265162 -0.00463802 -105.42801360 0.00000000 -105.43922672 -0.01121312 potential -96.11108240 -96.11543110 -0.00434870 -96.11542958 -0.00434718 -96.11405137 -0.00296897 -96.11108240 0.00000000 -96.12229552 -0.01121312 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -96.11108240 Difference in potential energy from amber=>gromacs conversion: -0.00434870 Difference in potential energy from amber=>lammps conversion: -0.00434718 Difference in potential energy from amber=>desmond conversion: -0.00296897 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.01121312 ======================================================================= INFO 2017-03-19 00:35:28 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8723116.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8723116.inpcrd') INFO 2017-03-19 00:35:28 Beginning InterMol conversion INFO 2017-03-19 00:35:28 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:35:28 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:35:28 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8739734.inpcrd INFO 2017-03-19 00:35:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8739734/mobley_8739734_converted.input INFO 2017-03-19 00:35:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8739734/mobley_8739734_converted.cms WARNING 2017-03-19 00:35:44 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:35:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8739734/mobley_8739734_converted.inp INFO 2017-03-19 00:35:44 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8739734/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8739734/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8739734/mobley_8739734_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8739734/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -58.80393570 -58.80393570 0.00000000 0.00000000 0.00000000 0.00000000 -26.47375792 -26.47375792 coulomb total -26.47467840 -26.46945706 0.00522134 -26.46945677 0.00522163 -26.46935242 0.00532598 -26.47375792 0.00092048 coulomb-14 32.33353360 32.33447864 0.00094504 0.00000000 -32.33353360 32.33455341 0.00101981 0.00000000 -32.33353360 improper 0.00000000 0.00605520 0.00605520 0.00000000 0.00000000 0.00000000 0.00000000 0.00606680 0.00606680 proper 11.77754160 11.77167792 -0.00586368 11.77773448 0.00019288 11.77773160 0.00019000 11.77168400 -0.00585760 vdw (SR) 0.00000000 -1.59108716 -1.59108716 0.00000000 0.00000000 0.00000000 0.00000000 5.67957080 5.67957080 vdw total 5.67936160 5.67947596 0.00011436 5.67947624 0.00011464 5.67954804 0.00018644 5.67957080 0.00020920 vdw-14 7.27053680 7.27056312 0.00002632 0.00000000 -7.27053680 7.27063107 0.00009427 0.00000000 -7.27053680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.95643840 1.95640542 -0.00003298 1.95640543 -0.00003297 1.95624255 -0.00019585 1.95639656 -0.00004184 bond 1.69326480 1.69346915 0.00020435 1.69346915 0.00020435 1.69364724 0.00038244 1.69347400 0.00020920 bonded 15.42724480 15.42760768 0.00036288 15.42760906 0.00036426 15.42762139 0.00037659 15.42762136 0.00037656 dihedral 11.77754160 11.77773311 0.00019151 11.77773448 0.00019288 11.77773160 0.00019000 11.77775080 0.00020920 nonbonded -20.79531680 -20.78998110 0.00533570 -20.78998053 0.00533627 -20.78980438 0.00551242 -20.79418712 0.00112968 potential -5.36807200 -5.36237342 0.00569858 -5.36237130 0.00570070 -5.36222214 0.00584986 -5.36660760 0.00146440 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -5.36807200 Difference in potential energy from amber=>gromacs conversion: 0.00569858 Difference in potential energy from amber=>lammps conversion: 0.00570070 Difference in potential energy from amber=>desmond conversion: 0.00584986 Difference in potential energy from amber=>charmm conversion: 0.00146440 ======================================================================= INFO 2017-03-19 00:35:44 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8739734.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8739734.inpcrd') INFO 2017-03-19 00:35:44 Beginning InterMol conversion INFO 2017-03-19 00:35:44 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:35:44 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:35:44 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8746821.inpcrd INFO 2017-03-19 00:35:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8746821/mobley_8746821_converted.input INFO 2017-03-19 00:35:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8746821/mobley_8746821_converted.cms WARNING 2017-03-19 00:36:00 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:36:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8746821/mobley_8746821_converted.inp INFO 2017-03-19 00:36:00 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8746821/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8746821/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8746821/mobley_8746821_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8746821/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -17.87611924 -17.87611924 0.00000000 0.00000000 0.00000000 0.00000000 -96.87771672 -96.87771672 coulomb total -96.85499760 -96.85608898 -0.00109138 -96.85608962 -0.00109202 -96.85628502 -0.00128742 -96.87771672 -0.02271912 coulomb-14 -78.97467360 -78.97996973 -0.00529613 0.00000000 78.97467360 -78.98009397 -0.00542037 0.00000000 78.97467360 improper 0.00000000 0.00012702 0.00012702 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00125520 0.00095604 -0.00029916 0.00108309 -0.00017211 0.00108433 -0.00017087 0.00096232 -0.00029288 vdw (SR) 0.00000000 23.34187980 23.34187980 0.00000000 0.00000000 0.00000000 0.00000000 49.16723000 49.16723000 vdw total 49.16702080 49.16694502 -0.00007578 49.16694549 -0.00007531 49.16657043 -0.00045037 49.16723000 0.00020920 vdw-14 25.82490320 25.82506522 0.00016202 0.00000000 -25.82490320 25.82537888 0.00047568 0.00000000 -25.82490320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.01752480 2.01734608 -0.00017872 2.01734606 -0.00017874 2.01750642 -0.00001838 2.01735744 -0.00016736 bond 1.99409440 1.99398938 -0.00010502 1.99398938 -0.00010502 1.99364892 -0.00044548 1.99396888 -0.00012552 bonded 4.01287440 4.01241851 -0.00045589 4.01241853 -0.00045587 4.01223967 -0.00063473 4.01241416 -0.00046024 dihedral 0.00125520 0.00108306 -0.00017214 0.00108309 -0.00017211 0.00108433 -0.00017087 0.00108784 -0.00016736 nonbonded -47.68797680 -47.68914395 -0.00116715 -47.68914414 -0.00116734 -47.68971458 -0.00173778 -47.71048672 -0.02250992 potential -43.67510240 -43.67672544 -0.00162304 -43.67672579 -0.00162339 -43.67752703 -0.00242463 -43.69807256 -0.02297016 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -43.67510240 Difference in potential energy from amber=>gromacs conversion: -0.00162304 Difference in potential energy from amber=>lammps conversion: -0.00162339 Difference in potential energy from amber=>desmond conversion: -0.00242463 Difference in potential energy from amber=>charmm conversion: -0.02297016 ======================================================================= INFO 2017-03-19 00:36:00 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8746821.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8746821.inpcrd') INFO 2017-03-19 00:36:00 Beginning InterMol conversion INFO 2017-03-19 00:36:00 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:36:00 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:36:00 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8754702.inpcrd INFO 2017-03-19 00:36:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8754702/mobley_8754702_converted.input INFO 2017-03-19 00:36:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8754702/mobley_8754702_converted.cms WARNING 2017-03-19 00:36:16 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:36:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8754702/mobley_8754702_converted.inp INFO 2017-03-19 00:36:16 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8754702/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8754702/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8754702/mobley_8754702_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8754702/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -14.90484515 -14.90484515 0.00000000 0.00000000 0.00000000 0.00000000 -26.58237456 -26.58237456 coulomb total -26.53367280 -26.53781758 -0.00414478 -26.53781747 -0.00414467 -26.53785190 -0.00417910 -26.58237456 -0.04870176 coulomb-14 -11.62733600 -11.63297243 -0.00563643 0.00000000 11.62733600 -11.63300398 -0.00566798 0.00000000 11.62733600 improper 0.00000000 0.00000961 0.00000961 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 9.93951040 9.93944397 -0.00006643 9.93945350 -0.00005690 9.93945141 -0.00005899 9.93946856 -0.00004184 vdw (SR) 0.00000000 -1.49422832 -1.49422832 0.00000000 0.00000000 0.00000000 0.00000000 5.79278984 5.79278984 vdw total 5.79274800 5.79272428 -0.00002372 5.79272457 -0.00002343 5.79271054 -0.00003746 5.79278984 0.00004184 vdw-14 7.28685440 7.28695260 0.00009820 0.00000000 -7.28685440 7.28692946 0.00007506 0.00000000 -7.28685440 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.41542320 2.41549762 0.00007442 2.41549763 0.00007443 2.41539072 -0.00003248 2.41554872 0.00012552 bond 1.91794560 1.91793530 -0.00001030 1.91793531 -0.00001029 1.91806734 0.00012174 1.91794560 0.00000000 bonded 14.27287920 14.27288649 0.00000729 14.27288644 0.00000724 14.27290946 0.00003026 14.27296288 0.00008368 dihedral 9.93951040 9.93945358 -0.00005682 9.93945350 -0.00005690 9.93945141 -0.00005899 9.93946856 -0.00004184 nonbonded -20.74092480 -20.74509330 -0.00416850 -20.74509290 -0.00416810 -20.74514136 -0.00421656 -20.78958472 -0.04865992 potential -6.46804560 -6.47220681 -0.00416121 -6.47220659 -0.00416099 -6.47226244 -0.00421684 -6.51662184 -0.04857624 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -6.46804560 Difference in potential energy from amber=>gromacs conversion: -0.00416121 Difference in potential energy from amber=>lammps conversion: -0.00416099 Difference in potential energy from amber=>desmond conversion: -0.00421684 Difference in potential energy from amber=>charmm conversion: -0.04857624 ======================================================================= INFO 2017-03-19 00:36:16 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8754702.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8754702.inpcrd') INFO 2017-03-19 00:36:16 Beginning InterMol conversion INFO 2017-03-19 00:36:16 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:36:16 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8764620.inpcrd INFO 2017-03-19 00:36:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8764620/mobley_8764620_converted.input INFO 2017-03-19 00:36:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8764620/mobley_8764620_converted.cms INFO 2017-03-19 00:36:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8764620/mobley_8764620_converted.rst7 WARNING 2017-03-19 00:36:32 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:36:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8764620/mobley_8764620_converted.inp INFO 2017-03-19 00:36:32 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8764620/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8764620/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8764620/mobley_8764620_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_8764620/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8764620/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 47.27912504 47.27912504 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -75.84470688 -75.84470688 coulomb total -75.84211280 -75.84076489 0.00134791 -75.84076555 0.00134725 -75.84088731 0.00122549 -75.84169440 0.00041840 -75.84470688 -0.00259408 coulomb-14 -123.12173120 -123.11988993 0.00184127 0.00000000 123.12173120 -123.12001199 0.00171921 -123.12131280 0.00041840 0.00000000 123.12173120 improper 0.00000000 0.00010451 0.00010451 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00083680 0.00088759 0.00005079 0.00099213 0.00015533 0.00099605 0.00015925 0.00083680 0.00000000 0.00087864 0.00004184 vdw (SR) 0.00000000 -1.97355211 -1.97355211 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 17.68338312 17.68338312 vdw total 17.68325760 17.68343271 0.00017511 17.68343291 0.00017531 17.68384454 0.00058694 17.68325760 0.00000000 17.68338312 0.00012552 vdw-14 19.65685040 19.65698483 0.00013443 0.00000000 -19.65685040 19.65739700 0.00054660 19.65685040 0.00000000 0.00000000 -19.65685040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.98614480 1.70830774 -0.27783706 1.70830774 -0.27783706 1.70821878 -0.27792602 1.98614480 0.00000000 1.70832720 -0.27781760 bond 2.52546240 2.52563326 0.00017086 2.52563327 0.00017087 2.52576092 0.00029852 2.52546240 0.00000000 2.52562976 0.00016736 bonded 4.51244400 4.23493311 -0.27751089 4.23493315 -0.27751085 4.23497574 -0.27746826 4.51244400 0.00000000 4.23491928 -0.27752472 dihedral 0.00083680 0.00099211 0.00015531 0.00099213 0.00015533 0.00099605 0.00015925 0.00083680 0.00000000 0.00096232 0.00012552 nonbonded -58.15885520 -58.15733217 0.00152303 -58.15733222 0.00152298 -58.15704276 0.00181244 -58.15843680 0.00041840 -58.16132376 -0.00246856 potential -53.64641120 -53.92239907 -0.27598787 -53.92239621 -0.27598501 -53.92212508 -0.27571388 -53.64599280 0.00041840 -53.92636264 -0.27995144 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -53.64641120 Difference in potential energy from amber=>gromacs conversion: -0.27598787 Difference in potential energy from amber=>lammps conversion: -0.27598501 Difference in potential energy from amber=>desmond conversion: -0.27571388 Difference in potential energy from amber=>amber conversion: 0.00041840 Difference in potential energy from amber=>charmm conversion: -0.27995144 ======================================================================= INFO 2017-03-19 00:36:32 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8764620.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8764620.inpcrd') INFO 2017-03-19 00:36:32 Beginning InterMol conversion INFO 2017-03-19 00:36:32 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:36:32 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:36:32 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8765203.inpcrd INFO 2017-03-19 00:36:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8765203/mobley_8765203_converted.input INFO 2017-03-19 00:36:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8765203/mobley_8765203_converted.cms WARNING 2017-03-19 00:36:48 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:36:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8765203/mobley_8765203_converted.inp INFO 2017-03-19 00:36:48 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8765203/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8765203/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8765203/mobley_8765203_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8765203/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 7.50221485 7.50221485 0.00000000 0.00000000 0.00000000 0.00000000 -15.70790752 -15.70790752 coulomb total -15.72263520 -15.71102169 0.01161351 -15.71102167 0.01161353 -15.71106899 0.01156621 -15.70790752 0.01472768 coulomb-14 -23.20781120 -23.21323654 -0.00542534 0.00000000 23.20781120 -23.21323404 -0.00542284 0.00000000 23.20781120 improper 0.00000000 0.00001299 0.00001299 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 38.40368080 38.40369362 0.00001282 38.40370632 0.00002552 38.40361147 -0.00006933 38.40368080 0.00000000 vdw (SR) 0.00000000 4.64392793 4.64392793 0.00000000 0.00000000 0.00000000 0.00000000 9.73290448 9.73290448 vdw total 9.73282080 9.73284168 0.00002088 9.73284172 0.00002092 9.73275687 -0.00006393 9.73290448 0.00008368 vdw-14 5.08899920 5.08891375 -0.00008545 0.00000000 -5.08899920 5.08885627 -0.00014293 0.00000000 -5.08899920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.32374560 4.32384899 0.00010339 4.32384894 0.00010334 4.32389606 0.00015046 4.32382928 0.00008368 bond 0.17656480 0.17662393 0.00005913 0.17662394 0.00005914 0.17678631 0.00022151 0.17660664 0.00004184 bonded 42.90399120 42.90417954 0.00018834 42.90417920 0.00018800 42.90429383 0.00030263 42.90411672 0.00012552 dihedral 38.40368080 38.40370661 0.00002581 38.40370632 0.00002552 38.40361147 -0.00006933 38.40368080 0.00000000 nonbonded -5.98981440 -5.97818001 0.01163439 -5.97817995 0.01163445 -5.97831212 0.01150228 -5.97500304 0.01481136 potential 36.91417680 36.92599953 0.01182273 36.92599953 0.01182273 36.92596083 0.01178403 36.92919736 0.01502056 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 36.91417680 Difference in potential energy from amber=>gromacs conversion: 0.01182273 Difference in potential energy from amber=>lammps conversion: 0.01182273 Difference in potential energy from amber=>desmond conversion: 0.01178403 Difference in potential energy from amber=>charmm conversion: 0.01502056 ======================================================================= INFO 2017-03-19 00:36:48 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8765203.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8765203.inpcrd') INFO 2017-03-19 00:36:48 Beginning InterMol conversion INFO 2017-03-19 00:36:48 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:36:48 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:36:48 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8772587.inpcrd INFO 2017-03-19 00:36:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8772587/mobley_8772587_converted.input INFO 2017-03-19 00:36:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8772587/mobley_8772587_converted.cms WARNING 2017-03-19 00:37:04 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:37:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8772587/mobley_8772587_converted.inp INFO 2017-03-19 00:37:04 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8772587/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8772587/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8772587/mobley_8772587_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8772587/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 6.89912365 6.89912365 0.00000000 0.00000000 0.00000000 0.00000000 4.23889408 4.23889408 coulomb total 4.23253440 4.23798140 0.00544700 4.23798155 0.00544715 4.23798119 0.00544679 4.23889408 0.00635968 coulomb-14 -2.66353440 -2.66114225 0.00239215 0.00000000 2.66353440 -2.66112347 0.00241093 0.00000000 2.66353440 proper 1.72171600 1.72175336 0.00003736 1.72175336 0.00003736 1.72174433 0.00002833 1.72175784 0.00004184 vdw (SR) 0.00000000 -1.16099607 -1.16099607 0.00000000 0.00000000 0.00000000 0.00000000 1.85313544 1.85313544 vdw total 1.85309360 1.85309124 -0.00000236 1.85309126 -0.00000234 1.85309878 0.00000518 1.85313544 0.00004184 vdw-14 3.01415360 3.01408731 -0.00006629 0.00000000 -3.01415360 3.01408802 -0.00006558 0.00000000 -3.01415360 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.66939200 2.66921995 -0.00017205 2.66921995 -0.00017205 2.66912622 -0.00026578 2.66922464 -0.00016736 bond 1.09076880 1.09094098 0.00017218 1.09094097 0.00017217 1.09067013 -0.00009867 1.09093616 0.00016736 bonded 5.48187680 5.48191430 0.00003750 5.48191429 0.00003749 5.48154068 -0.00033612 5.48191864 0.00004184 dihedral 1.72171600 1.72175336 0.00003736 1.72175336 0.00003736 1.72174433 0.00002833 1.72175784 0.00004184 nonbonded 6.08562800 6.09107264 0.00544464 6.09107264 0.00544464 6.09107997 0.00545197 6.09202952 0.00640152 potential 11.56750480 11.57298694 0.00548214 11.57298710 0.00548230 11.57257229 0.00506749 11.57399000 0.00648520 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 11.56750480 Difference in potential energy from amber=>gromacs conversion: 0.00548214 Difference in potential energy from amber=>lammps conversion: 0.00548230 Difference in potential energy from amber=>desmond conversion: 0.00506749 Difference in potential energy from amber=>charmm conversion: 0.00648520 ======================================================================= INFO 2017-03-19 00:37:04 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8772587.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8772587.inpcrd') INFO 2017-03-19 00:37:04 Beginning InterMol conversion INFO 2017-03-19 00:37:04 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:37:04 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:37:04 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8785107.inpcrd INFO 2017-03-19 00:37:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8785107/mobley_8785107_converted.input INFO 2017-03-19 00:37:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8785107/mobley_8785107_converted.cms WARNING 2017-03-19 00:37:20 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:37:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8785107/mobley_8785107_converted.inp INFO 2017-03-19 00:37:20 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8785107/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8785107/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8785107/mobley_8785107_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8785107/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 22.36830677 22.36830677 0.00000000 0.00000000 0.00000000 0.00000000 -52.09305936 -52.09305936 coulomb total -52.07573760 -52.09283592 -0.01709832 -52.09283342 -0.01709582 -52.09287581 -0.01713821 -52.09305936 -0.01732176 coulomb-14 -74.48063920 -74.46114269 0.01949651 0.00000000 74.48063920 -74.46115891 0.01948029 0.00000000 74.48063920 proper 40.45635120 40.45612700 -0.00022420 40.45612401 -0.00022719 40.45609321 -0.00025799 40.45664408 0.00029288 vdw (SR) 0.00000000 -2.46689852 -2.46689852 0.00000000 0.00000000 0.00000000 0.00000000 1.88719320 1.88719320 vdw total 1.88740240 1.88712035 -0.00028205 1.88712036 -0.00028204 1.88715811 -0.00024429 1.88719320 -0.00020920 vdw-14 4.35428880 4.35401887 -0.00026993 0.00000000 -4.35428880 4.35405563 -0.00023317 0.00000000 -4.35428880 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 19.91542160 19.91527890 -0.00014270 19.91527893 -0.00014267 19.91521286 -0.00020874 19.91521240 -0.00020920 bond 2.46144720 2.46124822 -0.00019898 2.46124821 -0.00019899 2.46141868 -0.00002852 2.46123800 -0.00020920 bonded 62.83322000 62.83265412 -0.00056588 62.83265114 -0.00056886 62.83272475 -0.00049525 62.83309448 -0.00012552 dihedral 40.45635120 40.45612700 -0.00022420 40.45612401 -0.00022719 40.45609321 -0.00025799 40.45664408 0.00029288 nonbonded -50.18833520 -50.20571557 -0.01738037 -50.20571554 -0.01738034 -50.20571769 -0.01738249 -50.20586616 -0.01753096 potential 12.64488480 12.62693855 -0.01794625 12.62693628 -0.01794852 12.62695586 -0.01792894 12.62727016 -0.01761464 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 12.64488480 Difference in potential energy from amber=>gromacs conversion: -0.01794625 Difference in potential energy from amber=>lammps conversion: -0.01794852 Difference in potential energy from amber=>desmond conversion: -0.01792894 Difference in potential energy from amber=>charmm conversion: -0.01761464 ======================================================================= INFO 2017-03-19 00:37:20 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8785107.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8785107.inpcrd') INFO 2017-03-19 00:37:20 Beginning InterMol conversion INFO 2017-03-19 00:37:20 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:37:21 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8789465.inpcrd INFO 2017-03-19 00:37:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8789465/mobley_8789465_converted.input INFO 2017-03-19 00:37:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8789465/mobley_8789465_converted.cms INFO 2017-03-19 00:37:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8789465/mobley_8789465_converted.rst7 WARNING 2017-03-19 00:37:36 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:37:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8789465/mobley_8789465_converted.inp INFO 2017-03-19 00:37:36 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8789465/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8789465/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8789465/mobley_8789465_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_8789465/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8789465/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -32.83478127 -32.83478127 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -43.65698568 -43.65698568 coulomb total -43.68765440 -43.68943171 -0.00177731 -43.68943260 -0.00177820 -43.68934059 -0.00168619 -43.68765440 0.00000000 -43.65698568 0.03066872 coulomb-14 -10.85413280 -10.85465044 -0.00051764 0.00000000 10.85413280 -10.85470320 -0.00057040 -10.85413280 0.00000000 0.00000000 10.85413280 improper 0.00000000 0.00004344 0.00004344 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00083680 0.00075623 -0.00008057 0.00079963 -0.00003717 0.00080178 -0.00003502 0.00083680 0.00000000 0.00075312 -0.00008368 vdw (SR) 0.00000000 -1.61927506 -1.61927506 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 14.95390888 14.95390888 vdw total 14.95403440 14.95389581 -0.00013859 14.95389591 -0.00013849 14.95390236 -0.00013204 14.95403440 0.00000000 14.95390888 -0.00012552 vdw-14 16.57324240 16.57317087 -0.00007153 0.00000000 -16.57324240 16.57317265 -0.00006975 16.57324240 0.00000000 0.00000000 -16.57324240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.55561120 1.55552329 -0.00008791 1.55552329 -0.00008791 1.55561733 0.00000613 1.55561120 0.00000000 1.55556936 -0.00004184 bond 0.80249120 0.80242786 -0.00006334 0.80242785 -0.00006335 0.80230824 -0.00018296 0.80249120 0.00000000 0.80240752 -0.00008368 bonded 2.35893920 2.35875081 -0.00018839 2.35875078 -0.00018842 2.35872735 -0.00021185 2.35893920 0.00000000 2.35877184 -0.00016736 dihedral 0.00083680 0.00079967 -0.00003713 0.00079963 -0.00003717 0.00080178 -0.00003502 0.00083680 0.00000000 0.00079496 -0.00004184 nonbonded -28.73362000 -28.73553590 -0.00191590 -28.73553544 -0.00191544 -28.73543823 -0.00181823 -28.73362000 0.00000000 -28.70307680 0.03054320 potential -26.37468080 -26.37678509 -0.00210429 -26.37678452 -0.00210372 -26.37678385 -0.00210305 -26.37468080 0.00000000 -26.34426312 0.03041768 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -26.37468080 Difference in potential energy from amber=>gromacs conversion: -0.00210429 Difference in potential energy from amber=>lammps conversion: -0.00210372 Difference in potential energy from amber=>desmond conversion: -0.00210305 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.03041768 ======================================================================= INFO 2017-03-19 00:37:36 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8789465.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8789465.inpcrd') INFO 2017-03-19 00:37:37 Beginning InterMol conversion INFO 2017-03-19 00:37:37 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:37:37 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:37:37 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8789864.inpcrd INFO 2017-03-19 00:37:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8789864/mobley_8789864_converted.input INFO 2017-03-19 00:37:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8789864/mobley_8789864_converted.cms WARNING 2017-03-19 00:37:52 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:37:52 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8789864/mobley_8789864_converted.inp INFO 2017-03-19 00:37:52 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8789864/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8789864/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8789864/mobley_8789864_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8789864/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 122.65488318 122.65488318 0.00000000 0.00000000 0.00000000 0.00000000 -222.98485744 -222.98485744 coulomb total -222.99255600 -222.99495263 -0.00239663 -222.99494925 -0.00239325 -222.99486138 -0.00230538 -222.98485744 0.00769856 coulomb-14 -345.64442400 -345.64983581 -0.00541181 0.00000000 345.64442400 -345.64985065 -0.00542665 0.00000000 345.64442400 proper 60.56256320 60.56240998 -0.00015322 60.56239166 -0.00017154 60.56233308 -0.00023012 60.56239584 -0.00016736 vdw (SR) 0.00000000 4.20531456 4.20531456 0.00000000 0.00000000 0.00000000 0.00000000 25.96330992 25.96330992 vdw total 25.96297520 25.96299801 0.00002281 25.96299821 0.00002301 25.96265186 -0.00032334 25.96330992 0.00033472 vdw-14 21.75763680 21.75768345 0.00004665 0.00000000 -21.75763680 21.75758086 -0.00005594 0.00000000 -21.75763680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.16768240 4.23874365 0.07106125 4.23874346 0.07106106 4.23898249 0.07130009 4.23885224 0.07116984 bond 3.83087040 3.83073025 -0.00014015 3.83073024 -0.00014016 3.83141445 0.00054405 3.83074488 -0.00012552 bonded 68.56111600 68.63188388 0.07076788 68.63186535 0.07074935 68.63273002 0.07161402 68.63199296 0.07087696 dihedral 60.56256320 60.56240998 -0.00015322 60.56239166 -0.00017154 60.56233308 -0.00023012 60.56239584 -0.00016736 nonbonded -197.02958080 -197.03195462 -0.00237382 -197.03195313 -0.00237233 -197.03220952 -0.00262872 -197.02154752 0.00803328 potential -128.46846480 -128.40007074 0.06839406 -128.40008987 0.06837493 -128.39956980 0.06889500 -128.38955456 0.07891024 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -128.46846480 Difference in potential energy from amber=>gromacs conversion: 0.06839406 Difference in potential energy from amber=>lammps conversion: 0.06837493 Difference in potential energy from amber=>desmond conversion: 0.06889500 Difference in potential energy from amber=>charmm conversion: 0.07891024 ======================================================================= INFO 2017-03-19 00:37:52 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8789864.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8789864.inpcrd') INFO 2017-03-19 00:37:53 Beginning InterMol conversion INFO 2017-03-19 00:37:53 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:37:53 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8798016.inpcrd INFO 2017-03-19 00:37:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8798016/mobley_8798016_converted.input INFO 2017-03-19 00:37:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8798016/mobley_8798016_converted.cms INFO 2017-03-19 00:38:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8798016/mobley_8798016_converted.rst7 WARNING 2017-03-19 00:38:08 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:38:08 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8798016/mobley_8798016_converted.inp INFO 2017-03-19 00:38:08 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8798016/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8798016/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8798016/mobley_8798016_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_8798016/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8798016/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -169.87901387 -169.87901387 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 13.83255504 13.83255504 coulomb total 13.78753520 13.77682237 -0.01071283 13.77682207 -0.01071313 13.77674717 -0.01078803 13.78753520 0.00000000 13.83255504 0.04501984 coulomb-14 183.65835360 183.65583623 -0.00251737 0.00000000 -183.65835360 183.65555158 -0.00280202 183.65835360 0.00000000 0.00000000 -183.65835360 improper 0.00000000 0.00031041 0.00031041 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00029288 0.00029288 proper 0.00167360 0.00142655 -0.00024705 0.00173709 0.00006349 0.00174021 0.00006661 0.00167360 0.00000000 0.00142256 -0.00025104 vdw (SR) 0.00000000 -0.91638178 -0.91638178 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 21.39639024 21.39639024 vdw total 21.39655760 21.39639462 -0.00016298 21.39639484 -0.00016276 21.39679684 0.00023924 21.39655760 0.00000000 21.39639024 -0.00016736 vdw-14 22.31285360 22.31277641 -0.00007719 0.00000000 -22.31285360 22.31314447 0.00029087 22.31285360 0.00000000 0.00000000 -22.31285360 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.97484800 1.97497713 0.00012913 1.97497712 0.00012912 1.97467313 -0.00017487 1.97484800 0.00000000 1.97497352 0.00012552 bond 3.37146720 3.37138846 -0.00007874 3.37138846 -0.00007874 3.37018526 -0.00128194 3.37146720 0.00000000 3.37138352 -0.00008368 bonded 5.34798880 5.34810255 0.00011375 5.34810267 0.00011387 5.34659861 -0.00139019 5.34798880 0.00000000 5.34807248 0.00008368 dihedral 0.00167360 0.00173696 0.00006336 0.00173709 0.00006349 0.00174021 0.00006661 0.00167360 0.00000000 0.00171544 0.00004184 nonbonded 35.18409280 35.17321699 -0.01087581 35.17321691 -0.01087589 35.17354401 -0.01054879 35.18409280 0.00000000 35.22894528 0.04485248 potential 40.53208160 40.52131954 -0.01076206 40.52131952 -0.01076208 40.52012277 -0.01195883 40.53208160 0.00000000 40.57701776 0.04493616 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 40.53208160 Difference in potential energy from amber=>gromacs conversion: -0.01076206 Difference in potential energy from amber=>lammps conversion: -0.01076208 Difference in potential energy from amber=>desmond conversion: -0.01195883 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.04493616 ======================================================================= INFO 2017-03-19 00:38:08 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8798016.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8798016.inpcrd') INFO 2017-03-19 00:38:09 Beginning InterMol conversion INFO 2017-03-19 00:38:09 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:38:09 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:38:09 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8809190.inpcrd INFO 2017-03-19 00:38:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8809190/mobley_8809190_converted.input INFO 2017-03-19 00:38:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8809190/mobley_8809190_converted.cms WARNING 2017-03-19 00:38:25 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:38:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8809190/mobley_8809190_converted.inp INFO 2017-03-19 00:38:25 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8809190/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8809190/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8809190/mobley_8809190_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8809190/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 7.26557330 7.26557330 0.00000000 0.00000000 0.00000000 0.00000000 -0.72968960 -0.72968960 coulomb total -0.72717920 -0.73389102 -0.00671182 -0.73389101 -0.00671181 -0.73389820 -0.00671900 -0.72968960 -0.00251040 coulomb-14 -7.99855280 -7.99946432 -0.00091152 0.00000000 7.99855280 -7.99947361 -0.00092081 0.00000000 7.99855280 improper 0.00000000 0.00001806 0.00001806 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 1.73719680 1.73732742 0.00013062 1.73734546 0.00014866 1.73733656 0.00013976 1.73732232 0.00012552 vdw (SR) 0.00000000 -4.82318738 -4.82318738 0.00000000 0.00000000 0.00000000 0.00000000 17.20398040 17.20398040 vdw total 17.20377120 17.20393696 0.00016576 17.20393689 0.00016569 17.20352849 -0.00024271 17.20398040 0.00020920 vdw-14 22.02708640 22.02712433 0.00003793 0.00000000 -22.02708640 22.02671147 -0.00037493 0.00000000 -22.02708640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.99997600 1.00009192 0.00011592 1.00009190 0.00011590 1.00004951 0.00007351 1.00005968 0.00008368 bond 1.44138800 1.44130605 -0.00008195 1.44130604 -0.00008196 1.44145955 0.00007155 1.44130432 -0.00008368 bonded 4.17856080 4.17874344 0.00018264 4.17874339 0.00018259 4.17884563 0.00028483 4.17868632 0.00012552 dihedral 1.73719680 1.73734547 0.00014867 1.73734546 0.00014866 1.73733656 0.00013976 1.73732232 0.00012552 nonbonded 16.47659200 16.47004593 -0.00654607 16.47004613 -0.00654587 16.46963028 -0.00696172 16.47429080 -0.00230120 potential 20.65515280 20.64878937 -0.00636343 20.64878935 -0.00636345 20.64838543 -0.00676737 20.65297712 -0.00217568 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 20.65515280 Difference in potential energy from amber=>gromacs conversion: -0.00636343 Difference in potential energy from amber=>lammps conversion: -0.00636345 Difference in potential energy from amber=>desmond conversion: -0.00676737 Difference in potential energy from amber=>charmm conversion: -0.00217568 ======================================================================= INFO 2017-03-19 00:38:25 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8809190.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8809190.inpcrd') INFO 2017-03-19 00:38:25 Beginning InterMol conversion INFO 2017-03-19 00:38:25 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:38:25 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:38:25 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8809274.inpcrd INFO 2017-03-19 00:38:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8809274/mobley_8809274_converted.input INFO 2017-03-19 00:38:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8809274/mobley_8809274_converted.cms WARNING 2017-03-19 00:38:41 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:38:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8809274/mobley_8809274_converted.inp INFO 2017-03-19 00:38:41 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8809274/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8809274/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8809274/mobley_8809274_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8809274/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -22.85619120 -22.85619120 0.00000000 0.00000000 0.00000000 0.00000000 50.57719616 50.57719616 coulomb total 50.55820080 50.56536787 0.00716707 50.56536799 0.00716719 50.56558987 0.00738907 50.57719616 0.01899536 coulomb-14 73.41413760 73.42155906 0.00742146 0.00000000 -73.41413760 73.42151525 0.00737765 0.00000000 -73.41413760 improper 0.00000000 0.00007041 0.00007041 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00083680 0.00070627 -0.00013053 0.00077663 -0.00006017 0.00077659 -0.00006021 0.00071128 -0.00012552 vdw (SR) 0.00000000 0.51321382 0.51321382 0.00000000 0.00000000 0.00000000 0.00000000 20.86841128 20.86841128 vdw total 20.86853680 20.86852266 -0.00001414 20.86852257 -0.00001423 20.86858565 0.00004885 20.86841128 -0.00012552 vdw-14 20.35516000 20.35530884 0.00014884 0.00000000 -20.35516000 20.35539129 0.00023129 0.00000000 -20.35516000 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.63427040 1.63426523 -0.00000517 1.63426521 -0.00000519 1.63415534 -0.00011506 1.63422856 -0.00004184 bond 3.60284240 3.60301919 0.00017679 3.60301917 0.00017677 3.60280843 -0.00003397 3.60300976 0.00016736 bonded 5.23794960 5.23806110 0.00011150 5.23806101 0.00011141 5.23774035 -0.00020925 5.23803328 0.00008368 dihedral 0.00083680 0.00077668 -0.00006012 0.00077663 -0.00006017 0.00077659 -0.00006021 0.00079496 -0.00004184 nonbonded 71.42673760 71.43389052 0.00715292 71.43388806 0.00715046 71.43417552 0.00743792 71.44560744 0.01886984 potential 76.66468720 76.67195162 0.00726442 76.67195062 0.00726342 76.67186569 0.00717849 76.68364072 0.01895352 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 76.66468720 Difference in potential energy from amber=>gromacs conversion: 0.00726442 Difference in potential energy from amber=>lammps conversion: 0.00726342 Difference in potential energy from amber=>desmond conversion: 0.00717849 Difference in potential energy from amber=>charmm conversion: 0.01895352 ======================================================================= INFO 2017-03-19 00:38:41 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8809274.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8809274.inpcrd') INFO 2017-03-19 00:38:41 Beginning InterMol conversion INFO 2017-03-19 00:38:41 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:38:41 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8823527.inpcrd INFO 2017-03-19 00:38:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8823527/mobley_8823527_converted.input INFO 2017-03-19 00:38:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8823527/mobley_8823527_converted.cms INFO 2017-03-19 00:38:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8823527/mobley_8823527_converted.rst7 WARNING 2017-03-19 00:38:57 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:38:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8823527/mobley_8823527_converted.inp INFO 2017-03-19 00:38:57 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8823527/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8823527/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8823527/mobley_8823527_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_8823527/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8823527/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -7.66170875 -7.66170875 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -20.51691344 -20.51691344 coulomb total -20.51457040 -20.51520521 -0.00063481 -20.51520511 -0.00063471 -20.51519294 -0.00062254 -20.51457040 0.00000000 -20.51691344 -0.00234304 coulomb-14 -12.85324800 -12.85349646 -0.00024846 0.00000000 12.85324800 -12.85349276 -0.00024476 -12.85324800 0.00000000 0.00000000 12.85324800 improper 0.00000000 0.00006811 0.00006811 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 33.47241840 33.47249929 0.00008089 33.47256735 0.00014895 33.47256312 0.00014472 33.47241840 0.00000000 33.47250208 0.00008368 vdw (SR) 0.00000000 -12.54386730 -12.54386730 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 26.54589008 26.54589008 vdw total 26.54580640 26.54587967 0.00007327 26.54587962 0.00007322 26.54596757 0.00016117 26.54580640 0.00000000 26.54589008 0.00008368 vdw-14 39.08985680 39.08974697 -0.00010983 0.00000000 -39.08985680 39.08984965 -0.00000715 39.08985680 0.00000000 0.00000000 -39.08985680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.82038640 4.82025767 -0.00012873 4.82025753 -0.00012887 4.82010310 -0.00028330 4.82038640 0.00000000 4.82030272 -0.00008368 bond 3.52543840 3.52562072 0.00018232 3.52562070 0.00018230 3.52492378 -0.00051462 3.52543840 0.00000000 3.52560576 0.00016736 bonded 41.81824320 41.81844579 0.00020259 41.81844558 0.00020238 41.81759001 -0.00065319 41.81824320 0.00000000 41.81849424 0.00025104 dihedral 33.47241840 33.47256740 0.00014900 33.47256735 0.00014895 33.47256312 0.00014472 33.47241840 0.00000000 33.47258576 0.00016736 nonbonded 6.03123600 6.03067446 -0.00056154 6.03067451 -0.00056149 6.03077463 -0.00046137 6.03123600 0.00000000 6.02897664 -0.00225936 potential 47.84947920 47.84912025 -0.00035895 47.84911938 -0.00035982 47.84810936 -0.00136984 47.84947920 0.00000000 47.84742904 -0.00205016 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 47.84947920 Difference in potential energy from amber=>gromacs conversion: -0.00035895 Difference in potential energy from amber=>lammps conversion: -0.00035982 Difference in potential energy from amber=>desmond conversion: -0.00136984 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.00205016 ======================================================================= INFO 2017-03-19 00:38:57 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8823527.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8823527.inpcrd') INFO 2017-03-19 00:38:57 Beginning InterMol conversion INFO 2017-03-19 00:38:57 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:38:57 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8827942.inpcrd INFO 2017-03-19 00:38:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8827942/mobley_8827942_converted.input INFO 2017-03-19 00:38:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8827942/mobley_8827942_converted.cms INFO 2017-03-19 00:39:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8827942/mobley_8827942_converted.rst7 WARNING 2017-03-19 00:39:13 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:39:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8827942/mobley_8827942_converted.inp INFO 2017-03-19 00:39:13 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8827942/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8827942/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8827942/mobley_8827942_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_8827942/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8827942/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -14.06163775 -14.06163775 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 24.11716176 24.11716176 coulomb total 24.10360560 24.10663157 0.00302597 24.10663147 0.00302587 24.10663243 0.00302683 24.10360560 0.00000000 24.11716176 0.01355616 coulomb-14 38.16728480 38.16826932 0.00098452 0.00000000 -38.16728480 38.16825202 0.00096722 38.16728480 0.00000000 0.00000000 -38.16728480 improper 0.00000000 0.00011376 0.00011376 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00125520 0.00099452 -0.00026068 0.00110827 -0.00014693 0.00111675 -0.00013845 0.00125520 0.00000000 0.00100416 -0.00025104 vdw (SR) 0.00000000 -10.78338595 -10.78338595 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 42.74244696 42.74244696 vdw total 42.74248880 42.74244671 -0.00004209 42.74244696 -0.00004184 42.74255051 0.00006171 42.74248880 0.00000000 42.74244696 -0.00004184 vdw-14 53.52591200 53.52583266 -0.00007934 0.00000000 -53.52591200 53.52594338 0.00003138 53.52591200 0.00000000 0.00000000 -53.52591200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 8.34540640 8.34536584 -0.00004056 8.34536582 -0.00004058 8.34608689 0.00068049 8.34540640 0.00000000 8.34536456 -0.00004184 bond 1.58992000 1.58984201 -0.00007799 1.58984201 -0.00007799 1.58998999 0.00006999 1.58992000 0.00000000 1.58983632 -0.00008368 bonded 9.93658160 9.93631613 -0.00026547 9.93631610 -0.00026550 9.93719363 0.00061203 9.93658160 0.00000000 9.93633056 -0.00025104 dihedral 0.00125520 0.00110828 -0.00014692 0.00110827 -0.00014693 0.00111675 -0.00013845 0.00125520 0.00000000 0.00112968 -0.00012552 nonbonded 66.84609440 66.84907828 0.00298388 66.84907759 0.00298319 66.84918295 0.00308855 66.84609440 0.00000000 66.85960872 0.01351432 potential 76.78267600 76.78539441 0.00271841 76.78539560 0.00271960 76.78616922 0.00349322 76.78267600 0.00000000 76.79593928 0.01326328 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 76.78267600 Difference in potential energy from amber=>gromacs conversion: 0.00271841 Difference in potential energy from amber=>lammps conversion: 0.00271960 Difference in potential energy from amber=>desmond conversion: 0.00349322 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.01326328 ======================================================================= INFO 2017-03-19 00:39:13 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8827942.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8827942.inpcrd') INFO 2017-03-19 00:39:13 Beginning InterMol conversion INFO 2017-03-19 00:39:13 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:39:13 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:39:13 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8861672.inpcrd INFO 2017-03-19 00:39:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8861672/mobley_8861672_converted.input INFO 2017-03-19 00:39:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8861672/mobley_8861672_converted.cms WARNING 2017-03-19 00:39:29 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:39:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8861672/mobley_8861672_converted.inp INFO 2017-03-19 00:39:29 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8861672/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8861672/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8861672/mobley_8861672_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8861672/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 122.12914028 122.12914028 0.00000000 0.00000000 0.00000000 0.00000000 -178.97018160 -178.97018160 coulomb total -178.92917840 -178.93689570 -0.00771730 -178.93689370 -0.00771530 -178.93709369 -0.00791529 -178.97018160 -0.04100320 coulomb-14 -301.06474080 -301.06603599 -0.00129519 0.00000000 301.06474080 -301.06619641 -0.00145561 0.00000000 301.06474080 improper 0.00000000 0.00012569 0.00012569 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00083680 0.00089964 0.00006284 0.00102538 0.00018858 0.00102847 0.00019167 0.00092048 0.00008368 vdw (SR) 0.00000000 -2.42800484 -2.42800484 0.00000000 0.00000000 0.00000000 0.00000000 21.23154064 21.23154064 vdw total 21.23170800 21.23153580 -0.00017220 21.23153562 -0.00017238 21.23189850 0.00019050 21.23154064 -0.00016736 vdw-14 23.65968320 23.65954064 -0.00014256 0.00000000 -23.65968320 23.65991169 0.00022849 0.00000000 -23.65968320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.00497280 2.00492454 -0.00004826 2.00492452 -0.00004828 2.00486941 -0.00010339 2.00493096 -0.00004184 bond 2.00162560 2.00149903 -0.00012657 2.00149903 -0.00012657 2.00095754 -0.00066806 2.00150008 -0.00012552 bonded 4.00743520 4.00744889 0.00001369 4.00744893 0.00001373 4.00685542 -0.00057978 4.00747704 0.00004184 dihedral 0.00083680 0.00102533 0.00018853 0.00102538 0.00018858 0.00102847 0.00019167 0.00104600 0.00020920 nonbonded -157.69747040 -157.70535990 -0.00788950 -157.70535724 -0.00788684 -157.70519519 -0.00772479 -157.73864096 -0.04117056 potential -153.69003520 -153.69791101 -0.00787581 -153.69790949 -0.00787429 -153.69839190 -0.00835670 -153.73120576 -0.04117056 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -153.69003520 Difference in potential energy from amber=>gromacs conversion: -0.00787581 Difference in potential energy from amber=>lammps conversion: -0.00787429 Difference in potential energy from amber=>desmond conversion: -0.00835670 Difference in potential energy from amber=>charmm conversion: -0.04117056 ======================================================================= INFO 2017-03-19 00:39:29 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8861672.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8861672.inpcrd') INFO 2017-03-19 00:39:29 Beginning InterMol conversion INFO 2017-03-19 00:39:29 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:39:30 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:39:30 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8882696.inpcrd INFO 2017-03-19 00:39:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8882696/mobley_8882696_converted.input INFO 2017-03-19 00:39:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8882696/mobley_8882696_converted.cms WARNING 2017-03-19 00:39:45 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:39:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8882696/mobley_8882696_converted.inp INFO 2017-03-19 00:39:45 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8882696/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8882696/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8882696/mobley_8882696_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8882696/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 11.16098010 11.16098010 0.00000000 0.00000000 0.00000000 0.00000000 0.99809320 0.99809320 coulomb total 1.01503840 1.00832557 -0.00671283 1.00832555 -0.00671285 1.00830965 -0.00672875 0.99809320 -0.01694520 coulomb-14 -10.14912880 -10.15265453 -0.00352573 0.00000000 10.14912880 -10.15267859 -0.00354979 0.00000000 10.14912880 proper 30.49843120 30.49859665 0.00016545 30.49859940 0.00016820 30.49856291 0.00013171 30.49968640 0.00125520 vdw (SR) 0.00000000 -0.32285795 -0.32285795 0.00000000 0.00000000 0.00000000 0.00000000 0.68667808 0.68667808 vdw total 0.68659440 0.68664447 0.00005007 0.68664448 0.00005008 0.68667956 0.00008516 0.68667808 0.00008368 vdw-14 1.00959920 1.00950243 -0.00009677 0.00000000 -1.00959920 1.00953829 -0.00006091 0.00000000 -1.00959920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 18.08241120 18.08244815 0.00003695 18.08244802 0.00003682 18.08229689 -0.00011431 18.08236936 -0.00004184 bond 2.29617920 2.29620235 0.00002315 2.29620234 0.00002314 2.29601885 -0.00016035 2.29622104 0.00004184 bonded 50.87702160 50.87724715 0.00022555 50.87724975 0.00022815 50.87687865 -0.00014295 50.87827680 0.00125520 dihedral 30.49843120 30.49859665 0.00016545 30.49859940 0.00016820 30.49856291 0.00013171 30.49968640 0.00125520 nonbonded 1.70163280 1.69497005 -0.00666275 1.69497007 -0.00666273 1.69498921 -0.00664359 1.68477128 -0.01686152 potential 52.57865440 52.57221719 -0.00643721 52.57221941 -0.00643499 52.57183950 -0.00681490 52.56300624 -0.01564816 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 52.57865440 Difference in potential energy from amber=>gromacs conversion: -0.00643721 Difference in potential energy from amber=>lammps conversion: -0.00643499 Difference in potential energy from amber=>desmond conversion: -0.00681490 Difference in potential energy from amber=>charmm conversion: -0.01564816 ======================================================================= INFO 2017-03-19 00:39:45 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8882696.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8882696.inpcrd') INFO 2017-03-19 00:39:46 Beginning InterMol conversion INFO 2017-03-19 00:39:46 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:39:46 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:39:46 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8883511.inpcrd INFO 2017-03-19 00:39:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8883511/mobley_8883511_converted.input INFO 2017-03-19 00:39:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8883511/mobley_8883511_converted.cms WARNING 2017-03-19 00:40:01 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:40:01 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8883511/mobley_8883511_converted.inp INFO 2017-03-19 00:40:01 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8883511/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8883511/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8883511/mobley_8883511_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8883511/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 41.16891085 41.16891085 0.00000000 0.00000000 0.00000000 0.00000000 11.40679736 11.40679736 coulomb total 11.43403520 11.43410676 0.00007156 11.43410675 0.00007155 11.43403662 0.00000142 11.40679736 -0.02723784 coulomb-14 -29.73359600 -29.73480408 -0.00120808 0.00000000 29.73359600 -29.73481685 -0.00122085 0.00000000 29.73359600 improper 0.00000000 0.00001605 0.00001605 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 8.37134720 8.37154630 0.00019910 8.37154217 0.00019497 8.37158958 0.00024238 8.37151456 0.00016736 vdw (SR) 0.00000000 2.61357533 2.61357533 0.00000000 0.00000000 0.00000000 0.00000000 24.88333584 24.88333584 vdw total 24.88350320 24.88327804 -0.00022516 24.88327810 -0.00022510 24.88324745 -0.00025575 24.88333584 -0.00016736 vdw-14 22.26975840 22.26970271 -0.00005569 0.00000000 -22.26975840 22.26971874 -0.00003966 0.00000000 -22.26975840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.16859120 1.16845353 -0.00013767 1.16845355 -0.00013765 1.16855023 -0.00004097 1.16846568 -0.00012552 bond 3.56644160 3.56638427 -0.00005733 3.56638428 -0.00005732 3.56633150 -0.00011010 3.56639976 -0.00004184 bonded 13.10638000 13.10640016 0.00002016 13.10638000 0.00000000 13.10647130 0.00009130 13.10638000 0.00000000 dihedral 8.37134720 8.37156235 0.00021515 8.37154217 0.00019497 8.37158958 0.00024238 8.37151456 0.00016736 nonbonded 36.31753840 36.31738480 -0.00015360 36.31738485 -0.00015355 36.31728407 -0.00025433 36.29013320 -0.02740520 potential 49.42391840 49.42378496 -0.00013344 49.42376359 -0.00015481 49.42369163 -0.00022677 49.39651320 -0.02740520 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 49.42391840 Difference in potential energy from amber=>gromacs conversion: -0.00013344 Difference in potential energy from amber=>lammps conversion: -0.00015481 Difference in potential energy from amber=>desmond conversion: -0.00022677 Difference in potential energy from amber=>charmm conversion: -0.02740520 ======================================================================= INFO 2017-03-19 00:40:01 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8883511.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8883511.inpcrd') INFO 2017-03-19 00:40:02 Beginning InterMol conversion INFO 2017-03-19 00:40:02 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:40:02 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:40:02 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8885088.inpcrd INFO 2017-03-19 00:40:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8885088/mobley_8885088_converted.input INFO 2017-03-19 00:40:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8885088/mobley_8885088_converted.cms WARNING 2017-03-19 00:40:17 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:40:17 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8885088/mobley_8885088_converted.inp INFO 2017-03-19 00:40:18 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8885088/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8885088/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8885088/mobley_8885088_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8885088/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 20.49728454 20.49728454 0.00000000 0.00000000 0.00000000 0.00000000 6.20508120 6.20508120 coulomb total 6.21909760 6.20287670 -0.01622090 6.20287665 -0.01622095 6.20289042 -0.01620718 6.20508120 -0.01401640 coulomb-14 -14.28710480 -14.29440784 -0.00730304 0.00000000 14.28710480 -14.29439492 -0.00729012 0.00000000 14.28710480 improper 0.00000000 0.01953915 0.01953915 0.00000000 0.00000000 0.00000000 0.00000000 0.01953928 0.01953928 proper 27.97422400 27.95479483 -0.01942917 27.97433362 0.00010962 27.97429626 0.00007226 27.95644200 -0.01778200 vdw (SR) 0.00000000 -0.25278584 -0.25278584 0.00000000 0.00000000 0.00000000 0.00000000 0.16685792 0.16685792 vdw total 0.16694160 0.16680764 -0.00013396 0.16680764 -0.00013396 0.16681431 -0.00012729 0.16685792 -0.00008368 vdw-14 0.41965520 0.41959348 -0.00006172 0.00000000 -0.41965520 0.41960042 -0.00005478 0.00000000 -0.41965520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 43.20440240 43.20436180 -0.00004060 43.20436056 -0.00004184 43.20450365 0.00010125 43.20419320 -0.00020920 bond 1.50958720 1.50955073 -0.00003647 1.50955072 -0.00003648 1.50949012 -0.00009708 1.50954536 -0.00004184 bonded 72.68821360 72.68824651 0.00003291 72.68824490 0.00003130 72.68829003 0.00007643 72.68971984 0.00150624 dihedral 27.97422400 27.97433398 0.00010998 27.97433362 0.00010962 27.97429626 0.00007226 27.97598128 0.00175728 nonbonded 6.38603920 6.36968434 -0.01635486 6.36968436 -0.01635484 6.36970473 -0.01633447 6.37193912 -0.01410008 potential 79.07425280 79.05793085 -0.01632195 79.05793102 -0.01632178 79.05797244 -0.01628036 79.06161712 -0.01263568 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 79.07425280 Difference in potential energy from amber=>gromacs conversion: -0.01632195 Difference in potential energy from amber=>lammps conversion: -0.01632178 Difference in potential energy from amber=>desmond conversion: -0.01628036 Difference in potential energy from amber=>charmm conversion: -0.01263568 ======================================================================= INFO 2017-03-19 00:40:18 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8885088.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8885088.inpcrd') INFO 2017-03-19 00:40:18 Beginning InterMol conversion INFO 2017-03-19 00:40:18 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:40:18 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:40:18 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8899867.inpcrd INFO 2017-03-19 00:40:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8899867/mobley_8899867_converted.input INFO 2017-03-19 00:40:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8899867/mobley_8899867_converted.cms WARNING 2017-03-19 00:40:34 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:40:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8899867/mobley_8899867_converted.inp INFO 2017-03-19 00:40:34 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8899867/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8899867/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8899867/mobley_8899867_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8899867/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 5.59217203 5.59217203 0.00000000 0.00000000 0.00000000 0.00000000 -27.51277064 -27.51277064 coulomb total -27.51942320 -27.50720308 0.01222012 -27.50720257 0.01222063 -27.50730127 0.01212193 -27.51277064 0.00665256 coulomb-14 -33.09544000 -33.09937511 -0.00393511 0.00000000 33.09544000 -33.09937087 -0.00393087 0.00000000 33.09544000 proper 38.73045120 38.73049698 0.00004578 38.73049681 0.00004561 38.73060567 0.00015447 38.73120432 0.00075312 vdw (SR) 0.00000000 -0.97391515 -0.97391515 0.00000000 0.00000000 0.00000000 0.00000000 4.63578832 4.63578832 vdw total 4.63587200 4.63570068 -0.00017132 4.63570087 -0.00017113 4.63573769 -0.00013431 4.63578832 -0.00008368 vdw-14 5.60990720 5.60961583 -0.00029137 0.00000000 -5.60990720 5.60965256 -0.00025464 0.00000000 -5.60990720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 17.19247440 17.19237609 -0.00009831 17.19237608 -0.00009832 17.19234009 -0.00013431 17.19222336 -0.00025104 bond 0.84809680 0.84793068 -0.00016612 0.84793070 -0.00016610 0.84791963 -0.00017717 0.84792944 -0.00016736 bonded 56.77102240 56.77080375 -0.00021865 56.77080358 -0.00021882 56.77086540 -0.00015700 56.77135712 0.00033472 dihedral 38.73045120 38.73049698 0.00004578 38.73049681 0.00004561 38.73060567 0.00015447 38.73120432 0.00075312 nonbonded -22.88355120 -22.87150241 0.01204879 -22.87150212 0.01204908 -22.87156358 0.01198762 -22.87698232 0.00656888 potential 33.88747120 33.89930135 0.01183015 33.89930188 0.01183068 33.89925732 0.01178612 33.89441664 0.00694544 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 33.88747120 Difference in potential energy from amber=>gromacs conversion: 0.01183015 Difference in potential energy from amber=>lammps conversion: 0.01183068 Difference in potential energy from amber=>desmond conversion: 0.01178612 Difference in potential energy from amber=>charmm conversion: 0.00694544 ======================================================================= INFO 2017-03-19 00:40:34 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8899867.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8899867.inpcrd') INFO 2017-03-19 00:40:34 Beginning InterMol conversion INFO 2017-03-19 00:40:34 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:40:34 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:40:34 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8916409.inpcrd INFO 2017-03-19 00:40:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8916409/mobley_8916409_converted.input INFO 2017-03-19 00:40:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8916409/mobley_8916409_converted.cms WARNING 2017-03-19 00:40:50 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:40:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8916409/mobley_8916409_converted.inp INFO 2017-03-19 00:40:50 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8916409/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8916409/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8916409/mobley_8916409_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8916409/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -489.75857460 -489.75857460 0.00000000 0.00000000 0.00000000 0.00000000 -302.95436072 -302.95436072 coulomb total -302.90779280 -302.91827595 -0.01048315 -302.91827372 -0.01048092 -302.91842309 -0.01063029 -302.95436072 -0.04656792 coulomb-14 186.83400960 186.84029865 0.00628905 0.00000000 -186.83400960 186.83998979 0.00598019 0.00000000 -186.83400960 improper 0.00000000 0.01492953 0.01492953 0.00000000 0.00000000 0.00000000 0.00000000 0.01493688 0.01493688 proper 94.60818960 94.59314157 -0.01504803 94.60806826 -0.00012134 94.60784275 -0.00034685 94.59291800 -0.01527160 vdw (SR) 0.00000000 -26.97479122 -26.97479122 0.00000000 0.00000000 0.00000000 0.00000000 -5.29878496 -5.29878496 vdw total -5.29861760 -5.29909587 -0.00047827 -5.29909583 -0.00047823 -5.29910432 -0.00048672 -5.29878496 -0.00016736 vdw-14 21.67604880 21.67569535 -0.00035345 0.00000000 -21.67604880 21.67562458 -0.00042422 0.00000000 -21.67604880 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 18.70164320 18.70171106 0.00006786 18.70171098 0.00006778 18.70209331 0.00045011 18.70160136 -0.00004184 bond 10.30310000 10.30314577 0.00004577 10.30314561 0.00004561 10.30269055 -0.00040945 10.30314184 0.00004184 bonded 123.61293280 123.61292794 -0.00000486 123.61292485 -0.00000795 123.61262661 -0.00030619 123.61259808 -0.00033472 dihedral 94.60818960 94.60807110 -0.00011850 94.60806826 -0.00012134 94.60784275 -0.00034685 94.60785488 -0.00033472 nonbonded -308.20641040 -308.21737182 -0.01096142 -308.21736830 -0.01095790 -308.21752741 -0.01111701 -308.25314568 -0.04673528 potential -184.59347760 -184.60444389 -0.01096629 -184.60444386 -0.01096626 -184.60525556 -0.01177796 -184.64050576 -0.04702816 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -184.59347760 Difference in potential energy from amber=>gromacs conversion: -0.01096629 Difference in potential energy from amber=>lammps conversion: -0.01096626 Difference in potential energy from amber=>desmond conversion: -0.01177796 Difference in potential energy from amber=>charmm conversion: -0.04702816 ======================================================================= INFO 2017-03-19 00:40:50 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8916409.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8916409.inpcrd') INFO 2017-03-19 00:40:50 Beginning InterMol conversion INFO 2017-03-19 00:40:50 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:40:50 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:40:50 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8966374.inpcrd INFO 2017-03-19 00:40:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8966374/mobley_8966374_converted.input INFO 2017-03-19 00:40:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8966374/mobley_8966374_converted.cms WARNING 2017-03-19 00:41:06 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:41:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8966374/mobley_8966374_converted.inp INFO 2017-03-19 00:41:06 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8966374/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8966374/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8966374/mobley_8966374_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8966374/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -4.14088656 -4.14088656 0.00000000 0.00000000 0.00000000 0.00000000 207.17753808 207.17753808 coulomb total 207.17201520 207.17755983 0.00554463 207.17755900 0.00554380 207.17718446 0.00516926 207.17753808 0.00552288 coulomb-14 211.32379840 211.31844639 -0.00535201 0.00000000 -211.32379840 211.31806465 -0.00573375 0.00000000 -211.32379840 improper 0.00000000 0.00008797 0.00008797 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00125520 0.00103282 -0.00022238 0.00112073 -0.00013447 0.00112274 -0.00013246 0.00104600 -0.00020920 vdw (SR) 0.00000000 -1.43298103 -1.43298103 0.00000000 0.00000000 0.00000000 0.00000000 24.69091368 24.69091368 vdw total 24.69103920 24.69097867 -0.00006053 24.69097853 -0.00006067 24.69034615 -0.00069305 24.69091368 -0.00012552 vdw-14 26.12405920 26.12395970 -0.00009950 0.00000000 -26.12405920 26.12333051 -0.00072869 0.00000000 -26.12405920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.61044560 0.61055435 0.00010875 0.61055434 0.00010874 0.61055825 0.00011265 0.61057112 0.00012552 bond 1.53385440 1.53375822 -0.00009618 1.53375821 -0.00009619 1.53403143 0.00017703 1.53377072 -0.00008368 bonded 2.14555520 2.14543337 -0.00012183 2.14543328 -0.00012192 2.14571241 0.00015721 2.14547152 -0.00008368 dihedral 0.00125520 0.00112080 -0.00013440 0.00112073 -0.00013447 0.00112274 -0.00013246 0.00112968 -0.00012552 nonbonded 231.86305440 231.86853850 0.00548410 231.86853544 0.00548104 231.86753061 0.00447621 231.86845176 0.00539736 potential 234.00860960 234.01397187 0.00536227 234.01396930 0.00535970 234.01321200 0.00460240 234.01388144 0.00527184 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 234.00860960 Difference in potential energy from amber=>gromacs conversion: 0.00536227 Difference in potential energy from amber=>lammps conversion: 0.00535970 Difference in potential energy from amber=>desmond conversion: 0.00460240 Difference in potential energy from amber=>charmm conversion: 0.00527184 ======================================================================= INFO 2017-03-19 00:41:06 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8966374.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8966374.inpcrd') INFO 2017-03-19 00:41:06 Beginning InterMol conversion INFO 2017-03-19 00:41:06 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:41:06 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:41:06 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_900088.inpcrd INFO 2017-03-19 00:41:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_900088/mobley_900088_converted.input INFO 2017-03-19 00:41:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_900088/mobley_900088_converted.cms WARNING 2017-03-19 00:41:22 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:41:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_900088/mobley_900088_converted.inp INFO 2017-03-19 00:41:22 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_900088/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_900088/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_900088/mobley_900088_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_900088/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -7.43192136 -7.43192136 0.00000000 0.00000000 0.00000000 0.00000000 -32.63352640 -32.63352640 coulomb total -32.65946720 -32.65144646 0.00802074 -32.65144605 0.00802115 -32.65144664 0.00802056 -32.63352640 0.02594080 coulomb-14 -25.20943680 -25.21952510 -0.01008830 0.00000000 25.20943680 -25.21950802 -0.01007122 0.00000000 25.20943680 improper 0.00000000 0.00006851 0.00006851 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 90.60117280 90.60110282 -0.00006998 90.60114770 -0.00002510 90.60116360 -0.00000920 90.60108912 -0.00008368 vdw (SR) 0.00000000 3.02600602 3.02600602 0.00000000 0.00000000 0.00000000 0.00000000 10.36598552 10.36598552 vdw total 10.36586000 10.36592147 0.00006147 10.36592150 0.00006150 10.36592225 0.00006225 10.36598552 0.00012552 vdw-14 7.33999120 7.33991545 -0.00007575 0.00000000 -7.33999120 7.33982120 -0.00017000 0.00000000 -7.33999120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.38146080 5.38154637 0.00008557 5.38154657 0.00008577 5.38141452 -0.00004628 5.38150264 0.00004184 bond 1.39034320 1.39018629 -0.00015691 1.39018630 -0.00015690 1.39027884 -0.00006436 1.39017584 -0.00016736 bonded 97.37297680 97.37290398 -0.00007282 97.37288057 -0.00009623 97.37285696 -0.00011984 97.37285128 -0.00012552 dihedral 90.60117280 90.60117132 -0.00000148 90.60114770 -0.00002510 90.60116360 -0.00000920 90.60117280 0.00000000 nonbonded -22.29360720 -22.28552499 0.00808221 -22.28552455 0.00808265 -22.28552439 0.00808281 -22.26754088 0.02606632 potential 75.07936960 75.08737899 0.00800939 75.08735686 0.00798726 75.08729744 0.00792784 75.10526856 0.02589896 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 75.07936960 Difference in potential energy from amber=>gromacs conversion: 0.00800939 Difference in potential energy from amber=>lammps conversion: 0.00798726 Difference in potential energy from amber=>desmond conversion: 0.00792784 Difference in potential energy from amber=>charmm conversion: 0.02589896 ======================================================================= INFO 2017-03-19 00:41:22 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_900088.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_900088.inpcrd') INFO 2017-03-19 00:41:22 Beginning InterMol conversion INFO 2017-03-19 00:41:22 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:41:22 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:41:22 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9007496.inpcrd INFO 2017-03-19 00:41:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9007496/mobley_9007496_converted.input INFO 2017-03-19 00:41:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9007496/mobley_9007496_converted.cms WARNING 2017-03-19 00:41:38 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:41:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9007496/mobley_9007496_converted.inp INFO 2017-03-19 00:41:38 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9007496/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9007496/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9007496/mobley_9007496_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9007496/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.24775449 0.24775449 0.00000000 0.00000000 0.00000000 0.00000000 -174.95839504 -174.95839504 coulomb total -174.93429520 -174.92936999 0.00492521 -174.92936645 0.00492875 -174.92932861 0.00496659 -174.95839504 -0.02409984 coulomb-14 -175.18408000 -175.17712448 0.00695552 0.00000000 175.18408000 -175.17714837 0.00693163 0.00000000 175.18408000 improper 0.00000000 0.00507074 0.00507074 0.00000000 0.00000000 0.00000000 0.00000000 0.00506264 0.00506264 proper 15.09670880 15.09168860 -0.00502020 15.09676068 0.00005188 15.09673976 0.00003096 15.09168800 -0.00502080 vdw (SR) 0.00000000 -9.79965390 -9.79965390 0.00000000 0.00000000 0.00000000 0.00000000 31.12770480 31.12770480 vdw total 31.12770480 31.12769222 -0.00001258 31.12769225 -0.00001255 31.12792325 0.00021845 31.12770480 0.00000000 vdw-14 40.92746960 40.92734613 -0.00012347 0.00000000 -40.92746960 40.92756864 0.00009904 0.00000000 -40.92746960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 8.47008960 8.47016777 0.00007817 8.47016784 0.00007824 8.46988132 -0.00020828 8.47021512 0.00012552 bond 12.43861360 12.43872758 0.00011398 12.43872740 0.00011380 12.43816390 -0.00044970 12.43873912 0.00012552 bonded 36.00541200 36.00565468 0.00024268 36.00565593 0.00024393 36.00478499 -0.00062701 36.00570488 0.00029288 dihedral 15.09670880 15.09675934 0.00005054 15.09676068 0.00005188 15.09673976 0.00003096 15.09675064 0.00004184 nonbonded -143.80659040 -143.80167777 0.00491263 -143.80167420 0.00491620 -143.80140537 0.00518503 -143.83069024 -0.02409984 potential -107.80117840 -107.79602309 0.00515531 -107.79601953 0.00515887 -107.79676093 0.00441747 -107.82498536 -0.02380696 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -107.80117840 Difference in potential energy from amber=>gromacs conversion: 0.00515531 Difference in potential energy from amber=>lammps conversion: 0.00515887 Difference in potential energy from amber=>desmond conversion: 0.00441747 Difference in potential energy from amber=>charmm conversion: -0.02380696 ======================================================================= INFO 2017-03-19 00:41:38 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9007496.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9007496.inpcrd') INFO 2017-03-19 00:41:38 Beginning InterMol conversion INFO 2017-03-19 00:41:38 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:41:39 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:41:39 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9015240.inpcrd INFO 2017-03-19 00:41:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9015240/mobley_9015240_converted.input INFO 2017-03-19 00:41:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9015240/mobley_9015240_converted.cms WARNING 2017-03-19 00:41:54 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:41:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9015240/mobley_9015240_converted.inp INFO 2017-03-19 00:41:54 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9015240/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9015240/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9015240/mobley_9015240_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9015240/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 9.38802803 9.38802803 0.00000000 0.00000000 0.00000000 0.00000000 4.72850576 4.72850576 coulomb total 4.72164400 4.72175330 0.00010930 4.72175320 0.00010920 4.72169806 0.00005406 4.72850576 0.00686176 coulomb-14 -4.66599680 -4.66627473 -0.00027793 0.00000000 4.66599680 -4.66628027 -0.00028347 0.00000000 4.66599680 proper 15.56531680 15.56513357 -0.00018323 15.56513354 -0.00018326 15.56516362 -0.00015318 15.56514944 -0.00016736 vdw (SR) 0.00000000 -3.90361633 -3.90361633 0.00000000 0.00000000 0.00000000 0.00000000 5.34510184 5.34510184 vdw total 5.34506000 5.34495453 -0.00010547 5.34495456 -0.00010544 5.34497653 -0.00008347 5.34510184 0.00004184 vdw-14 9.24873200 9.24857086 -0.00016114 0.00000000 -9.24873200 9.24858920 -0.00014280 0.00000000 -9.24873200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.88774880 4.88763467 -0.00011413 4.88763458 -0.00011422 4.88759847 -0.00015033 4.88762328 -0.00012552 bond 1.49912720 1.49903606 -0.00009114 1.49903607 -0.00009113 1.49899390 -0.00013330 1.49904352 -0.00008368 bonded 21.95219280 21.95180430 -0.00038850 21.95180419 -0.00038861 21.95175599 -0.00043681 21.95181624 -0.00037656 dihedral 15.56531680 15.56513357 -0.00018323 15.56513354 -0.00018326 15.56516362 -0.00015318 15.56514944 -0.00016736 nonbonded 10.06670400 10.06670783 0.00000383 10.06670777 0.00000377 10.06667458 -0.00002942 10.07360760 0.00690360 potential 32.01889680 32.01851213 -0.00038467 32.01851229 -0.00038451 32.01831455 -0.00058225 32.02542384 0.00652704 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 32.01889680 Difference in potential energy from amber=>gromacs conversion: -0.00038467 Difference in potential energy from amber=>lammps conversion: -0.00038451 Difference in potential energy from amber=>desmond conversion: -0.00058225 Difference in potential energy from amber=>charmm conversion: 0.00652704 ======================================================================= INFO 2017-03-19 00:41:54 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9015240.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9015240.inpcrd') INFO 2017-03-19 00:41:55 Beginning InterMol conversion INFO 2017-03-19 00:41:55 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:41:55 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:41:55 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9028462.inpcrd INFO 2017-03-19 00:41:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9028462/mobley_9028462_converted.input INFO 2017-03-19 00:41:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9028462/mobley_9028462_converted.cms WARNING 2017-03-19 00:42:10 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:42:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9028462/mobley_9028462_converted.inp INFO 2017-03-19 00:42:10 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9028462/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9028462/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9028462/mobley_9028462_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9028462/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -63.28306921 -63.28306921 0.00000000 0.00000000 0.00000000 0.00000000 193.36611224 193.36611224 coulomb total 193.33971120 193.34639321 0.00668201 193.34639305 0.00668185 193.34670183 0.00699063 193.36611224 0.02640104 coulomb-14 256.62061920 256.62946243 0.00884323 0.00000000 -256.62061920 256.62968718 0.00906798 0.00000000 -256.62061920 improper 0.00000000 0.00045672 0.00045672 0.00000000 0.00000000 0.00000000 0.00000000 0.00046024 0.00046024 proper 0.00292880 0.00245138 -0.00047742 0.00290835 -0.00002045 0.00290659 -0.00002221 0.00246856 -0.00046024 vdw (SR) 0.00000000 -1.08258745 -1.08258745 0.00000000 0.00000000 0.00000000 0.00000000 13.06805456 13.06805456 vdw total 13.06830560 13.06806515 -0.00024045 13.06806544 -0.00024016 13.06841043 0.00010483 13.06805456 -0.00025104 vdw-14 14.15070640 14.15065260 -0.00005380 0.00000000 -14.15070640 14.15100970 0.00030330 0.00000000 -14.15070640 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.62504160 2.62492588 -0.00011572 2.62492587 -0.00011573 2.62528448 0.00024288 2.62499976 -0.00004184 bond 1.97777680 1.97795877 0.00018197 1.97795876 0.00018196 1.97766568 -0.00011112 1.97794416 0.00016736 bonded 4.60574720 4.60579276 0.00004556 4.60579298 0.00004578 4.60585675 0.00010955 4.60587272 0.00012552 dihedral 0.00292880 0.00290810 -0.00002070 0.00290835 -0.00002045 0.00290659 -0.00002221 0.00292880 0.00000000 nonbonded 206.40801680 206.41445836 0.00644156 206.41445598 0.00643918 206.41511226 0.00709546 206.43416680 0.02615000 potential 211.01376400 211.02025112 0.00648712 211.02024920 0.00648520 211.02093705 0.00717305 211.03999768 0.02623368 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 211.01376400 Difference in potential energy from amber=>gromacs conversion: 0.00648712 Difference in potential energy from amber=>lammps conversion: 0.00648520 Difference in potential energy from amber=>desmond conversion: 0.00717305 Difference in potential energy from amber=>charmm conversion: 0.02623368 ======================================================================= INFO 2017-03-19 00:42:10 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9028462.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9028462.inpcrd') INFO 2017-03-19 00:42:11 Beginning InterMol conversion INFO 2017-03-19 00:42:11 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:42:11 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:42:11 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_902954.inpcrd INFO 2017-03-19 00:42:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_902954/mobley_902954_converted.input INFO 2017-03-19 00:42:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_902954/mobley_902954_converted.cms WARNING 2017-03-19 00:42:26 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:42:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_902954/mobley_902954_converted.inp INFO 2017-03-19 00:42:26 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_902954/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_902954/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_902954/mobley_902954_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_902954/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -5.22779892 -5.22779892 0.00000000 0.00000000 0.00000000 0.00000000 -16.86754496 -16.86754496 coulomb total -16.86486720 -16.86563155 -0.00076435 -16.86563120 -0.00076400 -16.86561216 -0.00074496 -16.86754496 -0.00267776 coulomb-14 -11.63737760 -11.63783262 -0.00045502 0.00000000 11.63737760 -11.63781257 -0.00043497 0.00000000 11.63737760 proper 4.94004880 4.93987687 -0.00017193 4.93987684 -0.00017196 4.93986893 -0.00017987 4.93988144 -0.00016736 vdw (SR) 0.00000000 -0.95749347 -0.95749347 0.00000000 0.00000000 0.00000000 0.00000000 14.70805704 14.70805704 vdw total 14.70801520 14.70793085 -0.00008435 14.70793110 -0.00008410 14.70786894 -0.00014626 14.70805704 0.00004184 vdw-14 15.66531440 15.66542432 0.00010992 0.00000000 -15.66531440 15.66538373 0.00006933 0.00000000 -15.66531440 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.15136480 4.15120505 -0.00015975 4.15120505 -0.00015975 4.15128593 -0.00007887 4.15128112 -0.00008368 bond 2.23509280 2.23529930 0.00020650 2.23529928 0.00020648 2.23490057 -0.00019223 2.23530200 0.00020920 bonded 11.32650640 11.32638121 -0.00012519 11.32638117 -0.00012523 11.32605544 -0.00045096 11.32646456 -0.00004184 dihedral 4.94004880 4.93987687 -0.00017193 4.93987684 -0.00017196 4.93986893 -0.00017987 4.93988144 -0.00016736 nonbonded -2.15685200 -2.15770070 -0.00084870 -2.15770026 -0.00084826 -2.15774322 -0.00089122 -2.15948792 -0.00263592 potential 9.16965440 9.16868051 -0.00097389 9.16868078 -0.00097362 9.16825862 -0.00139578 9.16697664 -0.00267776 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 9.16965440 Difference in potential energy from amber=>gromacs conversion: -0.00097389 Difference in potential energy from amber=>lammps conversion: -0.00097362 Difference in potential energy from amber=>desmond conversion: -0.00139578 Difference in potential energy from amber=>charmm conversion: -0.00267776 ======================================================================= INFO 2017-03-19 00:42:26 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_902954.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_902954.inpcrd') INFO 2017-03-19 00:42:27 Beginning InterMol conversion INFO 2017-03-19 00:42:27 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:42:27 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:42:27 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9073553.inpcrd INFO 2017-03-19 00:42:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9073553/mobley_9073553_converted.input INFO 2017-03-19 00:42:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9073553/mobley_9073553_converted.cms WARNING 2017-03-19 00:42:42 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:42:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9073553/mobley_9073553_converted.inp INFO 2017-03-19 00:42:42 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9073553/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9073553/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9073553/mobley_9073553_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9073553/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 13.88731841 13.88731841 0.00000000 0.00000000 0.00000000 0.00000000 7.52521688 7.52521688 coulomb total 7.50567760 7.52217458 0.01649698 7.52217469 0.01649709 7.52216448 0.01648688 7.52521688 0.01953928 coulomb-14 -6.36595600 -6.36514383 0.00081217 0.00000000 6.36595600 -6.36515301 0.00080299 0.00000000 6.36595600 proper 0.00000000 0.00002096 0.00002096 0.00002096 0.00002096 0.00002082 0.00002082 0.00004184 0.00004184 vdw (SR) 0.00000000 -0.27114163 -0.27114163 0.00000000 0.00000000 0.00000000 0.00000000 -0.27806864 -0.27806864 vdw total -0.27823600 -0.27808091 0.00015509 -0.27808091 0.00015509 -0.27806693 0.00016907 -0.27806864 0.00016736 vdw-14 -0.00711280 -0.00693928 0.00017352 0.00000000 0.00711280 -0.00692538 0.00018742 0.00000000 0.00711280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.25606080 0.25592114 -0.00013966 0.25592114 -0.00013966 0.25601085 -0.00004995 0.25593528 -0.00012552 bond 0.32174960 0.32181852 0.00006892 0.32181852 0.00006892 0.32205653 0.00030693 0.32183328 0.00008368 bonded 0.57781040 0.57776062 -0.00004978 0.57776062 -0.00004978 0.57808821 0.00027781 0.57781040 0.00000000 dihedral 0.00000000 0.00002096 0.00002096 0.00002096 0.00002096 0.00002082 0.00002082 0.00004184 0.00004184 nonbonded 7.22744160 7.24409366 0.01665206 7.24409350 0.01665190 7.24409755 0.01665595 7.24714824 0.01970664 potential 7.80525200 7.82185428 0.01660228 7.82185411 0.01660211 7.82217180 0.01691980 7.82491680 0.01966480 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 7.80525200 Difference in potential energy from amber=>gromacs conversion: 0.01660228 Difference in potential energy from amber=>lammps conversion: 0.01660211 Difference in potential energy from amber=>desmond conversion: 0.01691980 Difference in potential energy from amber=>charmm conversion: 0.01966480 ======================================================================= INFO 2017-03-19 00:42:42 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9073553.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9073553.inpcrd') INFO 2017-03-19 00:42:43 Beginning InterMol conversion INFO 2017-03-19 00:42:43 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:42:43 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:42:43 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9100956.inpcrd INFO 2017-03-19 00:42:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9100956/mobley_9100956_converted.input INFO 2017-03-19 00:42:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9100956/mobley_9100956_converted.cms WARNING 2017-03-19 00:42:58 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:42:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9100956/mobley_9100956_converted.inp INFO 2017-03-19 00:42:58 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9100956/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9100956/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9100956/mobley_9100956_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9100956/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 7.50687322 7.50687322 0.00000000 0.00000000 0.00000000 0.00000000 -1.75393280 -1.75393280 coulomb total -1.77108720 -1.75880395 0.01228325 -1.75880394 0.01228326 -1.75880185 0.01228535 -1.75393280 0.01715440 coulomb-14 -9.26588640 -9.26567717 0.00020923 0.00000000 9.26588640 -9.26566762 0.00021878 0.00000000 9.26588640 proper 15.09126960 15.09123221 -0.00003739 15.09123236 -0.00003724 15.09121061 -0.00005899 15.09122776 -0.00004184 vdw (SR) 0.00000000 -3.40890138 -3.40890138 0.00000000 0.00000000 0.00000000 0.00000000 12.08791072 12.08791072 vdw total 12.08799440 12.08780670 -0.00018770 12.08780696 -0.00018744 12.08775377 -0.00024063 12.08791072 -0.00008368 vdw-14 15.49669920 15.49670808 0.00000888 0.00000000 -15.49669920 15.49666163 -0.00003757 0.00000000 -15.49669920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.02129040 2.02125292 -0.00003748 2.02125291 -0.00003749 2.02115695 -0.00013345 2.02116488 -0.00012552 bond 0.88533440 0.88526042 -0.00007398 0.88526043 -0.00007397 0.88484859 -0.00048581 0.88525072 -0.00008368 bonded 17.99789440 17.99774555 -0.00014885 17.99774570 -0.00014870 17.99721615 -0.00067825 17.99764336 -0.00025104 dihedral 15.09126960 15.09123221 -0.00003739 15.09123236 -0.00003724 15.09121061 -0.00005899 15.09122776 -0.00004184 nonbonded 10.31690720 10.32900274 0.01209554 10.32900314 0.01209594 10.32895193 0.01204473 10.33397792 0.01707072 potential 28.31480160 28.32674830 0.01194670 28.32674859 0.01194699 28.32610978 0.01130818 28.33166312 0.01686152 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 28.31480160 Difference in potential energy from amber=>gromacs conversion: 0.01194670 Difference in potential energy from amber=>lammps conversion: 0.01194699 Difference in potential energy from amber=>desmond conversion: 0.01130818 Difference in potential energy from amber=>charmm conversion: 0.01686152 ======================================================================= INFO 2017-03-19 00:42:58 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9100956.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9100956.inpcrd') INFO 2017-03-19 00:42:59 Beginning InterMol conversion INFO 2017-03-19 00:42:59 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:42:59 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:42:59 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9112978.inpcrd INFO 2017-03-19 00:42:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9112978/mobley_9112978_converted.input INFO 2017-03-19 00:42:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9112978/mobley_9112978_converted.cms WARNING 2017-03-19 00:43:14 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:43:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9112978/mobley_9112978_converted.inp INFO 2017-03-19 00:43:14 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9112978/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9112978/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9112978/mobley_9112978_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9112978/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 6.65937810 6.65937810 0.00000000 0.00000000 0.00000000 0.00000000 5.01222280 5.01222280 coulomb total 5.00531920 5.01150646 0.00618726 5.01150650 0.00618730 5.01146253 0.00614333 5.01222280 0.00690360 coulomb-14 -1.64891440 -1.64787165 0.00104275 0.00000000 1.64891440 -1.64788953 0.00102487 0.00000000 1.64891440 improper 0.00000000 0.00099179 0.00099179 0.00000000 0.00000000 0.00000000 0.00000000 0.00100416 0.00100416 proper 32.03856160 32.03757942 -0.00098218 32.03855867 -0.00000293 32.03841922 -0.00014238 32.03755744 -0.00100416 vdw (SR) 0.00000000 3.15445780 3.15445780 0.00000000 0.00000000 0.00000000 0.00000000 7.55609480 7.55609480 vdw total 7.55588560 7.55603029 0.00014469 7.55603037 0.00014477 7.55603742 0.00015182 7.55609480 0.00020920 vdw-14 4.40156800 4.40157249 0.00000449 0.00000000 -4.40156800 4.40160352 0.00003552 0.00000000 -4.40156800 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.14055840 1.14045902 -0.00009938 1.14045903 -0.00009937 1.14064017 0.00008177 1.14043288 -0.00012552 bond 1.47025760 1.47024446 -0.00001314 1.47024446 -0.00001314 1.46974621 -0.00051139 1.47025760 0.00000000 bonded 34.64937760 34.64927470 -0.00010290 34.64926216 -0.00011544 34.64880561 -0.00057199 34.64925208 -0.00012552 dihedral 32.03856160 32.03857121 0.00000961 32.03855867 -0.00000293 32.03841922 -0.00014238 32.03856160 0.00000000 nonbonded 12.56120480 12.56753675 0.00633195 12.56753687 0.00633207 12.56749995 0.00629515 12.56831760 0.00711280 potential 47.21058240 47.21681144 0.00622904 47.21679982 0.00621742 47.21627641 0.00569401 47.21756968 0.00698728 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 47.21058240 Difference in potential energy from amber=>gromacs conversion: 0.00622904 Difference in potential energy from amber=>lammps conversion: 0.00621742 Difference in potential energy from amber=>desmond conversion: 0.00569401 Difference in potential energy from amber=>charmm conversion: 0.00698728 ======================================================================= INFO 2017-03-19 00:43:14 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9112978.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9112978.inpcrd') INFO 2017-03-19 00:43:15 Beginning InterMol conversion INFO 2017-03-19 00:43:15 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:43:15 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:43:15 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9114381.inpcrd INFO 2017-03-19 00:43:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9114381/mobley_9114381_converted.input INFO 2017-03-19 00:43:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9114381/mobley_9114381_converted.cms WARNING 2017-03-19 00:43:30 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:43:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9114381/mobley_9114381_converted.inp INFO 2017-03-19 00:43:31 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9114381/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9114381/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9114381/mobley_9114381_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9114381/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 83.55253379 83.55253379 0.00000000 0.00000000 0.00000000 0.00000000 -161.38771656 -161.38771656 coulomb total -161.41035200 -161.40226186 0.00809014 -161.40226014 0.00809186 -161.40226265 0.00808935 -161.38771656 0.02263544 coulomb-14 -244.94893280 -244.95479565 -0.00586285 0.00000000 244.94893280 -244.95458246 -0.00564966 0.00000000 244.94893280 improper 0.00000000 0.00000346 0.00000346 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 3.25054960 3.25040305 -0.00014655 3.25040647 -0.00014313 3.25042550 -0.00012410 3.25038224 -0.00016736 vdw (SR) 0.00000000 -1.94861583 -1.94861583 0.00000000 0.00000000 0.00000000 0.00000000 8.54326776 8.54326776 vdw total 8.54330960 8.54319641 -0.00011319 8.54319663 -0.00011297 8.54334902 0.00003942 8.54326776 -0.00004184 vdw-14 10.49179840 10.49181224 0.00001384 0.00000000 -10.49179840 10.49193915 0.00014075 0.00000000 -10.49179840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.35140800 2.38438383 0.03297583 2.38438382 0.03297582 2.38426314 0.03285514 2.38441976 0.03301176 bond 3.58359600 3.58370073 0.00010473 3.58370073 0.00010473 3.58469153 0.00109553 3.58372152 0.00012552 bonded 9.18555360 9.21849107 0.03293747 9.21849101 0.03293741 9.21938018 0.03382658 9.21852352 0.03296992 dihedral 3.25054960 3.25040651 -0.00014309 3.25040647 -0.00014313 3.25042550 -0.00012410 3.25038224 -0.00016736 nonbonded -152.86704240 -152.85906545 0.00797695 -152.85906351 0.00797889 -152.85891363 0.00812877 -152.84444880 0.02259360 potential -143.68148880 -143.64057438 0.04091442 -143.64057346 0.04091534 -143.63957098 0.04191782 -143.62592528 0.05556352 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -143.68148880 Difference in potential energy from amber=>gromacs conversion: 0.04091442 Difference in potential energy from amber=>lammps conversion: 0.04091534 Difference in potential energy from amber=>desmond conversion: 0.04191782 Difference in potential energy from amber=>charmm conversion: 0.05556352 ======================================================================= INFO 2017-03-19 00:43:31 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9114381.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9114381.inpcrd') INFO 2017-03-19 00:43:31 Beginning InterMol conversion INFO 2017-03-19 00:43:31 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:43:31 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:43:31 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9121449.inpcrd INFO 2017-03-19 00:43:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9121449/mobley_9121449_converted.input INFO 2017-03-19 00:43:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9121449/mobley_9121449_converted.cms WARNING 2017-03-19 00:43:46 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:43:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9121449/mobley_9121449_converted.inp INFO 2017-03-19 00:43:46 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9121449/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9121449/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9121449/mobley_9121449_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9121449/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.33090992 0.33090992 0.00000000 0.00000000 0.00000000 0.00000000 -2.41630184 -2.41630184 coulomb total -2.41165760 -2.41163494 0.00002266 -2.41163492 0.00002268 -2.41163316 0.00002444 -2.41630184 -0.00464424 coulomb-14 -2.74261200 -2.74254486 0.00006714 0.00000000 2.74261200 -2.74253973 0.00007227 0.00000000 2.74261200 proper 0.01087840 0.01084721 -0.00003119 0.01084721 -0.00003119 0.01084635 -0.00003205 0.01083656 -0.00004184 vdw (SR) 0.00000000 -0.61687014 -0.61687014 0.00000000 0.00000000 0.00000000 0.00000000 0.52358576 0.52358576 vdw total 0.52383680 0.52357801 -0.00025879 0.52357802 -0.00025878 0.52359245 -0.00024435 0.52358576 -0.00025104 vdw-14 1.14055840 1.14044815 -0.00011025 0.00000000 -1.14055840 1.14046185 -0.00009655 0.00000000 -1.14055840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.42718640 0.57564491 0.14845851 0.57564493 0.14845853 0.57560835 0.14842195 0.57567656 0.14849016 bond 1.88405520 1.88418928 0.00013408 1.88418930 0.00013410 1.88435390 0.00029870 1.88418072 0.00012552 bonded 2.32212000 2.47068140 0.14856140 2.47068144 0.14856144 2.47080860 0.14868860 2.47069384 0.14857384 dihedral 0.01087840 0.01084721 -0.00003119 0.01084721 -0.00003119 0.01084635 -0.00003205 0.01083656 -0.00004184 nonbonded -1.88782080 -1.88805693 -0.00023613 -1.88805690 -0.00023610 -1.88804072 -0.00021992 -1.89271608 -0.00489528 potential 0.43429920 0.58262447 0.14832527 0.58262451 0.14832531 0.58274678 0.14844758 0.57801960 0.14372040 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 0.43429920 Difference in potential energy from amber=>gromacs conversion: 0.14832527 Difference in potential energy from amber=>lammps conversion: 0.14832531 Difference in potential energy from amber=>desmond conversion: 0.14844758 Difference in potential energy from amber=>charmm conversion: 0.14372040 ======================================================================= INFO 2017-03-19 00:43:46 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9121449.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9121449.inpcrd') INFO 2017-03-19 00:43:47 Beginning InterMol conversion INFO 2017-03-19 00:43:47 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:43:47 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:43:47 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9139060.inpcrd INFO 2017-03-19 00:43:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9139060/mobley_9139060_converted.input INFO 2017-03-19 00:43:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9139060/mobley_9139060_converted.cms WARNING 2017-03-19 00:44:03 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:44:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9139060/mobley_9139060_converted.inp INFO 2017-03-19 00:44:03 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9139060/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9139060/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9139060/mobley_9139060_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9139060/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 9.38591002 9.38591002 0.00000000 0.00000000 0.00000000 0.00000000 -5.88471232 -5.88471232 coulomb total -5.87935680 -5.89167583 -0.01231903 -5.89167575 -0.01231895 -5.89171759 -0.01236079 -5.88471232 -0.00535552 coulomb-14 -15.27829440 -15.27758585 0.00070855 0.00000000 15.27829440 -15.27759019 0.00070421 0.00000000 15.27829440 proper 18.30416320 18.30402321 -0.00013999 18.30402304 -0.00014016 18.30408132 -0.00008188 18.30403768 -0.00012552 vdw (SR) 0.00000000 -4.48663870 -4.48663870 0.00000000 0.00000000 0.00000000 0.00000000 14.10451504 14.10451504 vdw total 14.10468240 14.10439009 -0.00029231 14.10439036 -0.00029204 14.10437057 -0.00031183 14.10451504 -0.00016736 vdw-14 18.59118560 18.59102878 -0.00015682 0.00000000 -18.59118560 18.59103414 -0.00015146 0.00000000 -18.59118560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.60035600 2.60019509 -0.00016091 2.60019508 -0.00016092 2.60002969 -0.00032631 2.60010496 -0.00025104 bond 0.75060960 0.75043215 -0.00017745 0.75043216 -0.00017744 0.75021434 -0.00039526 0.75044224 -0.00016736 bonded 21.65512880 21.65465045 -0.00047835 21.65465028 -0.00047852 21.65432535 -0.00080345 21.65458488 -0.00054392 dihedral 18.30416320 18.30402321 -0.00013999 18.30402304 -0.00014016 18.30408132 -0.00008188 18.30403768 -0.00012552 nonbonded 8.22532560 8.21271426 -0.01261134 8.21271461 -0.01261099 8.21265298 -0.01267262 8.21980272 -0.00552288 potential 29.88045440 29.86736471 -0.01308969 29.86736517 -0.01308923 29.86690180 -0.01355260 29.87438760 -0.00606680 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 29.88045440 Difference in potential energy from amber=>gromacs conversion: -0.01308969 Difference in potential energy from amber=>lammps conversion: -0.01308923 Difference in potential energy from amber=>desmond conversion: -0.01355260 Difference in potential energy from amber=>charmm conversion: -0.00606680 ======================================================================= INFO 2017-03-19 00:44:03 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9139060.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9139060.inpcrd') INFO 2017-03-19 00:44:03 Beginning InterMol conversion INFO 2017-03-19 00:44:03 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:44:03 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:44:03 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9185328.inpcrd INFO 2017-03-19 00:44:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9185328/mobley_9185328_converted.input INFO 2017-03-19 00:44:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9185328/mobley_9185328_converted.cms WARNING 2017-03-19 00:44:19 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:44:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9185328/mobley_9185328_converted.inp INFO 2017-03-19 00:44:19 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9185328/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9185328/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9185328/mobley_9185328_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9185328/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -2.20798255 -2.20798255 0.00000000 0.00000000 0.00000000 0.00000000 1.16993008 1.16993008 coulomb total 1.17695920 1.14877381 -0.02818539 1.14877381 -0.02818539 1.14882693 -0.02813227 1.16993008 -0.00702912 coulomb-14 3.36435440 3.35675636 -0.00759804 0.00000000 -3.36435440 3.35684845 -0.00750595 0.00000000 -3.36435440 proper 4.98523600 4.98507586 -0.00016014 4.98507575 -0.00016025 4.98505944 -0.00017656 4.98506864 -0.00016736 vdw (SR) 0.00000000 -0.54280102 -0.54280102 0.00000000 0.00000000 0.00000000 0.00000000 1.13834088 1.13834088 vdw total 1.13846640 1.13833273 -0.00013367 1.13833276 -0.00013364 1.13827097 -0.00019543 1.13834088 -0.00012552 vdw-14 1.68113120 1.68113375 0.00000255 0.00000000 -1.68113120 1.68107105 -0.00006015 0.00000000 -1.68113120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 21.50534160 21.50529274 -0.00004886 21.50529265 -0.00004895 21.50539905 0.00005745 21.50546712 0.00012552 bond 2.23802160 2.23797516 -0.00004644 2.23797516 -0.00004644 2.23834422 0.00032262 2.23797976 -0.00004184 bonded 28.72859920 28.72834375 -0.00025545 28.72834356 -0.00025564 28.72880270 0.00020350 28.72851552 -0.00008368 dihedral 4.98523600 4.98507586 -0.00016014 4.98507575 -0.00016025 4.98505944 -0.00017656 4.98506864 -0.00016736 nonbonded 2.31542560 2.28710654 -0.02831906 2.28710653 -0.02831907 2.28709789 -0.02832771 2.30827096 -0.00715464 potential 31.04402480 31.01545030 -0.02857450 31.01545017 -0.02857463 31.01587953 -0.02814527 31.03682832 -0.00719648 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 31.04402480 Difference in potential energy from amber=>gromacs conversion: -0.02857450 Difference in potential energy from amber=>lammps conversion: -0.02857463 Difference in potential energy from amber=>desmond conversion: -0.02814527 Difference in potential energy from amber=>charmm conversion: -0.00719648 ======================================================================= INFO 2017-03-19 00:44:19 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9185328.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9185328.inpcrd') INFO 2017-03-19 00:44:19 Beginning InterMol conversion INFO 2017-03-19 00:44:19 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:44:19 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:44:19 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9197172.inpcrd INFO 2017-03-19 00:44:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9197172/mobley_9197172_converted.input INFO 2017-03-19 00:44:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9197172/mobley_9197172_converted.cms WARNING 2017-03-19 00:44:35 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:44:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9197172/mobley_9197172_converted.inp INFO 2017-03-19 00:44:35 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9197172/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9197172/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9197172/mobley_9197172_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9197172/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 9.48205824 9.48205824 0.00000000 0.00000000 0.00000000 0.00000000 10.74618560 10.74618560 coulomb total 10.76124800 10.75511274 -0.00613526 10.75511258 -0.00613542 10.75504113 -0.00620687 10.74618560 -0.01506240 coulomb-14 1.27444640 1.27305450 -0.00139190 0.00000000 -1.27444640 1.27303348 -0.00141292 0.00000000 -1.27444640 improper 0.00000000 0.00110233 0.00110233 0.00000000 0.00000000 0.00000000 0.00000000 0.00108784 0.00108784 proper 17.30544240 17.30416144 -0.00128096 17.30526207 -0.00018033 17.30524843 -0.00019397 17.30414536 -0.00129704 vdw (SR) 0.00000000 -2.96854772 -2.96854772 0.00000000 0.00000000 0.00000000 0.00000000 5.30920312 5.30920312 vdw total 5.30907760 5.30910289 0.00002529 5.30910312 0.00002552 5.30911144 0.00003384 5.30920312 0.00012552 vdw-14 8.27762560 8.27765061 0.00002501 0.00000000 -8.27762560 8.27766133 0.00003573 0.00000000 -8.27762560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.57690160 3.57688421 -0.00001739 3.57688419 -0.00001741 3.57669333 -0.00020827 3.57681792 -0.00008368 bond 1.30247920 1.30259203 0.00011283 1.30259204 0.00011284 1.30259679 0.00011759 1.30260472 0.00012552 bonded 22.18482320 22.18474000 -0.00008320 22.18473831 -0.00008489 22.18453855 -0.00028465 22.18465584 -0.00016736 dihedral 17.30544240 17.30526377 -0.00017863 17.30526207 -0.00018033 17.30524843 -0.00019397 17.30523320 -0.00020920 nonbonded 16.07032560 16.06421563 -0.00610997 16.06421570 -0.00610990 16.06415257 -0.00617303 16.05538872 -0.01493688 potential 38.25514880 38.24895563 -0.00619317 38.24895397 -0.00619483 38.24861858 -0.00653022 38.24008640 -0.01506240 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 38.25514880 Difference in potential energy from amber=>gromacs conversion: -0.00619317 Difference in potential energy from amber=>lammps conversion: -0.00619483 Difference in potential energy from amber=>desmond conversion: -0.00653022 Difference in potential energy from amber=>charmm conversion: -0.01506240 ======================================================================= INFO 2017-03-19 00:44:35 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9197172.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9197172.inpcrd') INFO 2017-03-19 00:44:35 Beginning InterMol conversion INFO 2017-03-19 00:44:35 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:44:35 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:44:35 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9201263.inpcrd INFO 2017-03-19 00:44:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9201263/mobley_9201263_converted.input INFO 2017-03-19 00:44:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9201263/mobley_9201263_converted.cms WARNING 2017-03-19 00:44:51 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:44:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9201263/mobley_9201263_converted.inp INFO 2017-03-19 00:44:51 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9201263/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9201263/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9201263/mobley_9201263_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9201263/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -54.38906897 -54.38906897 0.00000000 0.00000000 0.00000000 0.00000000 -356.95670480 -356.95670480 coulomb total -357.01569920 -357.07466705 -0.05896785 -357.07466431 -0.05896511 -357.07431913 -0.05861993 -356.95670480 0.05899440 coulomb-14 -302.66428400 -302.68559808 -0.02131408 0.00000000 302.66428400 -302.68527429 -0.02099029 0.00000000 302.66428400 proper 17.42301280 17.42301449 0.00000169 17.42301531 0.00000251 17.42299991 -0.00001289 17.42292912 -0.00008368 vdw (SR) 0.00000000 -1.20729655 -1.20729655 0.00000000 0.00000000 0.00000000 0.00000000 -1.33390104 -1.33390104 vdw total -1.33427760 -1.33391736 0.00036024 -1.33391736 0.00036024 -1.33395737 0.00032023 -1.33390104 0.00037656 vdw-14 -0.12677520 -0.12662081 0.00015439 0.00000000 0.12677520 -0.12665801 0.00011719 0.00000000 0.12677520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.26479920 2.26474124 -0.00005796 2.26474125 -0.00005795 2.26490408 0.00010488 2.26484104 0.00004184 bond 6.12621280 6.12634799 0.00013519 6.12634794 0.00013514 6.12654484 0.00033204 6.12633832 0.00012552 bonded 25.81402480 25.81410371 0.00007891 25.81410451 0.00007971 25.81444883 0.00042403 25.81410848 0.00008368 dihedral 17.42301280 17.42301449 0.00000169 17.42301531 0.00000251 17.42299991 -0.00001289 17.42292912 -0.00008368 nonbonded -358.34997680 -358.40858441 -0.05860761 -358.40858209 -0.05860529 -358.40827651 -0.05829971 -358.29060584 0.05937096 potential -332.53595200 -332.59448070 -0.05852870 -332.59447779 -0.05852579 -332.59385647 -0.05790447 -332.47645552 0.05949648 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -332.53595200 Difference in potential energy from amber=>gromacs conversion: -0.05852870 Difference in potential energy from amber=>lammps conversion: -0.05852579 Difference in potential energy from amber=>desmond conversion: -0.05790447 Difference in potential energy from amber=>charmm conversion: 0.05949648 ======================================================================= INFO 2017-03-19 00:44:51 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9201263.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9201263.inpcrd') INFO 2017-03-19 00:44:51 Beginning InterMol conversion INFO 2017-03-19 00:44:51 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:44:51 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:44:51 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9209581.inpcrd INFO 2017-03-19 00:44:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9209581/mobley_9209581_converted.input INFO 2017-03-19 00:44:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9209581/mobley_9209581_converted.cms WARNING 2017-03-19 00:45:07 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:45:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9209581/mobley_9209581_converted.inp INFO 2017-03-19 00:45:07 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9209581/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9209581/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9209581/mobley_9209581_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9209581/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 11.29959375 11.29959375 0.00000000 0.00000000 0.00000000 0.00000000 45.19703240 45.19703240 coulomb total 45.13531840 45.20010848 0.06479008 45.20010764 0.06478924 45.20006174 0.06474334 45.19703240 0.06171400 coulomb-14 33.85860160 33.90051473 0.04191313 0.00000000 -33.85860160 33.90049461 0.04189301 0.00000000 -33.85860160 proper 0.09581360 0.09574356 -0.00007004 0.09574356 -0.00007004 0.09573523 -0.00007837 0.09572992 -0.00008368 vdw (SR) 0.00000000 -0.33496126 -0.33496126 0.00000000 0.00000000 0.00000000 0.00000000 6.16068896 6.16068896 vdw total 6.16052160 6.16061745 0.00009585 6.16061741 0.00009581 6.16052789 0.00000629 6.16068896 0.00016736 vdw-14 6.49566000 6.49557870 -0.00008130 0.00000000 -6.49566000 6.49549138 -0.00016862 0.00000000 -6.49566000 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.58408640 0.58424981 0.00016341 0.58424983 0.00016343 0.58415787 0.00007147 0.58421192 0.00012552 bond 0.77822400 0.77827844 0.00005444 0.77827843 0.00005443 0.77829385 0.00006985 0.77826584 0.00004184 bonded 1.45812400 1.45827182 0.00014782 1.45827182 0.00014782 1.45818695 0.00006295 1.45820768 0.00008368 dihedral 0.09581360 0.09574356 -0.00007004 0.09574356 -0.00007004 0.09573523 -0.00007837 0.09572992 -0.00008368 nonbonded 51.29584000 51.36072593 0.06488593 51.36072547 0.06488547 51.36058963 0.06474963 51.35772136 0.06188136 potential 52.75396400 52.81899774 0.06503374 52.81899591 0.06503191 52.81875868 0.06479468 52.81597088 0.06200688 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 52.75396400 Difference in potential energy from amber=>gromacs conversion: 0.06503374 Difference in potential energy from amber=>lammps conversion: 0.06503191 Difference in potential energy from amber=>desmond conversion: 0.06479468 Difference in potential energy from amber=>charmm conversion: 0.06200688 ======================================================================= INFO 2017-03-19 00:45:07 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9209581.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9209581.inpcrd') INFO 2017-03-19 00:45:07 Beginning InterMol conversion INFO 2017-03-19 00:45:07 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:45:07 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:45:07 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9246215.inpcrd INFO 2017-03-19 00:45:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9246215/mobley_9246215_converted.input INFO 2017-03-19 00:45:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9246215/mobley_9246215_converted.cms WARNING 2017-03-19 00:45:23 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:45:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9246215/mobley_9246215_converted.inp INFO 2017-03-19 00:45:23 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9246215/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9246215/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9246215/mobley_9246215_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9246215/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.48303031 0.48303031 0.00000000 0.00000000 0.00000000 0.00000000 18.05144960 18.05144960 coulomb total 18.03555040 18.05195381 0.01640341 18.05195377 0.01640337 18.05192863 0.01637823 18.05144960 0.01589920 coulomb-14 17.56443200 17.56892351 0.00449151 0.00000000 -17.56443200 17.56895319 0.00452119 0.00000000 -17.56443200 improper 0.00000000 0.00398934 0.00398934 0.00000000 0.00000000 0.00000000 0.00000000 0.00397480 0.00397480 proper 24.08603280 24.08197902 -0.00405378 24.08596837 -0.00006443 24.08592469 -0.00010811 24.08197432 -0.00405848 vdw (SR) 0.00000000 -0.70378349 -0.70378349 0.00000000 0.00000000 0.00000000 0.00000000 1.73046056 1.73046056 vdw total 1.73050240 1.73044651 -0.00005589 1.73044654 -0.00005586 1.73042428 -0.00007812 1.73046056 -0.00004184 vdw-14 2.43425120 2.43423000 -0.00002120 0.00000000 -2.43425120 2.43421460 -0.00003660 0.00000000 -2.43425120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.54473280 1.54471761 -0.00001519 1.54471761 -0.00001519 1.54480370 0.00007090 1.54464912 -0.00008368 bond 1.27277280 1.27279573 0.00002293 1.27279573 0.00002293 1.27299647 0.00022367 1.27281464 0.00004184 bonded 26.90353840 26.90348170 -0.00005670 26.90348171 -0.00005669 26.90372486 0.00018646 26.90341288 -0.00012552 dihedral 24.08603280 24.08596836 -0.00006444 24.08596837 -0.00006443 24.08592469 -0.00010811 24.08594912 -0.00008368 nonbonded 19.76605280 19.78240032 0.01634752 19.78240011 0.01634731 19.78235292 0.01630012 19.78191016 0.01585736 potential 46.66959120 46.68588202 0.01629082 46.68588370 0.01629250 46.68605566 0.01646446 46.68536488 0.01577368 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 46.66959120 Difference in potential energy from amber=>gromacs conversion: 0.01629082 Difference in potential energy from amber=>lammps conversion: 0.01629250 Difference in potential energy from amber=>desmond conversion: 0.01646446 Difference in potential energy from amber=>charmm conversion: 0.01577368 ======================================================================= INFO 2017-03-19 00:45:23 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9246215.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9246215.inpcrd') INFO 2017-03-19 00:45:23 Beginning InterMol conversion INFO 2017-03-19 00:45:23 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:45:23 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9257453.inpcrd INFO 2017-03-19 00:45:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9257453/mobley_9257453_converted.input INFO 2017-03-19 00:45:24 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9257453/mobley_9257453_converted.cms INFO 2017-03-19 00:45:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9257453/mobley_9257453_converted.rst7 WARNING 2017-03-19 00:45:39 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:45:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9257453/mobley_9257453_converted.inp INFO 2017-03-19 00:45:39 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9257453/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9257453/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9257453/mobley_9257453_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_9257453/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9257453/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 56.69681524 56.69681524 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -75.07702656 -75.07702656 coulomb total -75.07602240 -75.07840330 -0.00238090 -75.07840310 -0.00238070 -75.07897505 -0.00295265 -75.07560400 0.00041840 -75.07702656 -0.00100416 coulomb-14 -131.77089600 -131.77521853 -0.00432253 0.00000000 131.77089600 -131.77517540 -0.00427940 -131.77047760 0.00041840 0.00000000 131.77089600 improper 0.00000000 0.00000994 0.00000994 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00000000 0.00009640 0.00009640 0.00010632 0.00010632 0.00011123 0.00011123 0.00000000 0.00000000 0.00008368 0.00008368 vdw (SR) 0.00000000 -2.13038015 -2.13038015 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 15.32795848 15.32795848 vdw total 15.32766560 15.32795526 0.00028966 15.32795513 0.00028953 15.32794198 0.00027638 15.32766560 0.00000000 15.32795848 0.00029288 vdw-14 17.45815840 17.45833540 0.00017700 0.00000000 -17.45815840 17.45831881 0.00016041 17.45815840 0.00000000 0.00000000 -17.45815840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.76439280 1.76435036 -0.00004244 1.76435037 -0.00004243 1.76449066 0.00009786 1.76439280 0.00000000 1.76439280 0.00000000 bond 0.74224160 0.74225798 0.00001638 0.74225796 0.00001636 0.74215170 -0.00008990 0.74224160 0.00000000 0.74224160 0.00000000 bonded 2.50663440 2.50671468 0.00008028 2.50671466 0.00008026 2.50675358 0.00011918 2.50663440 0.00000000 2.50671808 0.00008368 dihedral 0.00000000 0.00010634 0.00010634 0.00010632 0.00010632 0.00011123 0.00011123 0.00000000 0.00000000 0.00008368 0.00008368 nonbonded -59.74835680 -59.75044804 -0.00209124 -59.75044880 -0.00209200 -59.75103307 -0.00267627 -59.74793840 0.00041840 -59.74906808 -0.00071128 potential -57.24172240 -57.24373336 -0.00201096 -57.24373072 -0.00200832 -57.24434409 -0.00262169 -57.24130400 0.00041840 -57.24230816 -0.00058576 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -57.24172240 Difference in potential energy from amber=>gromacs conversion: -0.00201096 Difference in potential energy from amber=>lammps conversion: -0.00200832 Difference in potential energy from amber=>desmond conversion: -0.00262169 Difference in potential energy from amber=>amber conversion: 0.00041840 Difference in potential energy from amber=>charmm conversion: -0.00058576 ======================================================================= INFO 2017-03-19 00:45:39 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9257453.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9257453.inpcrd') INFO 2017-03-19 00:45:39 Beginning InterMol conversion INFO 2017-03-19 00:45:39 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:45:40 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:45:40 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9281946.inpcrd INFO 2017-03-19 00:45:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9281946/mobley_9281946_converted.input INFO 2017-03-19 00:45:40 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9281946/mobley_9281946_converted.cms WARNING 2017-03-19 00:45:55 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:45:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9281946/mobley_9281946_converted.inp INFO 2017-03-19 00:45:55 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9281946/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9281946/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9281946/mobley_9281946_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9281946/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 101.08025978 101.08025978 0.00000000 0.00000000 0.00000000 0.00000000 -301.41071576 -301.41071576 coulomb total -301.42916720 -301.44242253 -0.01325533 -301.44241793 -0.01325073 -301.44193133 -0.01276413 -301.41071576 0.01845144 coulomb-14 -402.50289200 -402.52268231 -0.01979031 0.00000000 402.50289200 -402.52284424 -0.01995224 0.00000000 402.50289200 improper 0.00000000 0.00002763 0.00002763 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 45.92149200 45.92128674 -0.00020526 45.92130372 -0.00018828 45.92137527 -0.00011673 45.92128280 -0.00020920 vdw (SR) 0.00000000 -5.05656984 -5.05656984 0.00000000 0.00000000 0.00000000 0.00000000 24.15590560 24.15590560 vdw total 24.15590560 24.15560026 -0.00030534 24.15560017 -0.00030543 24.15544963 -0.00045597 24.15590560 -0.00000000 vdw-14 29.21226960 29.21217010 -0.00009950 0.00000000 -29.21226960 29.21205513 -0.00021447 0.00000000 -29.21226960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.77564160 3.77554996 -0.00009164 3.77554997 -0.00009163 3.77612286 0.00048126 3.77564160 0.00000000 bond 17.64267280 17.64247316 -0.00019964 17.64247322 -0.00019958 17.64450100 0.00182820 17.64246360 -0.00020920 bonded 67.33980640 67.33933748 -0.00046892 67.33932691 -0.00047949 67.34199912 0.00219272 67.33942984 -0.00037656 dihedral 45.92149200 45.92131437 -0.00017763 45.92130372 -0.00018828 45.92137527 -0.00011673 45.92132464 -0.00016736 nonbonded -277.27326160 -277.28682227 -0.01356067 -277.28681776 -0.01355616 -277.28648170 -0.01322010 -277.25481016 0.01845144 potential -209.93345520 -209.94748479 -0.01402959 -209.94749252 -0.01403732 -209.94476204 -0.01130684 -209.91538032 0.01807488 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -209.93345520 Difference in potential energy from amber=>gromacs conversion: -0.01402959 Difference in potential energy from amber=>lammps conversion: -0.01403732 Difference in potential energy from amber=>desmond conversion: -0.01130684 Difference in potential energy from amber=>charmm conversion: 0.01807488 ======================================================================= INFO 2017-03-19 00:45:55 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9281946.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9281946.inpcrd') INFO 2017-03-19 00:45:56 Beginning InterMol conversion INFO 2017-03-19 00:45:56 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:45:56 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:45:56 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_929676.inpcrd INFO 2017-03-19 00:45:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_929676/mobley_929676_converted.input INFO 2017-03-19 00:45:56 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_929676/mobley_929676_converted.cms WARNING 2017-03-19 00:46:11 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:46:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_929676/mobley_929676_converted.inp INFO 2017-03-19 00:46:11 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_929676/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_929676/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_929676/mobley_929676_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_929676/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 7.45713983 7.45713983 0.00000000 0.00000000 0.00000000 0.00000000 4.27165480 4.27165480 coulomb total 4.27228240 4.26620724 -0.00607516 4.26620723 -0.00607517 4.26616941 -0.00611299 4.27165480 -0.00062760 coulomb-14 -3.18904480 -3.19093260 -0.00188780 0.00000000 3.18904480 -3.19093768 -0.00189288 0.00000000 3.18904480 proper 12.21518800 12.21523567 0.00004767 12.21523570 0.00004770 12.21524097 0.00005297 12.21527168 0.00008368 vdw (SR) 0.00000000 -2.44189198 -2.44189198 0.00000000 0.00000000 0.00000000 0.00000000 3.71806976 3.71806976 vdw total 3.71832080 3.71798871 -0.00033209 3.71798876 -0.00033204 3.71800985 -0.00031095 3.71806976 -0.00025104 vdw-14 6.16010320 6.15988069 -0.00022251 0.00000000 -6.16010320 6.15990705 -0.00019615 0.00000000 -6.16010320 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.77396800 3.77415338 0.00018538 3.77415339 0.00018539 3.77411012 0.00014212 3.77417720 0.00020920 bond 1.25729200 1.25747961 0.00018761 1.25747961 0.00018761 1.25768894 0.00039694 1.25745936 0.00016736 bonded 17.24644800 17.24686865 0.00042065 17.24686870 0.00042070 17.24704003 0.00059203 17.24690824 0.00046024 dihedral 12.21518800 12.21523567 0.00004767 12.21523570 0.00004770 12.21524097 0.00005297 12.21527168 0.00008368 nonbonded 7.99060320 7.98419595 -0.00640725 7.98419582 -0.00640738 7.98417925 -0.00642395 7.98972456 -0.00087864 potential 25.23705120 25.23106460 -0.00598660 25.23106473 -0.00598647 25.23114435 -0.00590685 25.23667464 -0.00037656 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 25.23705120 Difference in potential energy from amber=>gromacs conversion: -0.00598660 Difference in potential energy from amber=>lammps conversion: -0.00598647 Difference in potential energy from amber=>desmond conversion: -0.00590685 Difference in potential energy from amber=>charmm conversion: -0.00037656 ======================================================================= INFO 2017-03-19 00:46:11 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_929676.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_929676.inpcrd') INFO 2017-03-19 00:46:12 Beginning InterMol conversion INFO 2017-03-19 00:46:12 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:46:12 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:46:12 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9407874.inpcrd INFO 2017-03-19 00:46:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9407874/mobley_9407874_converted.input INFO 2017-03-19 00:46:12 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9407874/mobley_9407874_converted.cms WARNING 2017-03-19 00:46:28 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:46:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9407874/mobley_9407874_converted.inp INFO 2017-03-19 00:46:28 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9407874/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9407874/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9407874/mobley_9407874_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9407874/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -3.47902956 -3.47902956 0.00000000 0.00000000 0.00000000 0.00000000 -60.82925136 -60.82925136 coulomb total -60.85084080 -60.85270061 -0.00185981 -60.85269850 -0.00185770 -60.85265883 -0.00181803 -60.82925136 0.02158944 coulomb-14 -57.37184480 -57.37367105 -0.00182625 0.00000000 57.37184480 -57.37375061 -0.00190581 0.00000000 57.37184480 improper 0.00000000 0.00188052 0.00188052 0.00000000 0.00000000 0.00000000 0.00000000 0.00188280 0.00188280 proper 19.24388960 19.24191698 -0.00197262 19.24379881 -0.00009079 19.24377663 -0.00011297 19.24192312 -0.00196648 vdw (SR) 0.00000000 -2.92824351 -2.92824351 0.00000000 0.00000000 0.00000000 0.00000000 9.31383504 9.31383504 vdw total 9.31358400 9.31367454 0.00009054 9.31367479 0.00009079 9.31360042 0.00001642 9.31383504 0.00025104 vdw-14 12.24196560 12.24191805 -0.00004755 0.00000000 -12.24196560 12.24188790 -0.00007770 0.00000000 -12.24196560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.32335120 3.32330195 -0.00004925 3.32330195 -0.00004925 3.32365314 0.00030194 3.32326752 -0.00008368 bond 1.72799200 1.72783297 -0.00015903 1.72783297 -0.00015903 1.72804363 0.00005163 1.72782464 -0.00016736 bonded 24.29523280 24.29493243 -0.00030037 24.29493373 -0.00029907 24.29547340 0.00024060 24.29489808 -0.00033472 dihedral 19.24388960 19.24379750 -0.00009210 19.24379881 -0.00009079 19.24377663 -0.00011297 19.24380592 -0.00008368 nonbonded -51.53725680 -51.53902607 -0.00176927 -51.53902663 -0.00176983 -51.53905841 -0.00180161 -51.51541632 0.02184048 potential -27.24202400 -27.24409365 -0.00206965 -27.24409173 -0.00206773 -27.24366860 -0.00164460 -27.22056008 0.02146392 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -27.24202400 Difference in potential energy from amber=>gromacs conversion: -0.00206965 Difference in potential energy from amber=>lammps conversion: -0.00206773 Difference in potential energy from amber=>desmond conversion: -0.00164460 Difference in potential energy from amber=>charmm conversion: 0.02146392 ======================================================================= INFO 2017-03-19 00:46:28 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9407874.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9407874.inpcrd') INFO 2017-03-19 00:46:28 Beginning InterMol conversion INFO 2017-03-19 00:46:28 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:46:28 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:46:28 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9414831.inpcrd INFO 2017-03-19 00:46:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9414831/mobley_9414831_converted.input INFO 2017-03-19 00:46:28 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9414831/mobley_9414831_converted.cms WARNING 2017-03-19 00:46:44 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:46:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9414831/mobley_9414831_converted.inp INFO 2017-03-19 00:46:44 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9414831/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9414831/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9414831/mobley_9414831_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9414831/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -11.99613618 -11.99613618 0.00000000 0.00000000 0.00000000 0.00000000 -1.72690416 -1.72690416 coulomb total -1.73050240 -1.72384020 0.00666220 -1.72384017 0.00666223 -1.72402306 0.00647934 -1.72690416 0.00359824 coulomb-14 10.27255680 10.27229597 -0.00026083 0.00000000 -10.27255680 10.27232760 -0.00022920 0.00000000 -10.27255680 improper 0.00000000 0.00004862 0.00004862 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00051085 0.00009245 0.00055945 0.00014105 0.00055064 0.00013224 0.00050208 0.00008368 vdw (SR) 0.00000000 6.09732990 6.09732990 0.00000000 0.00000000 0.00000000 0.00000000 40.63894096 40.63894096 vdw total 40.63877360 40.63885863 0.00008503 40.63885895 0.00008535 40.63879552 0.00002192 40.63894096 0.00016736 vdw-14 34.54143040 34.54152873 0.00009833 0.00000000 -34.54143040 34.54164320 0.00021280 0.00000000 -34.54143040 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.65391120 2.65403222 0.00012102 2.65403220 0.00012100 2.65410241 0.00019121 2.65403672 0.00012552 bond 5.08021280 5.08022685 0.00001405 5.08022703 0.00001423 5.07982524 -0.00038756 5.08021280 0.00000000 bonded 7.73454240 7.73481853 0.00027613 7.73481868 0.00027628 7.73447829 -0.00006411 7.73479344 0.00025104 dihedral 0.00041840 0.00055946 0.00014106 0.00055945 0.00014105 0.00055064 0.00013224 0.00054392 0.00012552 nonbonded 38.90827120 38.91501843 0.00674723 38.91501874 0.00674754 38.91477247 0.00650127 38.91203680 0.00376560 potential 46.64281360 46.64983696 0.00702336 46.64983854 0.00702494 46.64916533 0.00635173 46.64687208 0.00405848 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 46.64281360 Difference in potential energy from amber=>gromacs conversion: 0.00702336 Difference in potential energy from amber=>lammps conversion: 0.00702494 Difference in potential energy from amber=>desmond conversion: 0.00635173 Difference in potential energy from amber=>charmm conversion: 0.00405848 ======================================================================= INFO 2017-03-19 00:46:44 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9414831.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9414831.inpcrd') INFO 2017-03-19 00:46:44 Beginning InterMol conversion INFO 2017-03-19 00:46:44 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:46:44 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:46:44 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9434451.inpcrd INFO 2017-03-19 00:46:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9434451/mobley_9434451_converted.input INFO 2017-03-19 00:46:44 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9434451/mobley_9434451_converted.cms WARNING 2017-03-19 00:47:00 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:47:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9434451/mobley_9434451_converted.inp INFO 2017-03-19 00:47:00 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9434451/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9434451/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9434451/mobley_9434451_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9434451/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 8.74123802 8.74123802 0.00000000 0.00000000 0.00000000 0.00000000 -13.03968704 -13.03968704 coulomb total -13.03441520 -13.04181456 -0.00739936 -13.04181460 -0.00739940 -13.04183264 -0.00741744 -13.03968704 -0.00527184 coulomb-14 -21.78525120 -21.78305258 0.00219862 0.00000000 21.78525120 -21.78304807 0.00220313 0.00000000 21.78525120 proper 13.86033680 13.86015729 -0.00017951 13.86015731 -0.00017949 13.86014019 -0.00019661 13.86016944 -0.00016736 vdw (SR) 0.00000000 -0.18607380 -0.18607380 0.00000000 0.00000000 0.00000000 0.00000000 1.57753536 1.57753536 vdw total 1.57736800 1.57748225 0.00011425 1.57748227 0.00011427 1.57745139 0.00008339 1.57753536 0.00016736 vdw-14 1.76355600 1.76355604 0.00000004 0.00000000 -1.76355600 1.76352819 -0.00002781 0.00000000 -1.76355600 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.28950880 1.28967380 0.00016500 1.28967382 0.00016502 1.28989081 0.00038201 1.28971800 0.00020920 bond 0.91378560 0.91379213 0.00000653 0.91379213 0.00000653 0.91409403 0.00030843 0.91378560 0.00000000 bonded 16.06363120 16.06362322 -0.00000798 16.06362325 -0.00000795 16.06412504 0.00049384 16.06367304 0.00004184 dihedral 13.86033680 13.86015729 -0.00017951 13.86015731 -0.00017949 13.86014019 -0.00019661 13.86016944 -0.00016736 nonbonded -11.45704720 -11.46433231 -0.00728511 -11.46433196 -0.00728476 -11.46438124 -0.00733404 -11.46215168 -0.00510448 potential 4.60658400 4.59929091 -0.00729309 4.59929129 -0.00729271 4.59971626 -0.00686774 4.60152136 -0.00506264 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 4.60658400 Difference in potential energy from amber=>gromacs conversion: -0.00729309 Difference in potential energy from amber=>lammps conversion: -0.00729271 Difference in potential energy from amber=>desmond conversion: -0.00686774 Difference in potential energy from amber=>charmm conversion: -0.00506264 ======================================================================= INFO 2017-03-19 00:47:00 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9434451.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9434451.inpcrd') INFO 2017-03-19 00:47:00 Beginning InterMol conversion INFO 2017-03-19 00:47:00 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:47:00 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:47:00 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9460824.inpcrd INFO 2017-03-19 00:47:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9460824/mobley_9460824_converted.input INFO 2017-03-19 00:47:00 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9460824/mobley_9460824_converted.cms WARNING 2017-03-19 00:47:16 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:47:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9460824/mobley_9460824_converted.inp INFO 2017-03-19 00:47:16 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9460824/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9460824/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9460824/mobley_9460824_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9460824/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -32.71345159 -32.71345159 0.00000000 0.00000000 0.00000000 0.00000000 -215.21295192 -215.21295192 coulomb total -215.20696880 -215.20745831 -0.00048951 -215.20745414 -0.00048534 -215.20731461 -0.00034581 -215.21295192 -0.00598312 coulomb-14 -182.49896720 -182.49400672 0.00496048 0.00000000 182.49896720 -182.49397276 0.00499444 0.00000000 182.49896720 proper 70.04350720 70.04333962 -0.00016758 70.04333566 -0.00017154 70.04324528 -0.00026192 70.04333984 -0.00016736 vdw (SR) 0.00000000 -10.22595180 -10.22595180 0.00000000 0.00000000 0.00000000 0.00000000 -9.29509072 -9.29509072 vdw total -9.29517440 -9.29521425 -0.00003985 -9.29521457 -0.00004017 -9.29517599 -0.00000159 -9.29509072 0.00008368 vdw-14 0.93094000 0.93073755 -0.00020245 0.00000000 -0.93094000 0.93076569 -0.00017431 0.00000000 -0.93094000 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 10.65079040 10.65060840 -0.00018200 10.65060840 -0.00018200 10.65053438 -0.00025602 10.65049752 -0.00029288 bond 7.99269520 7.99254215 -0.00015305 7.99254207 -0.00015313 7.99319674 0.00050154 7.99252784 -0.00016736 bonded 88.68699280 88.68649017 -0.00050263 88.68648612 -0.00050668 88.68697640 -0.00001640 88.68636520 -0.00062760 dihedral 70.04350720 70.04333962 -0.00016758 70.04333566 -0.00017154 70.04324528 -0.00026192 70.04333984 -0.00016736 nonbonded -224.50214320 -224.50267256 -0.00052936 -224.50267038 -0.00052718 -224.50249060 -0.00034740 -224.50804264 -0.00589944 potential -135.81515040 -135.81618239 -0.00103199 -135.81618385 -0.00103345 -135.81573867 -0.00058827 -135.82163560 -0.00648520 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -135.81515040 Difference in potential energy from amber=>gromacs conversion: -0.00103199 Difference in potential energy from amber=>lammps conversion: -0.00103345 Difference in potential energy from amber=>desmond conversion: -0.00058827 Difference in potential energy from amber=>charmm conversion: -0.00648520 ======================================================================= INFO 2017-03-19 00:47:16 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9460824.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9460824.inpcrd') INFO 2017-03-19 00:47:16 Beginning InterMol conversion INFO 2017-03-19 00:47:16 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:47:16 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:47:16 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9478823.inpcrd INFO 2017-03-19 00:47:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9478823/mobley_9478823_converted.input INFO 2017-03-19 00:47:16 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9478823/mobley_9478823_converted.cms WARNING 2017-03-19 00:47:32 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:47:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9478823/mobley_9478823_converted.inp INFO 2017-03-19 00:47:32 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9478823/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9478823/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9478823/mobley_9478823_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9478823/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.33521938 0.33521938 0.00000000 0.00000000 0.00000000 0.00000000 -14.04798920 -14.04798920 coulomb total -14.04861680 -14.05508735 -0.00647055 -14.05508736 -0.00647056 -14.05517051 -0.00655371 -14.04798920 0.00062760 coulomb-14 -14.39170480 -14.39030673 0.00139807 0.00000000 14.39170480 -14.39031077 0.00139403 0.00000000 14.39170480 improper 0.00000000 0.00002862 0.00002862 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00027041 -0.00014799 0.00029898 -0.00011942 0.00029727 -0.00012113 0.00025104 -0.00016736 vdw (SR) 0.00000000 23.93254342 23.93254342 0.00000000 0.00000000 0.00000000 0.00000000 46.03203328 46.03203328 vdw total 46.03194960 46.03170751 -0.00024209 46.03170693 -0.00024267 46.03260979 0.00066019 46.03203328 0.00008368 vdw-14 22.09905120 22.09916409 0.00011289 0.00000000 -22.09905120 22.09924333 0.00019213 0.00000000 -22.09905120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.94349200 0.94355543 0.00006343 0.94355543 0.00006343 0.94351131 0.00001931 0.94353384 0.00004184 bond 1.85936960 1.85950180 0.00013220 1.85950181 0.00013221 1.85933639 -0.00003321 1.85949512 0.00012552 bonded 2.80328000 2.80335625 0.00007625 2.80335623 0.00007623 2.80314497 -0.00013503 2.80332184 0.00004184 dihedral 0.00041840 0.00029902 -0.00011938 0.00029898 -0.00011942 0.00029727 -0.00012113 0.00029288 -0.00012552 nonbonded 31.98333280 31.97662016 -0.00671264 31.97662041 -0.00671239 31.97743929 -0.00589351 31.98404408 0.00071128 potential 34.78661280 34.77997642 -0.00663638 34.77997698 -0.00663582 34.78053625 -0.00607655 34.78736592 0.00075312 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 34.78661280 Difference in potential energy from amber=>gromacs conversion: -0.00663638 Difference in potential energy from amber=>lammps conversion: -0.00663582 Difference in potential energy from amber=>desmond conversion: -0.00607655 Difference in potential energy from amber=>charmm conversion: 0.00075312 ======================================================================= INFO 2017-03-19 00:47:32 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9478823.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9478823.inpcrd') INFO 2017-03-19 00:47:32 Beginning InterMol conversion INFO 2017-03-19 00:47:32 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:47:32 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:47:32 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9507933.inpcrd INFO 2017-03-19 00:47:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9507933/mobley_9507933_converted.input INFO 2017-03-19 00:47:32 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9507933/mobley_9507933_converted.cms WARNING 2017-03-19 00:47:48 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:47:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9507933/mobley_9507933_converted.inp INFO 2017-03-19 00:47:48 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9507933/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9507933/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9507933/mobley_9507933_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9507933/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -3.12639948 -3.12639948 0.00000000 0.00000000 0.00000000 0.00000000 -99.45999784 -99.45999784 coulomb total -99.44740400 -99.45070040 -0.00329640 -99.45070099 -0.00329699 -99.45073502 -0.00333102 -99.45999784 -0.01259384 coulomb-14 -96.32111920 -96.32430092 -0.00318172 0.00000000 96.32111920 -96.32429402 -0.00317482 0.00000000 96.32111920 improper 0.00000000 0.00019675 0.00019675 0.00000000 0.00000000 0.00000000 0.00000000 0.00020920 0.00020920 proper 0.00167360 0.00146184 -0.00021176 0.00165855 -0.00001505 0.00166191 -0.00001169 0.00146440 -0.00020920 vdw (SR) 0.00000000 -2.37962644 -2.37962644 0.00000000 0.00000000 0.00000000 0.00000000 20.90656936 20.90656936 vdw total 20.90661120 20.90659804 -0.00001316 20.90659823 -0.00001297 20.90692539 0.00031419 20.90656936 -0.00004184 vdw-14 23.28605200 23.28622448 0.00017248 0.00000000 -23.28605200 23.28656500 0.00051300 0.00000000 -23.28605200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.94681520 1.94665294 -0.00016226 1.94665294 -0.00016226 1.94663291 -0.00018229 1.94664784 -0.00016736 bond 2.14597360 2.14598606 0.00001246 2.14598607 0.00001247 2.14556126 -0.00041234 2.14597360 0.00000000 bonded 4.09446240 4.09429759 -0.00016481 4.09429757 -0.00016483 4.09385608 -0.00060632 4.09429504 -0.00016736 dihedral 0.00167360 0.00165860 -0.00001500 0.00165855 -0.00001505 0.00166191 -0.00001169 0.00167360 0.00000000 nonbonded -78.54079280 -78.54410236 -0.00330956 -78.54410234 -0.00330954 -78.54380963 -0.00301683 -78.55342848 -0.01263568 potential -74.44633040 -74.44980477 -0.00347437 -74.44980312 -0.00347272 -74.45000479 -0.00367439 -74.45909160 -0.01276120 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -74.44633040 Difference in potential energy from amber=>gromacs conversion: -0.00347437 Difference in potential energy from amber=>lammps conversion: -0.00347272 Difference in potential energy from amber=>desmond conversion: -0.00367439 Difference in potential energy from amber=>charmm conversion: -0.01276120 ======================================================================= INFO 2017-03-19 00:47:48 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9507933.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9507933.inpcrd') INFO 2017-03-19 00:47:48 Beginning InterMol conversion INFO 2017-03-19 00:47:48 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:47:48 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9510785.inpcrd INFO 2017-03-19 00:47:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9510785/mobley_9510785_converted.input INFO 2017-03-19 00:47:49 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9510785/mobley_9510785_converted.cms INFO 2017-03-19 00:48:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9510785/mobley_9510785_converted.rst7 WARNING 2017-03-19 00:48:04 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:48:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9510785/mobley_9510785_converted.inp INFO 2017-03-19 00:48:04 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9510785/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9510785/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9510785/mobley_9510785_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_9510785/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9510785/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.41207733 0.41207733 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 3.75405216 3.75405216 coulomb total 3.75388480 3.75396438 0.00007958 3.75396434 0.00007954 3.75397660 0.00009180 3.75388480 0.00000000 3.75405216 0.00016736 coulomb-14 3.34176080 3.34188705 0.00012625 0.00000000 -3.34176080 3.34188858 0.00012778 3.34176080 0.00000000 0.00000000 -3.34176080 improper 0.00000000 0.00034496 0.00034496 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00033472 0.00033472 proper 33.47576560 33.47544639 -0.00031921 33.47579112 0.00002552 33.47578367 0.00001807 33.47576560 0.00000000 33.47543088 -0.00033472 vdw (SR) 0.00000000 -11.44384417 -11.44384417 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 31.51192152 31.51192152 vdw total 31.51221440 31.51191502 -0.00029938 31.51191524 -0.00029916 31.51211390 -0.00010050 31.51221440 0.00000000 31.51192152 -0.00029288 vdw-14 42.95587280 42.95575919 -0.00011361 0.00000000 -42.95587280 42.95594937 0.00007657 42.95587280 0.00000000 0.00000000 -42.95587280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 3.70702400 3.70706209 0.00003809 3.70706207 0.00003807 3.70705521 0.00003121 3.70702400 0.00000000 3.70710768 0.00008368 bond 4.40533360 4.40550074 0.00016714 4.40550054 0.00016694 4.40524197 -0.00009163 4.40533360 0.00000000 4.40550096 0.00016736 bonded 41.58812320 41.58835418 0.00023098 41.58835374 0.00023054 41.58808085 -0.00004235 41.58812320 0.00000000 41.58837424 0.00025104 dihedral 33.47576560 33.47579135 0.00002575 33.47579112 0.00002552 33.47578367 0.00001807 33.47576560 0.00000000 33.47576560 -0.00000000 nonbonded 35.26609920 35.26587940 -0.00021980 35.26587954 -0.00021966 35.26609050 -0.00000870 35.26609920 0.00000000 35.26597368 -0.00012552 potential 76.85422240 76.85423359 0.00001119 76.85423495 0.00001255 76.85395044 -0.00027196 76.85422240 0.00000000 76.85438976 0.00016736 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 76.85422240 Difference in potential energy from amber=>gromacs conversion: 0.00001119 Difference in potential energy from amber=>lammps conversion: 0.00001255 Difference in potential energy from amber=>desmond conversion: -0.00027196 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00016736 ======================================================================= INFO 2017-03-19 00:48:04 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9510785.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9510785.inpcrd') INFO 2017-03-19 00:48:04 Beginning InterMol conversion INFO 2017-03-19 00:48:04 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:48:05 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:48:05 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_951560.inpcrd INFO 2017-03-19 00:48:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_951560/mobley_951560_converted.input INFO 2017-03-19 00:48:05 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_951560/mobley_951560_converted.cms WARNING 2017-03-19 00:48:20 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:48:20 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_951560/mobley_951560_converted.inp INFO 2017-03-19 00:48:20 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_951560/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_951560/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_951560/mobley_951560_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_951560/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -118.41061385 -118.41061385 0.00000000 0.00000000 0.00000000 0.00000000 233.75539392 233.75539392 coulomb total 233.64083600 233.64869148 0.00785548 233.64868937 0.00785337 233.64875296 0.00791696 233.75539392 0.11455792 coulomb-14 352.04719920 352.05930533 0.01210613 0.00000000 -352.04719920 352.05930016 0.01210096 0.00000000 -352.04719920 proper 12.54028480 12.54009785 -0.00018695 12.54009778 -0.00018702 12.54012091 -0.00016389 12.54024296 -0.00004184 vdw (SR) 0.00000000 -1.48465811 -1.48465811 0.00000000 0.00000000 0.00000000 0.00000000 11.89113720 11.89113720 vdw total 11.89134640 11.89116828 -0.00017812 11.89116858 -0.00017782 11.89119173 -0.00015467 11.89113720 -0.00020920 vdw-14 13.37582960 13.37582638 -0.00000322 0.00000000 -13.37582960 13.37585090 0.00002130 0.00000000 -13.37582960 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.50370560 2.50377779 0.00007219 2.50377782 0.00007222 2.50376423 0.00005863 2.50370560 0.00000000 bond 0.44141200 0.44151061 0.00009861 0.44151062 0.00009862 0.44164246 0.00023046 0.44149568 0.00008368 bonded 15.48540240 15.48538625 -0.00001615 15.48538621 -0.00001619 15.48552761 0.00012521 15.48544424 0.00004184 dihedral 12.54028480 12.54009785 -0.00018695 12.54009778 -0.00018702 12.54012091 -0.00016389 12.54024296 -0.00004184 nonbonded 245.53218240 245.53985976 0.00767736 245.53985586 0.00767346 245.53994469 0.00776229 245.64653112 0.11434872 potential 261.01758480 261.02524601 0.00766121 261.02524570 0.00766090 261.02543440 0.00784960 261.13197536 0.11439056 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 261.01758480 Difference in potential energy from amber=>gromacs conversion: 0.00766121 Difference in potential energy from amber=>lammps conversion: 0.00766090 Difference in potential energy from amber=>desmond conversion: 0.00784960 Difference in potential energy from amber=>charmm conversion: 0.11439056 ======================================================================= INFO 2017-03-19 00:48:20 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_951560.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_951560.inpcrd') INFO 2017-03-19 00:48:21 Beginning InterMol conversion INFO 2017-03-19 00:48:21 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:48:21 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:48:21 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9534740.inpcrd INFO 2017-03-19 00:48:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9534740/mobley_9534740_converted.input INFO 2017-03-19 00:48:21 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9534740/mobley_9534740_converted.cms WARNING 2017-03-19 00:48:36 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:48:36 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9534740/mobley_9534740_converted.inp INFO 2017-03-19 00:48:36 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9534740/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9534740/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9534740/mobley_9534740_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9534740/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -435.53372433 -435.53372433 0.00000000 0.00000000 0.00000000 0.00000000 114.95251304 114.95251304 coulomb total 114.89766080 114.90174696 0.00408616 114.90174438 0.00408358 114.90278620 0.00512540 114.95251304 0.05485224 coulomb-14 550.41649680 550.43547129 0.01897449 0.00000000 -550.41649680 550.43566370 0.01916690 0.00000000 -550.41649680 proper 55.85891040 55.85889227 -0.00001813 55.85889366 -0.00001674 55.85894052 0.00003012 55.85945432 0.00054392 vdw (SR) 0.00000000 -7.31315136 -7.31315136 0.00000000 0.00000000 0.00000000 0.00000000 11.19182344 11.19182344 vdw total 11.19178160 11.19158060 -0.00020100 11.19158077 -0.00020083 11.19156684 -0.00021476 11.19182344 0.00004184 vdw-14 18.50499520 18.50473197 -0.00026323 0.00000000 -18.50499520 18.50471688 -0.00027832 0.00000000 -18.50499520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.63294320 4.63280464 -0.00013856 4.63280471 -0.00013849 4.63278291 -0.00016029 4.63269216 -0.00025104 bond 0.95395200 0.95392695 -0.00002505 0.95392694 -0.00002506 0.95409842 0.00014642 0.95391016 -0.00004184 bonded 61.44580560 61.44562386 -0.00018174 61.44562531 -0.00018029 61.44582186 0.00001626 61.44605664 0.00025104 dihedral 55.85891040 55.85889227 -0.00001813 55.85889366 -0.00001674 55.85894052 0.00003012 55.85945432 0.00054392 nonbonded 126.08944240 126.09332757 0.00388517 126.09332515 0.00388275 126.09435304 0.00491064 126.14433648 0.05489408 potential 187.53524800 187.53895143 0.00370343 187.53895084 0.00370284 187.54009014 0.00484214 187.59039312 0.05514512 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 187.53524800 Difference in potential energy from amber=>gromacs conversion: 0.00370343 Difference in potential energy from amber=>lammps conversion: 0.00370284 Difference in potential energy from amber=>desmond conversion: 0.00484214 Difference in potential energy from amber=>charmm conversion: 0.05514512 ======================================================================= INFO 2017-03-19 00:48:36 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9534740.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9534740.inpcrd') INFO 2017-03-19 00:48:37 Beginning InterMol conversion INFO 2017-03-19 00:48:37 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:48:37 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:48:37 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9557440.inpcrd INFO 2017-03-19 00:48:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9557440/mobley_9557440_converted.input INFO 2017-03-19 00:48:37 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9557440/mobley_9557440_converted.cms WARNING 2017-03-19 00:48:53 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:48:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9557440/mobley_9557440_converted.inp INFO 2017-03-19 00:48:53 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9557440/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9557440/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9557440/mobley_9557440_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9557440/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 234.97215974 234.97215974 0.00000000 0.00000000 0.00000000 0.00000000 -634.07172752 -634.07172752 coulomb total -633.67893360 -633.70335396 -0.02442036 -633.70332632 -0.02439272 -633.70319996 -0.02426636 -634.07172752 -0.39279392 coulomb-14 -868.64526080 -868.67551370 -0.03025290 0.00000000 868.64526080 -868.67525590 -0.02999510 0.00000000 868.64526080 improper 0.00000000 0.00009262 0.00009262 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 50.20841840 50.20840596 -0.00001244 50.20849790 0.00007950 50.20849664 0.00007824 50.20841840 0.00000000 vdw (SR) 0.00000000 -1.94676064 -1.94676064 0.00000000 0.00000000 0.00000000 0.00000000 14.58082160 14.58082160 vdw total 14.58082160 14.58085184 0.00003024 14.58085172 0.00003012 14.58085704 0.00003544 14.58082160 0.00000000 vdw-14 16.52763680 16.52761248 -0.00002432 0.00000000 -16.52763680 16.52761199 -0.00002481 0.00000000 -16.52763680 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 10.29933440 10.29944744 0.00011304 10.29944737 0.00011297 10.30049195 0.00115755 10.29941808 0.00008368 bond 19.17903760 19.17895307 -0.00008453 19.17895308 -0.00008452 19.17996938 0.00093178 19.17895392 -0.00008368 bonded 79.68679040 79.68689908 0.00010868 79.68689835 0.00010795 79.68895796 0.00216756 79.68687408 0.00008368 dihedral 50.20841840 50.20849857 0.00008017 50.20849790 0.00007950 50.20849664 0.00007824 50.20850208 0.00008368 nonbonded -619.09811200 -619.12250212 -0.02439012 -619.12250472 -0.02439272 -619.12234292 -0.02423092 -619.49090592 -0.39279392 potential -539.41132160 -539.43560304 -0.02428144 -539.43558880 -0.02426720 -539.43345914 -0.02213754 -539.80403184 -0.39271024 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -539.41132160 Difference in potential energy from amber=>gromacs conversion: -0.02428144 Difference in potential energy from amber=>lammps conversion: -0.02426720 Difference in potential energy from amber=>desmond conversion: -0.02213754 Difference in potential energy from amber=>charmm conversion: -0.39271024 ======================================================================= INFO 2017-03-19 00:48:53 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9557440.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9557440.inpcrd') INFO 2017-03-19 00:48:53 Beginning InterMol conversion INFO 2017-03-19 00:48:53 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:48:53 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:48:53 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9565165.inpcrd INFO 2017-03-19 00:48:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9565165/mobley_9565165_converted.input INFO 2017-03-19 00:48:53 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9565165/mobley_9565165_converted.cms WARNING 2017-03-19 00:49:09 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:49:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9565165/mobley_9565165_converted.inp INFO 2017-03-19 00:49:09 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9565165/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9565165/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9565165/mobley_9565165_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9565165/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -5.29975952 -5.29975952 0.00000000 0.00000000 0.00000000 0.00000000 0.62257920 0.62257920 coulomb total 0.58910720 0.59623495 0.00712775 0.59623494 0.00712774 0.59616414 0.00705694 0.62257920 0.03347200 coulomb-14 5.89609280 5.89599447 -0.00009833 0.00000000 -5.89609280 5.89596653 -0.00012627 0.00000000 -5.89609280 improper 0.00000000 0.00013229 0.00013229 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 proper 0.00125520 0.00100238 -0.00025282 0.00113469 -0.00012051 0.00111974 -0.00013546 0.00100416 -0.00025104 vdw (SR) 0.00000000 -6.27941362 -6.27941362 0.00000000 0.00000000 0.00000000 0.00000000 23.32851960 23.32851960 vdw total 23.32872880 23.32857415 -0.00015465 23.32857399 -0.00015481 23.32852228 -0.00020652 23.32851960 -0.00020920 vdw-14 29.60807600 29.60798777 -0.00008823 0.00000000 -29.60807600 29.60793914 -0.00013686 0.00000000 -29.60807600 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 79.40813600 79.40804382 -0.00009218 79.40804395 -0.00009205 79.40845273 0.00031673 79.40796864 -0.00016736 bond 6.34419920 6.34418154 -0.00001766 6.34418163 -0.00001757 6.34444350 0.00024430 6.34419920 0.00000000 bonded 85.75359040 85.75336002 -0.00023038 85.75336027 -0.00023013 85.75401597 0.00042557 85.75329752 -0.00029288 dihedral 0.00125520 0.00113467 -0.00012053 0.00113469 -0.00012051 0.00111974 -0.00013546 0.00112968 -0.00012552 nonbonded 23.91783600 23.92480910 0.00697310 23.92480905 0.00697305 23.92468642 0.00685042 23.95109880 0.03326280 potential 109.67142640 109.67816912 0.00674272 109.67817101 0.00674461 109.67858146 0.00715506 109.70439632 0.03296992 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 109.67142640 Difference in potential energy from amber=>gromacs conversion: 0.00674272 Difference in potential energy from amber=>lammps conversion: 0.00674461 Difference in potential energy from amber=>desmond conversion: 0.00715506 Difference in potential energy from amber=>charmm conversion: 0.03296992 ======================================================================= INFO 2017-03-19 00:49:09 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9565165.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9565165.inpcrd') INFO 2017-03-19 00:49:09 Beginning InterMol conversion INFO 2017-03-19 00:49:09 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:49:09 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:49:09 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9571888.inpcrd INFO 2017-03-19 00:49:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9571888/mobley_9571888_converted.input INFO 2017-03-19 00:49:09 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9571888/mobley_9571888_converted.cms WARNING 2017-03-19 00:49:25 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:49:25 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9571888/mobley_9571888_converted.inp INFO 2017-03-19 00:49:25 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9571888/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9571888/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9571888/mobley_9571888_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9571888/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -41.45184396 -41.45184396 0.00000000 0.00000000 0.00000000 0.00000000 -65.88846048 -65.88846048 coulomb total -65.77582720 -65.77806154 -0.00223434 -65.77806146 -0.00223426 -65.77812271 -0.00229551 -65.88846048 -0.11263328 coulomb-14 -24.32535760 -24.32621758 -0.00085998 0.00000000 24.32535760 -24.32629277 -0.00093517 0.00000000 24.32535760 improper 0.00000000 0.00907668 0.00907668 0.00000000 0.00000000 0.00000000 0.00000000 0.00907928 0.00907928 proper 58.07810400 58.06902682 -0.00907718 58.07810400 0.00000000 58.07815839 0.00005439 58.06839712 -0.00970688 vdw (SR) 0.00000000 -17.51881288 -17.51881288 0.00000000 0.00000000 0.00000000 0.00000000 7.31886200 7.31886200 vdw total 7.31865280 7.31866506 0.00001226 7.31866535 0.00001255 7.31860096 -0.00005184 7.31886200 0.00020920 vdw-14 24.83747920 24.83747794 -0.00000126 0.00000000 -24.83747920 24.83730858 -0.00017062 0.00000000 -24.83747920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 174.82551120 174.82540551 -0.00010569 174.82540660 -0.00010460 174.82521204 -0.00029916 174.82513464 -0.00037656 bond 30.65867840 30.65877711 0.00009871 30.65877714 0.00009874 30.65789511 -0.00078329 30.65876208 0.00008368 bonded 263.56229360 263.56228612 -0.00000748 263.56228774 -0.00000586 263.56126555 -0.00102805 263.56137312 -0.00092048 dihedral 58.07810400 58.07810350 -0.00000050 58.07810400 0.00000000 58.07815839 0.00005439 58.07747640 -0.00062760 nonbonded -58.45717440 -58.45939648 -0.00222208 -58.45939610 -0.00222170 -58.45952175 -0.00234735 -58.56959848 -0.11242408 potential 205.10511920 205.10288963 -0.00222957 205.10288913 -0.00223007 205.10138707 -0.00373213 204.99181648 -0.11330272 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 205.10511920 Difference in potential energy from amber=>gromacs conversion: -0.00222957 Difference in potential energy from amber=>lammps conversion: -0.00223007 Difference in potential energy from amber=>desmond conversion: -0.00373213 Difference in potential energy from amber=>charmm conversion: -0.11330272 ======================================================================= INFO 2017-03-19 00:49:25 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9571888.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9571888.inpcrd') INFO 2017-03-19 00:49:25 Beginning InterMol conversion INFO 2017-03-19 00:49:25 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:49:25 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:49:25 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9617923.inpcrd INFO 2017-03-19 00:49:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9617923/mobley_9617923_converted.input INFO 2017-03-19 00:49:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9617923/mobley_9617923_converted.cms WARNING 2017-03-19 00:49:41 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:49:41 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9617923/mobley_9617923_converted.inp INFO 2017-03-19 00:49:41 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9617923/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9617923/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9617923/mobley_9617923_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9617923/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -1.37289572 -1.37289572 0.00000000 0.00000000 0.00000000 0.00000000 -60.21102352 -60.21102352 coulomb total -60.22909840 -60.22760039 0.00149801 -60.22760053 0.00149787 -60.22760794 0.00149046 -60.21102352 0.01807488 coulomb-14 -58.84921520 -58.85470467 -0.00548947 0.00000000 58.84921520 -58.85473682 -0.00552162 0.00000000 58.84921520 improper 0.00000000 0.00003048 0.00003048 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 22.73209040 22.73187181 -0.00021859 22.73190379 -0.00018661 22.73189547 -0.00019493 22.73188120 -0.00020920 vdw (SR) 0.00000000 -4.41923599 -4.41923599 0.00000000 0.00000000 0.00000000 0.00000000 11.18261864 11.18261864 vdw total 11.18257680 11.18240175 -0.00017505 11.18240191 -0.00017489 11.18239116 -0.00018564 11.18261864 0.00004184 vdw-14 15.60171760 15.60163774 -0.00007986 0.00000000 -15.60171760 15.60162836 -0.00008924 0.00000000 -15.60171760 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.52462560 2.52476223 0.00013663 2.52476225 0.00013665 2.52490420 0.00027860 2.52470928 0.00008368 bond 1.82380560 1.82396613 0.00016053 1.82396614 0.00016054 1.82396367 0.00015807 1.82397296 0.00016736 bonded 27.08052160 27.08063065 0.00010905 27.08063218 0.00011058 27.08076333 0.00024173 27.08060528 0.00008368 dihedral 22.73209040 22.73190229 -0.00018811 22.73190379 -0.00018661 22.73189547 -0.00019493 22.73192304 -0.00016736 nonbonded -49.04652160 -49.04519864 0.00132296 -49.04519946 0.00132214 -49.04521679 0.00130481 -49.02840488 0.01811672 potential -21.96600000 -21.96456798 0.00143202 -21.96456572 0.00143428 -21.96458376 0.00141624 -21.94784144 0.01815856 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -21.96600000 Difference in potential energy from amber=>gromacs conversion: 0.00143202 Difference in potential energy from amber=>lammps conversion: 0.00143428 Difference in potential energy from amber=>desmond conversion: 0.00141624 Difference in potential energy from amber=>charmm conversion: 0.01815856 ======================================================================= INFO 2017-03-19 00:49:41 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9617923.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9617923.inpcrd') INFO 2017-03-19 00:49:41 Beginning InterMol conversion INFO 2017-03-19 00:49:41 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:49:42 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:49:42 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9624458.inpcrd INFO 2017-03-19 00:49:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9624458/mobley_9624458_converted.input INFO 2017-03-19 00:49:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9624458/mobley_9624458_converted.cms WARNING 2017-03-19 00:49:57 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:49:57 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9624458/mobley_9624458_converted.inp INFO 2017-03-19 00:49:57 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9624458/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9624458/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9624458/mobley_9624458_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9624458/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -2.22164743 -2.22164743 0.00000000 0.00000000 0.00000000 0.00000000 -4.24667632 -4.24667632 coulomb total -4.23546320 -4.23543079 0.00003241 -4.23543056 0.00003264 -4.23542679 0.00003641 -4.24667632 -0.01121312 coulomb-14 -2.01375920 -2.01378336 -0.00002416 0.00000000 2.01375920 -2.01379416 -0.00003496 0.00000000 2.01375920 proper 3.12419280 3.12427767 0.00008487 3.12427765 0.00008485 3.12428693 0.00009413 3.12427648 0.00008368 vdw (SR) 0.00000000 -0.86447705 -0.86447705 0.00000000 0.00000000 0.00000000 0.00000000 1.00754904 1.00754904 vdw total 1.00750720 1.00751532 0.00000812 1.00751536 0.00000816 1.00759364 0.00008644 1.00754904 0.00004184 vdw-14 1.87192160 1.87199237 0.00007077 0.00000000 -1.87192160 1.87205843 0.00013683 0.00000000 -1.87192160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.51118880 4.51115347 -0.00003533 4.51115365 -0.00003515 4.51109947 -0.00008933 4.51123064 0.00004184 bond 0.39371440 0.39389338 0.00017898 0.39389337 0.00017897 0.39395372 0.00023932 0.39388176 0.00016736 bonded 8.02909600 8.02932452 0.00022852 8.02932468 0.00022868 8.02934012 0.00024412 8.02938888 0.00029288 dihedral 3.12419280 3.12427767 0.00008487 3.12427765 0.00008485 3.12428693 0.00009413 3.12427648 0.00008368 nonbonded -3.22795600 -3.22791546 0.00004054 -3.22791537 0.00004063 -3.22783315 0.00012285 -3.23912728 -0.01117128 potential 4.80114000 4.80140905 0.00026905 4.80140903 0.00026903 4.80147405 0.00033405 4.79030344 -0.01083656 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 4.80114000 Difference in potential energy from amber=>gromacs conversion: 0.00026905 Difference in potential energy from amber=>lammps conversion: 0.00026903 Difference in potential energy from amber=>desmond conversion: 0.00033405 Difference in potential energy from amber=>charmm conversion: -0.01083656 ======================================================================= INFO 2017-03-19 00:49:57 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9624458.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9624458.inpcrd') INFO 2017-03-19 00:49:58 Beginning InterMol conversion INFO 2017-03-19 00:49:58 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:49:58 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:49:58 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9626434.inpcrd INFO 2017-03-19 00:49:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9626434/mobley_9626434_converted.input INFO 2017-03-19 00:49:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9626434/mobley_9626434_converted.cms WARNING 2017-03-19 00:50:13 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:50:13 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9626434/mobley_9626434_converted.inp INFO 2017-03-19 00:50:13 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9626434/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9626434/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9626434/mobley_9626434_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9626434/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -54.40139060 -54.40139060 0.00000000 0.00000000 0.00000000 0.00000000 42.64625680 42.64625680 coulomb total 42.66006400 42.65809149 -0.00197251 42.65808915 -0.00197485 42.65821132 -0.00185268 42.64625680 -0.01380720 coulomb-14 97.05415600 97.05948209 0.00532609 0.00000000 -97.05415600 97.05963578 0.00547978 0.00000000 -97.05415600 proper 8.80773840 8.80777883 0.00004043 8.80777898 0.00004058 8.80778618 0.00004778 8.80778024 0.00004184 vdw (SR) 0.00000000 -1.86763197 -1.86763197 0.00000000 0.00000000 0.00000000 0.00000000 3.39418632 3.39418632 vdw total 3.39406080 3.39409050 0.00002970 3.39409055 0.00002975 3.39419044 0.00012964 3.39418632 0.00012552 vdw-14 5.26179840 5.26172248 -0.00007592 0.00000000 -5.26179840 5.26182999 0.00003159 0.00000000 -5.26179840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.04976560 1.04975663 -0.00000897 1.04975665 -0.00000895 1.04958640 -0.00017920 1.04976560 0.00000000 bond 1.80330400 1.80320277 -0.00010123 1.80320279 -0.00010121 1.80309748 -0.00020652 1.80322032 -0.00008368 bonded 11.66080800 11.66073823 -0.00006977 11.66073842 -0.00006958 11.66047006 -0.00033794 11.66076616 -0.00004184 dihedral 8.80773840 8.80777883 0.00004043 8.80777898 0.00004058 8.80778618 0.00004778 8.80778024 0.00004184 nonbonded 46.05412480 46.05218200 -0.00194280 46.05218342 -0.00194138 46.05240177 -0.00172303 46.04044312 -0.01368168 potential 57.71493280 57.71292023 -0.00201257 57.71292030 -0.00201250 57.71283327 -0.00209953 57.70116744 -0.01376536 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 57.71493280 Difference in potential energy from amber=>gromacs conversion: -0.00201257 Difference in potential energy from amber=>lammps conversion: -0.00201250 Difference in potential energy from amber=>desmond conversion: -0.00209953 Difference in potential energy from amber=>charmm conversion: -0.01376536 ======================================================================= INFO 2017-03-19 00:50:13 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9626434.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9626434.inpcrd') INFO 2017-03-19 00:50:14 Beginning InterMol conversion INFO 2017-03-19 00:50:14 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:50:14 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:50:14 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9653690.inpcrd INFO 2017-03-19 00:50:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9653690/mobley_9653690_converted.input INFO 2017-03-19 00:50:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9653690/mobley_9653690_converted.cms WARNING 2017-03-19 00:50:29 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:50:29 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9653690/mobley_9653690_converted.inp INFO 2017-03-19 00:50:29 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9653690/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9653690/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9653690/mobley_9653690_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9653690/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -28.63848664 -28.63848664 0.00000000 0.00000000 0.00000000 0.00000000 -40.83165600 -40.83165600 coulomb total -40.85676000 -40.85835180 -0.00159180 -40.85835118 -0.00159118 -40.85850013 -0.00174013 -40.83165600 0.02510400 coulomb-14 -12.21937200 -12.21986516 -0.00049316 0.00000000 12.21937200 -12.21986868 -0.00049668 0.00000000 12.21937200 improper 0.00000000 0.00426187 0.00426187 0.00000000 0.00000000 0.00000000 0.00000000 0.00426768 0.00426768 proper 71.84053520 71.83622967 -0.00430553 71.84051846 -0.00001674 71.84070340 0.00016820 71.83693696 -0.00359824 vdw (SR) 0.00000000 -3.39601607 -3.39601607 0.00000000 0.00000000 0.00000000 0.00000000 19.56032552 19.56032552 vdw total 19.56061840 19.56015975 -0.00045865 19.56016025 -0.00045815 19.56020338 -0.00041502 19.56032552 -0.00029288 vdw-14 22.95635280 22.95617582 -0.00017698 0.00000000 -22.95635280 22.95619326 -0.00015954 0.00000000 -22.95635280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.91201600 4.91184995 -0.00016605 4.91184990 -0.00016610 4.91194207 -0.00007393 4.91168128 -0.00033472 bond 2.38404320 2.38414575 0.00010255 2.38414575 0.00010255 2.38381878 -0.00022442 2.38412688 0.00008368 bonded 79.13659440 79.13648722 -0.00010718 79.13651411 -0.00008029 79.13646424 -0.00013016 79.13701280 0.00041840 dihedral 71.84053520 71.84049153 -0.00004367 71.84051846 -0.00001674 71.84070340 0.00016820 71.84120464 0.00066944 nonbonded -21.29614160 -21.29819205 -0.00205045 -21.29819134 -0.00204974 -21.29829674 -0.00215514 -21.27133048 0.02481112 potential 57.84045280 57.83829517 -0.00215763 57.83832314 -0.00212966 57.83805830 -0.00239450 57.86568232 0.02522952 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 57.84045280 Difference in potential energy from amber=>gromacs conversion: -0.00215763 Difference in potential energy from amber=>lammps conversion: -0.00212966 Difference in potential energy from amber=>desmond conversion: -0.00239450 Difference in potential energy from amber=>charmm conversion: 0.02522952 ======================================================================= INFO 2017-03-19 00:50:29 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9653690.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9653690.inpcrd') INFO 2017-03-19 00:50:30 Beginning InterMol conversion INFO 2017-03-19 00:50:30 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:50:30 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:50:30 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_967099.inpcrd INFO 2017-03-19 00:50:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_967099/mobley_967099_converted.input INFO 2017-03-19 00:50:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_967099/mobley_967099_converted.cms WARNING 2017-03-19 00:50:45 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:50:45 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_967099/mobley_967099_converted.inp INFO 2017-03-19 00:50:46 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_967099/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_967099/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_967099/mobley_967099_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_967099/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -50.67789006 -50.67789006 0.00000000 0.00000000 0.00000000 0.00000000 1.27063896 1.27063896 coulomb total 1.26900720 1.27338043 0.00437323 1.27338040 0.00437320 1.27346149 0.00445429 1.27063896 0.00163176 coulomb-14 51.93724720 51.95127049 0.01402329 0.00000000 -51.93724720 51.95127071 0.01402351 0.00000000 -51.93724720 proper 0.05439200 0.05454602 0.00015402 0.05454600 0.00015400 0.05455222 0.00016022 0.05455936 0.00016736 vdw (SR) 0.00000000 0.17068281 0.17068281 0.00000000 0.00000000 0.00000000 0.00000000 8.85740248 8.85740248 vdw total 8.85752800 8.85729999 -0.00022801 8.85729997 -0.00022803 8.85733961 -0.00018839 8.85740248 -0.00012552 vdw-14 8.68682080 8.68661718 -0.00020362 0.00000000 -8.68682080 8.68661675 -0.00020405 0.00000000 -8.68682080 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.63719920 1.63702213 -0.00017707 1.63702213 -0.00017707 1.63701347 -0.00018573 1.63707368 -0.00012552 bond 10.18092720 10.18100809 0.00008089 10.18100795 0.00008075 10.18201726 0.00109006 10.18101088 0.00008368 bonded 11.87251840 11.87257623 0.00005783 11.87257609 0.00005769 11.87358294 0.00106454 11.87264392 0.00012552 dihedral 0.05439200 0.05454602 0.00015402 0.05454600 0.00015400 0.05455222 0.00016022 0.05455936 0.00016736 nonbonded 10.12653520 10.13068042 0.00414522 10.13068071 0.00414551 10.13080109 0.00426589 10.12804144 0.00150624 potential 21.99905360 22.00325665 0.00420305 22.00325685 0.00420325 22.00435063 0.00529703 22.00068536 0.00163176 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 21.99905360 Difference in potential energy from amber=>gromacs conversion: 0.00420305 Difference in potential energy from amber=>lammps conversion: 0.00420325 Difference in potential energy from amber=>desmond conversion: 0.00529703 Difference in potential energy from amber=>charmm conversion: 0.00163176 ======================================================================= INFO 2017-03-19 00:50:46 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_967099.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_967099.inpcrd') INFO 2017-03-19 00:50:46 Beginning InterMol conversion INFO 2017-03-19 00:50:46 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:50:46 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:50:46 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9671033.inpcrd INFO 2017-03-19 00:50:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9671033/mobley_9671033_converted.input INFO 2017-03-19 00:50:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9671033/mobley_9671033_converted.cms WARNING 2017-03-19 00:51:02 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:51:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9671033/mobley_9671033_converted.inp INFO 2017-03-19 00:51:02 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9671033/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9671033/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9671033/mobley_9671033_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9671033/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -6.57007521 -6.57007521 0.00000000 0.00000000 0.00000000 0.00000000 -11.40186024 -11.40186024 coulomb total -11.39847120 -11.39896893 -0.00049773 -11.39896868 -0.00049748 -11.39899278 -0.00052158 -11.40186024 -0.00338904 coulomb-14 -4.82875440 -4.82889372 -0.00013932 0.00000000 4.82875440 -4.82887210 -0.00011770 0.00000000 4.82875440 proper 0.03430880 0.03414949 -0.00015931 0.03414948 -0.00015932 0.03414722 -0.00016158 0.03414144 -0.00016736 vdw (SR) 0.00000000 -1.91741083 -1.91741083 0.00000000 0.00000000 0.00000000 0.00000000 1.69602624 1.69602624 vdw total 1.69577520 1.69598620 0.00021100 1.69598620 0.00021100 1.69598886 0.00021366 1.69602624 0.00025104 vdw-14 3.61330240 3.61339703 0.00009463 0.00000000 -3.61330240 3.61339275 0.00009035 0.00000000 -3.61330240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.66562640 2.66546243 -0.00016397 2.66546243 -0.00016397 2.66510528 -0.00052112 2.66554272 -0.00008368 bond 11.35579440 11.35571470 -0.00007970 11.35571490 -0.00007950 11.35540525 -0.00038915 11.35571072 -0.00008368 bonded 14.05572960 14.05532661 -0.00040299 14.05532681 -0.00040279 14.05465775 -0.00107185 14.05539488 -0.00033472 dihedral 0.03430880 0.03414949 -0.00015931 0.03414948 -0.00015932 0.03414722 -0.00016158 0.03414144 -0.00016736 nonbonded -9.70269600 -9.70298274 -0.00028674 -9.70298260 -0.00028660 -9.70300391 -0.00030791 -9.70583400 -0.00313800 potential 4.35303360 4.35234388 -0.00068972 4.35234408 -0.00068952 4.35162100 -0.00141260 4.34960272 -0.00343088 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 4.35303360 Difference in potential energy from amber=>gromacs conversion: -0.00068972 Difference in potential energy from amber=>lammps conversion: -0.00068952 Difference in potential energy from amber=>desmond conversion: -0.00141260 Difference in potential energy from amber=>charmm conversion: -0.00343088 ======================================================================= INFO 2017-03-19 00:51:02 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9671033.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9671033.inpcrd') INFO 2017-03-19 00:51:02 Beginning InterMol conversion INFO 2017-03-19 00:51:02 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:51:02 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:51:02 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9705941.inpcrd INFO 2017-03-19 00:51:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9705941/mobley_9705941_converted.input INFO 2017-03-19 00:51:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9705941/mobley_9705941_converted.cms WARNING 2017-03-19 00:51:18 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:51:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9705941/mobley_9705941_converted.inp INFO 2017-03-19 00:51:18 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9705941/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9705941/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9705941/mobley_9705941_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9705941/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 12.47398902 12.47398902 0.00000000 0.00000000 0.00000000 0.00000000 -4.16734768 -4.16734768 coulomb total -4.18358160 -4.18402689 -0.00044529 -4.18402678 -0.00044518 -4.18408343 -0.00050183 -4.16734768 0.01623392 coulomb-14 -16.65734080 -16.65801591 -0.00067511 0.00000000 16.65734080 -16.65803476 -0.00069396 0.00000000 16.65734080 improper 0.00000000 0.00006512 0.00006512 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00041840 0.00041697 -0.00000143 0.00048229 0.00006389 0.00048381 0.00006541 0.00041840 0.00000000 vdw (SR) 0.00000000 -0.59862612 -0.59862612 0.00000000 0.00000000 0.00000000 0.00000000 -0.78663384 -0.78663384 vdw total -0.78659200 -0.78667393 -0.00008193 -0.78667392 -0.00008192 -0.78664346 -0.00005146 -0.78663384 -0.00004184 vdw-14 -0.18786160 -0.18804781 -0.00018621 0.00000000 0.18786160 -0.18801532 -0.00015372 0.00000000 0.18786160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 10.49514560 10.49528017 0.00013457 10.49528032 0.00013472 10.49481841 -0.00032719 10.49535480 0.00020920 bond 2.24136880 2.24156606 0.00019726 2.24156608 0.00019728 2.24215966 0.00079086 2.24157800 0.00020920 bonded 12.73693280 12.73732832 0.00039552 12.73732869 0.00039589 12.73746188 0.00052908 12.73743488 0.00050208 dihedral 0.00041840 0.00048209 0.00006369 0.00048229 0.00006389 0.00048381 0.00006541 0.00050208 0.00008368 nonbonded -4.97017360 -4.97070081 -0.00052721 -4.97070078 -0.00052718 -4.97072689 -0.00055329 -4.95398152 0.01619208 potential 7.76675920 7.76662750 -0.00013170 7.76662782 -0.00013138 7.76670067 -0.00005853 7.78341152 0.01665232 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 7.76675920 Difference in potential energy from amber=>gromacs conversion: -0.00013170 Difference in potential energy from amber=>lammps conversion: -0.00013138 Difference in potential energy from amber=>desmond conversion: -0.00005853 Difference in potential energy from amber=>charmm conversion: 0.01665232 ======================================================================= INFO 2017-03-19 00:51:18 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9705941.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9705941.inpcrd') INFO 2017-03-19 00:51:18 Beginning InterMol conversion INFO 2017-03-19 00:51:18 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:51:18 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9717937.inpcrd INFO 2017-03-19 00:51:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9717937/mobley_9717937_converted.input INFO 2017-03-19 00:51:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9717937/mobley_9717937_converted.cms INFO 2017-03-19 00:51:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9717937/mobley_9717937_converted.rst7 WARNING 2017-03-19 00:51:34 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:51:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9717937/mobley_9717937_converted.inp INFO 2017-03-19 00:51:34 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9717937/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9717937/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9717937/mobley_9717937_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_9717937/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9717937/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -6.08305317 -6.08305317 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 10.59635656 10.59635656 coulomb total 10.59179600 10.59880310 0.00700710 10.59880294 0.00700694 10.59881709 0.00702109 10.59179600 0.00000000 10.59635656 0.00456056 coulomb-14 16.67993440 16.68185627 0.00192187 0.00000000 -16.67993440 16.68184126 0.00190686 16.67993440 0.00000000 0.00000000 -16.67993440 improper 0.00000000 0.00023144 0.00023144 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00025104 0.00025104 proper 33.47409200 33.47385668 -0.00023532 33.47408823 -0.00000377 33.47407614 -0.00001586 33.47409200 0.00000000 33.47384096 -0.00025104 vdw (SR) 0.00000000 -8.91703850 -8.91703850 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 25.88929496 25.88929496 vdw total 25.88933680 25.88934311 0.00000631 25.88934308 0.00000628 25.88950713 0.00017033 25.88933680 0.00000000 25.88929496 -0.00004184 vdw-14 34.80627760 34.80638161 0.00010401 0.00000000 -34.80627760 34.80654379 0.00026619 34.80627760 0.00000000 0.00000000 -34.80627760 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.38864560 2.38845603 -0.00018957 2.38845602 -0.00018958 2.38825873 -0.00038687 2.38864560 0.00000000 2.38847824 -0.00016736 bond 3.75806880 3.75789155 -0.00017725 3.75789157 -0.00017723 3.75739062 -0.00067818 3.75806880 0.00000000 3.75790144 -0.00016736 bonded 39.62080640 39.62043570 -0.00037070 39.62043582 -0.00037058 39.61972548 -0.00108092 39.62080640 0.00000000 39.62047168 -0.00033472 dihedral 33.47409200 33.47408812 -0.00000388 33.47408823 -0.00000377 33.47407614 -0.00001586 33.47409200 0.00000000 33.47409200 -0.00000000 nonbonded 36.48113280 36.48814621 0.00701341 36.48814602 0.00701322 36.48832422 0.00719142 36.48113280 0.00000000 36.48565152 0.00451872 potential 76.10193920 76.10858191 0.00664271 76.10858339 0.00664419 76.10792399 0.00598479 76.10193920 0.00000000 76.10608136 0.00414216 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 76.10193920 Difference in potential energy from amber=>gromacs conversion: 0.00664271 Difference in potential energy from amber=>lammps conversion: 0.00664419 Difference in potential energy from amber=>desmond conversion: 0.00598479 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00414216 ======================================================================= INFO 2017-03-19 00:51:34 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9717937.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9717937.inpcrd') INFO 2017-03-19 00:51:34 Beginning InterMol conversion INFO 2017-03-19 00:51:34 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:51:34 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:51:34 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9729792.inpcrd INFO 2017-03-19 00:51:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9729792/mobley_9729792_converted.input INFO 2017-03-19 00:51:34 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9729792/mobley_9729792_converted.cms WARNING 2017-03-19 00:51:50 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:51:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9729792/mobley_9729792_converted.inp INFO 2017-03-19 00:51:50 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9729792/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9729792/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9729792/mobley_9729792_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9729792/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -5.87008838 -5.87008838 0.00000000 0.00000000 0.00000000 0.00000000 11.15818408 11.15818408 coulomb total 11.15872800 11.15900556 0.00027756 11.15900540 0.00027740 11.15899536 0.00026736 11.15818408 -0.00054392 coulomb-14 17.02846160 17.02909394 0.00063234 0.00000000 -17.02846160 17.02911167 0.00065007 0.00000000 -17.02846160 improper 0.00000000 0.06186716 0.06186716 0.00000000 0.00000000 0.00000000 0.00000000 0.06188136 0.06188136 proper 4.64507680 4.58322063 -0.06185617 4.64508726 0.00001046 4.64485957 -0.00021723 4.58323728 -0.06183952 vdw (SR) 0.00000000 -1.41866993 -1.41866993 0.00000000 0.00000000 0.00000000 0.00000000 3.77681312 3.77681312 vdw total 3.77689680 3.77680311 -0.00009369 3.77680312 -0.00009368 3.77688957 -0.00000723 3.77681312 -0.00008368 vdw-14 5.19569120 5.19547304 -0.00021816 0.00000000 -5.19569120 5.19555915 -0.00013205 0.00000000 -5.19569120 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 32.96489920 32.96493444 0.00003524 32.96493435 0.00003515 32.96515388 0.00025468 32.96498288 0.00008368 bond 0.92717440 0.92726141 0.00008701 0.92726139 0.00008699 0.92727311 0.00009871 0.92725808 0.00008368 bonded 38.53715040 38.53728364 0.00013324 38.53728299 0.00013259 38.53728656 0.00013616 38.53735960 0.00020920 dihedral 4.64507680 4.64508779 0.00001099 4.64508726 0.00001046 4.64485957 -0.00021723 4.64511864 0.00004184 nonbonded 14.93562480 14.93580867 0.00018387 14.93580848 0.00018368 14.93588493 0.00026013 14.93499720 -0.00062760 potential 53.47277520 53.47309231 0.00031711 53.47309318 0.00031798 53.47313126 0.00035606 53.47231496 -0.00046024 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 53.47277520 Difference in potential energy from amber=>gromacs conversion: 0.00031711 Difference in potential energy from amber=>lammps conversion: 0.00031798 Difference in potential energy from amber=>desmond conversion: 0.00035606 Difference in potential energy from amber=>charmm conversion: -0.00046024 ======================================================================= INFO 2017-03-19 00:51:50 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9729792.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9729792.inpcrd') INFO 2017-03-19 00:51:50 Beginning InterMol conversion INFO 2017-03-19 00:51:50 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:51:50 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:51:50 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9733743.inpcrd INFO 2017-03-19 00:51:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9733743/mobley_9733743_converted.input INFO 2017-03-19 00:51:50 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9733743/mobley_9733743_converted.cms WARNING 2017-03-19 00:52:06 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:52:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9733743/mobley_9733743_converted.inp INFO 2017-03-19 00:52:06 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9733743/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9733743/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9733743/mobley_9733743_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9733743/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 10.55559700 10.55559700 0.00000000 0.00000000 0.00000000 0.00000000 0.17171136 0.17171136 coulomb total 0.23095680 0.21328837 -0.01766843 0.21328837 -0.01766843 0.21329660 -0.01766020 0.17171136 -0.05924544 coulomb-14 -10.33824560 -10.34230862 -0.00406302 0.00000000 10.33824560 -10.34227718 -0.00403158 0.00000000 10.33824560 proper 6.68352160 6.68369975 0.00017815 6.68369984 0.00017824 6.68369122 0.00016962 6.68368896 0.00016736 vdw (SR) 0.00000000 -1.09600067 -1.09600067 0.00000000 0.00000000 0.00000000 0.00000000 2.29279016 2.29279016 vdw total 2.29283200 2.29273206 -0.00009994 2.29273209 -0.00009991 2.29275344 -0.00007856 2.29279016 -0.00004184 vdw-14 3.38862160 3.38873273 0.00011113 0.00000000 -3.38862160 3.38875654 0.00013494 0.00000000 -3.38862160 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 21.62542240 21.62524620 -0.00017620 21.62524625 -0.00017615 21.62551997 0.00009757 21.62538056 -0.00004184 bond 2.34513200 2.34531804 0.00018604 2.34531806 0.00018606 2.34499090 -0.00014110 2.34529936 0.00016736 bonded 30.65407600 30.65426399 0.00018799 30.65426415 0.00018815 30.65420209 0.00012609 30.65436888 0.00029288 dihedral 6.68352160 6.68369975 0.00017815 6.68369984 0.00017824 6.68369122 0.00016962 6.68368896 0.00016736 nonbonded 2.52378880 2.50602043 -0.01776837 2.50602044 -0.01776836 2.50605004 -0.01773876 2.46450152 -0.05928728 potential 33.17786480 33.16028442 -0.01758038 33.16028447 -0.01758033 33.16021974 -0.01764506 33.11895408 -0.05891072 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 33.17786480 Difference in potential energy from amber=>gromacs conversion: -0.01758038 Difference in potential energy from amber=>lammps conversion: -0.01758033 Difference in potential energy from amber=>desmond conversion: -0.01764506 Difference in potential energy from amber=>charmm conversion: -0.05891072 ======================================================================= INFO 2017-03-19 00:52:06 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9733743.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9733743.inpcrd') INFO 2017-03-19 00:52:06 Beginning InterMol conversion INFO 2017-03-19 00:52:06 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:52:06 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9740891.inpcrd INFO 2017-03-19 00:52:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9740891/mobley_9740891_converted.input INFO 2017-03-19 00:52:06 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9740891/mobley_9740891_converted.cms INFO 2017-03-19 00:52:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9740891/mobley_9740891_converted.rst7 WARNING 2017-03-19 00:52:22 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:52:22 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9740891/mobley_9740891_converted.inp INFO 2017-03-19 00:52:22 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9740891/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9740891/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9740891/mobley_9740891_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_9740891/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9740891/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 45.03753767 45.03753767 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 5.13996032 5.13996032 coulomb total 5.12498160 5.12761586 0.00263426 5.12761585 0.00263425 5.12761564 0.00263404 5.12498160 0.00000000 5.13996032 0.01497872 coulomb-14 -39.91201280 -39.90992181 0.00209099 0.00000000 39.91201280 -39.90993523 0.00207757 -39.91201280 0.00000000 0.00000000 39.91201280 improper 0.00000000 0.00005212 0.00005212 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00056106 0.00014266 0.00061313 0.00019473 0.00061349 0.00019509 0.00041840 0.00000000 0.00054392 0.00012552 vdw (SR) 0.00000000 -4.42215861 -4.42215861 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 18.74871320 18.74871320 vdw total 18.74892240 18.74871887 -0.00020353 18.74871906 -0.00020334 18.74888633 -0.00003607 18.74892240 0.00000000 18.74871320 -0.00020920 vdw-14 23.17099200 23.17087748 -0.00011452 0.00000000 -23.17099200 23.17104509 0.00005309 23.17099200 0.00000000 0.00000000 -23.17099200 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.12505360 1.84466517 -0.28038843 1.84466518 -0.28038842 1.84472863 -0.28032497 2.12505360 0.00000000 1.84468376 -0.28036984 bond 1.31126560 1.31139075 0.00012515 1.31139074 0.00012514 1.31109848 -0.00016712 1.31126560 0.00000000 1.31139112 0.00012552 bonded 3.43673760 3.15666910 -0.28006850 3.15666906 -0.28006854 3.15644060 -0.28029700 3.43673760 0.00000000 3.15666064 -0.28007696 dihedral 0.00041840 0.00061318 0.00019478 0.00061313 0.00019473 0.00061349 0.00019509 0.00041840 0.00000000 0.00058576 0.00016736 nonbonded 23.87390400 23.87633473 0.00243073 23.87633449 0.00243049 23.87650197 0.00259797 23.87390400 0.00000000 23.88867352 0.01476952 potential 27.31064160 27.03300383 -0.27763777 27.03300391 -0.27763769 27.03285655 -0.27778505 27.31064160 0.00000000 27.04533416 -0.26530744 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 27.31064160 Difference in potential energy from amber=>gromacs conversion: -0.27763777 Difference in potential energy from amber=>lammps conversion: -0.27763769 Difference in potential energy from amber=>desmond conversion: -0.27778505 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.26530744 ======================================================================= INFO 2017-03-19 00:52:22 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9740891.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9740891.inpcrd') INFO 2017-03-19 00:52:22 Beginning InterMol conversion INFO 2017-03-19 00:52:22 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:52:23 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:52:23 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9741965.inpcrd INFO 2017-03-19 00:52:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9741965/mobley_9741965_converted.input INFO 2017-03-19 00:52:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9741965/mobley_9741965_converted.cms WARNING 2017-03-19 00:52:38 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:52:38 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9741965/mobley_9741965_converted.inp INFO 2017-03-19 00:52:38 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9741965/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9741965/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9741965/mobley_9741965_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9741965/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 52.58541996 52.58541996 0.00000000 0.00000000 0.00000000 0.00000000 -88.36645656 -88.36645656 coulomb total -88.36608000 -88.36925974 -0.00317974 -88.36925984 -0.00317984 -88.36923976 -0.00315976 -88.36645656 -0.00037656 coulomb-14 -140.94975520 -140.95467970 -0.00492450 0.00000000 140.94975520 -140.95464881 -0.00489361 0.00000000 140.94975520 proper 12.34991280 12.34996090 0.00004810 12.34996092 0.00004812 12.34991590 0.00000310 12.34974544 -0.00016736 vdw (SR) 0.00000000 7.10719653 7.10719653 0.00000000 0.00000000 0.00000000 0.00000000 37.54462192 37.54462192 vdw total 37.54470560 37.54431369 -0.00039191 37.54431398 -0.00039162 37.54451008 -0.00019552 37.54462192 -0.00008368 vdw-14 30.43734480 30.43711715 -0.00022765 0.00000000 -30.43734480 30.43711732 -0.00022748 0.00000000 -30.43734480 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 8.31653680 8.31640411 -0.00013269 8.31640417 -0.00013263 8.31608618 -0.00045062 8.31653680 0.00000000 bond 3.44594240 3.44580735 -0.00013505 3.44580734 -0.00013506 3.44669772 0.00075532 3.44581688 -0.00012552 bonded 24.11239200 24.11217236 -0.00021964 24.11217242 -0.00021958 24.11269980 0.00030780 24.11209912 -0.00029288 dihedral 12.34991280 12.34996090 0.00004810 12.34996092 0.00004812 12.34991590 0.00000310 12.34974544 -0.00016736 nonbonded -50.82137440 -50.82494605 -0.00357165 -50.82494335 -0.00356895 -50.82472968 -0.00335528 -50.82183464 -0.00046024 potential -26.70898240 -26.71277369 -0.00379129 -26.71277227 -0.00378987 -26.71214513 -0.00316273 -26.70973552 -0.00075312 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -26.70898240 Difference in potential energy from amber=>gromacs conversion: -0.00379129 Difference in potential energy from amber=>lammps conversion: -0.00378987 Difference in potential energy from amber=>desmond conversion: -0.00316273 Difference in potential energy from amber=>charmm conversion: -0.00075312 ======================================================================= INFO 2017-03-19 00:52:38 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9741965.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9741965.inpcrd') INFO 2017-03-19 00:52:39 Beginning InterMol conversion INFO 2017-03-19 00:52:39 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:52:39 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:52:39 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9794857.inpcrd INFO 2017-03-19 00:52:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9794857/mobley_9794857_converted.input INFO 2017-03-19 00:52:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9794857/mobley_9794857_converted.cms WARNING 2017-03-19 00:52:54 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:52:54 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9794857/mobley_9794857_converted.inp INFO 2017-03-19 00:52:54 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9794857/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9794857/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9794857/mobley_9794857_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9794857/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 40.68502355 40.68502355 0.00000000 0.00000000 0.00000000 0.00000000 -65.44006120 -65.44006120 coulomb total -65.44403600 -65.43329233 0.01074367 -65.43329149 0.01074451 -65.43345621 0.01057979 -65.44006120 0.00397480 coulomb-14 -106.07067600 -106.11831588 -0.04763988 0.00000000 106.07067600 -106.11822800 -0.04755200 0.00000000 106.07067600 proper 10.77380000 10.77375771 -0.00004229 10.77375774 -0.00004226 10.77375205 -0.00004795 10.77375816 -0.00004184 vdw (SR) 0.00000000 55.46924874 55.46924874 0.00000000 0.00000000 0.00000000 0.00000000 75.13761088 75.13761088 vdw total 75.13752720 75.13689566 -0.00063154 75.13689542 -0.00063178 75.13507998 -0.00244722 75.13761088 0.00008368 vdw-14 19.66772880 19.66764692 -0.00008188 0.00000000 -19.66772880 19.66706647 -0.00066233 0.00000000 -19.66772880 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.50331120 1.50319599 -0.00011521 1.50319597 -0.00011523 1.50320661 -0.00010459 1.50322752 -0.00008368 bond 0.99997600 1.00000013 0.00002413 1.00000014 0.00002414 0.99959524 -0.00038076 1.00001784 0.00004184 bonded 13.27708720 13.27695383 -0.00013337 13.27695386 -0.00013334 13.27655390 -0.00053330 13.27700352 -0.00008368 dihedral 10.77380000 10.77375771 -0.00004229 10.77375774 -0.00004226 10.77375205 -0.00004795 10.77375816 -0.00004184 nonbonded 9.69349120 9.70360333 0.01011213 9.70360518 0.01011398 9.70162377 0.00813257 9.69754968 0.00405848 potential 22.97057840 22.98055717 0.00997877 22.98055891 0.00998051 22.97814207 0.00756367 22.97451136 0.00393296 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 22.97057840 Difference in potential energy from amber=>gromacs conversion: 0.00997877 Difference in potential energy from amber=>lammps conversion: 0.00998051 Difference in potential energy from amber=>desmond conversion: 0.00756367 Difference in potential energy from amber=>charmm conversion: 0.00393296 ======================================================================= INFO 2017-03-19 00:52:54 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9794857.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9794857.inpcrd') INFO 2017-03-19 00:52:55 Beginning InterMol conversion INFO 2017-03-19 00:52:55 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:52:55 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9821936.inpcrd INFO 2017-03-19 00:52:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9821936/mobley_9821936_converted.input INFO 2017-03-19 00:52:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9821936/mobley_9821936_converted.cms INFO 2017-03-19 00:53:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9821936/mobley_9821936_converted.rst7 WARNING 2017-03-19 00:53:10 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:53:10 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9821936/mobley_9821936_converted.inp INFO 2017-03-19 00:53:10 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9821936/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9821936/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9821936/mobley_9821936_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_9821936/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9821936/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 6.33015344 6.33015344 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 20.71946088 20.71946088 coulomb total 20.72000480 20.71857949 -0.00142531 20.71857931 -0.00142549 20.71857529 -0.00142951 20.72000480 0.00000000 20.71946088 -0.00054392 coulomb-14 14.38961280 14.38842605 -0.00118675 0.00000000 -14.38961280 14.38841726 -0.00119554 14.38961280 0.00000000 0.00000000 -14.38961280 improper 0.00000000 0.00009009 0.00009009 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.00083680 0.00074510 -0.00009170 0.00083519 -0.00000161 0.00083295 -0.00000385 0.00083680 0.00000000 0.00075312 -0.00008368 vdw (SR) 0.00000000 -17.86757710 -17.86757710 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 55.46770640 55.46770640 vdw total 55.46770640 55.46751510 -0.00019130 55.46751394 -0.00019246 55.46755105 -0.00015535 55.46728800 -0.00041840 55.46770640 0.00000000 vdw-14 73.33547840 73.33509220 -0.00038620 0.00000000 -73.33547840 73.33513113 -0.00034727 73.33506000 -0.00041840 0.00000000 -73.33547840 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 8.37176560 8.37195386 0.00018826 8.37195388 0.00018828 8.37247470 0.00070910 8.37176560 0.00000000 8.37201664 0.00025104 bond 2.93298400 2.93307923 0.00009523 2.93307923 0.00009523 2.93343417 0.00045017 2.93298400 0.00000000 2.93306768 0.00008368 bonded 11.30558640 11.30586828 0.00028188 11.30586830 0.00028190 11.30674182 0.00115542 11.30558640 0.00000000 11.30592112 0.00033472 dihedral 0.00083680 0.00083519 -0.00000161 0.00083519 -0.00000161 0.00083295 -0.00000385 0.00083680 0.00000000 0.00083680 0.00000000 nonbonded 76.18771120 76.18609459 -0.00161661 76.18609618 -0.00161502 76.18612634 -0.00158486 76.18729280 -0.00041840 76.18716728 -0.00054392 potential 87.49329760 87.49196287 -0.00133473 87.49196290 -0.00133470 87.49245076 -0.00084684 87.49287920 -0.00041840 87.49308840 -0.00020920 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 87.49329760 Difference in potential energy from amber=>gromacs conversion: -0.00133473 Difference in potential energy from amber=>lammps conversion: -0.00133470 Difference in potential energy from amber=>desmond conversion: -0.00084684 Difference in potential energy from amber=>amber conversion: -0.00041840 Difference in potential energy from amber=>charmm conversion: -0.00020920 ======================================================================= INFO 2017-03-19 00:53:10 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9821936.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9821936.inpcrd') INFO 2017-03-19 00:53:11 Beginning InterMol conversion INFO 2017-03-19 00:53:11 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:53:11 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:53:11 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9838013.inpcrd INFO 2017-03-19 00:53:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9838013/mobley_9838013_converted.input INFO 2017-03-19 00:53:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9838013/mobley_9838013_converted.cms WARNING 2017-03-19 00:53:27 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:53:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9838013/mobley_9838013_converted.inp INFO 2017-03-19 00:53:27 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9838013/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9838013/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9838013/mobley_9838013_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9838013/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 42.51669996 42.51669996 0.00000000 0.00000000 0.00000000 0.00000000 -81.76335144 -81.76335144 coulomb total -81.74657360 -81.74960615 -0.00303255 -81.74960700 -0.00303340 -81.74973085 -0.00315725 -81.76335144 -0.01677784 coulomb-14 -124.26187120 -124.26630611 -0.00443491 0.00000000 124.26187120 -124.26632381 -0.00445261 0.00000000 124.26187120 proper 14.75864160 14.75863754 -0.00000406 14.75863532 -0.00000628 14.75864687 0.00000527 14.75864160 0.00000000 vdw (SR) 0.00000000 2.30040730 2.30040730 0.00000000 0.00000000 0.00000000 0.00000000 10.95237312 10.95237312 vdw total 10.95203840 10.95218472 0.00014632 10.95218484 0.00014644 10.95220750 0.00016910 10.95237312 0.00033472 vdw-14 8.65167520 8.65177742 0.00010222 0.00000000 -8.65167520 8.65177867 0.00010347 0.00000000 -8.65167520 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.43169280 4.43166433 -0.00002847 4.43166435 -0.00002845 4.43159310 -0.00009970 4.43165096 -0.00004184 bond 0.49496720 0.49508420 0.00011700 0.49508418 0.00011698 0.49486268 -0.00010452 0.49509272 0.00012552 bonded 19.68530160 19.68538607 0.00008447 19.68538386 0.00008226 19.68510265 -0.00019895 19.68538528 0.00008368 dihedral 14.75864160 14.75863754 -0.00000406 14.75863532 -0.00000628 14.75864687 0.00000527 14.75864160 0.00000000 nonbonded -70.79453520 -70.79742143 -0.00288623 -70.79742216 -0.00288696 -70.79752335 -0.00298815 -70.81097832 -0.01644312 potential -51.10923360 -51.11203536 -0.00280176 -51.11203688 -0.00280328 -51.11245821 -0.00322461 -51.12563488 -0.01640128 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -51.10923360 Difference in potential energy from amber=>gromacs conversion: -0.00280176 Difference in potential energy from amber=>lammps conversion: -0.00280328 Difference in potential energy from amber=>desmond conversion: -0.00322461 Difference in potential energy from amber=>charmm conversion: -0.01640128 ======================================================================= INFO 2017-03-19 00:53:27 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9838013.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9838013.inpcrd') INFO 2017-03-19 00:53:27 Beginning InterMol conversion INFO 2017-03-19 00:53:27 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:53:27 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:53:27 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9883303.inpcrd INFO 2017-03-19 00:53:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9883303/mobley_9883303_converted.input INFO 2017-03-19 00:53:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9883303/mobley_9883303_converted.cms WARNING 2017-03-19 00:53:43 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:53:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9883303/mobley_9883303_converted.inp INFO 2017-03-19 00:53:43 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9883303/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9883303/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9883303/mobley_9883303_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9883303/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 1.66867381 1.66867381 0.00000000 0.00000000 0.00000000 0.00000000 -1.14034920 -1.14034920 coulomb total -1.15060000 -1.14072486 0.00987514 -1.14072484 0.00987516 -1.14078219 0.00981781 -1.14034920 0.01025080 coulomb-14 -2.80955600 -2.80939868 0.00015732 0.00000000 2.80955600 -2.80938694 0.00016906 0.00000000 2.80955600 proper 10.13825040 10.13823506 -0.00001534 10.13823241 -0.00001799 10.13821057 -0.00003983 10.13825040 0.00000000 vdw (SR) 0.00000000 3.02680563 3.02680563 0.00000000 0.00000000 0.00000000 0.00000000 12.68488384 12.68488384 vdw total 12.68505120 12.68468620 -0.00036500 12.68468636 -0.00036484 12.68472615 -0.00032505 12.68488384 -0.00016736 vdw-14 9.65792720 9.65788057 -0.00004663 0.00000000 -9.65792720 9.65791348 -0.00001372 0.00000000 -9.65792720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 8.02700400 8.02682340 -0.00018060 8.02682325 -0.00018075 8.02679283 -0.00021117 8.02679480 -0.00020920 bond 0.97278000 0.97289458 0.00011458 0.97289460 0.00011460 0.97306553 0.00028553 0.97290552 0.00012552 bonded 19.13803440 19.13795305 -0.00008135 19.13795026 -0.00008414 19.13806893 0.00003453 19.13795072 -0.00008368 dihedral 10.13825040 10.13823506 -0.00001534 10.13823241 -0.00001799 10.13821057 -0.00003983 10.13825040 0.00000000 nonbonded 11.53445120 11.54396134 0.00951014 11.54396143 0.00951023 11.54394396 0.00949276 11.54453464 0.01008344 potential 30.67248560 30.68191439 0.00942879 30.68191215 0.00942655 30.68194859 0.00946299 30.68248536 0.00999976 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 30.67248560 Difference in potential energy from amber=>gromacs conversion: 0.00942879 Difference in potential energy from amber=>lammps conversion: 0.00942655 Difference in potential energy from amber=>desmond conversion: 0.00946299 Difference in potential energy from amber=>charmm conversion: 0.00999976 ======================================================================= INFO 2017-03-19 00:53:43 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9883303.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9883303.inpcrd') INFO 2017-03-19 00:53:43 Beginning InterMol conversion INFO 2017-03-19 00:53:43 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:53:43 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:53:43 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9897248.inpcrd INFO 2017-03-19 00:53:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9897248/mobley_9897248_converted.input INFO 2017-03-19 00:53:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9897248/mobley_9897248_converted.cms WARNING 2017-03-19 00:53:59 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:53:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9897248/mobley_9897248_converted.inp INFO 2017-03-19 00:53:59 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9897248/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9897248/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9897248/mobley_9897248_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9897248/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 47.66151934 47.66151934 0.00000000 0.00000000 0.00000000 0.00000000 -37.89038768 -37.89038768 coulomb total -37.89114080 -37.86489386 0.02624694 -37.86489331 0.02624749 -37.86509666 0.02604414 -37.89038768 0.00075312 coulomb-14 -85.51719440 -85.52641320 -0.00921880 0.00000000 85.51719440 -85.52650129 -0.00930689 0.00000000 85.51719440 improper 0.00000000 0.01348829 0.01348829 0.00000000 0.00000000 0.00000000 0.00000000 0.01347248 0.01347248 proper 115.15957920 115.14599368 -0.01358552 115.15949134 -0.00008786 115.15949175 -0.00008745 115.14602304 -0.01355616 vdw (SR) 0.00000000 -3.41667726 -3.41667726 0.00000000 0.00000000 0.00000000 0.00000000 7.86253096 7.86253096 vdw total 7.86257280 7.86236787 -0.00020493 7.86236778 -0.00020502 7.86238275 -0.00019005 7.86253096 -0.00004184 vdw-14 11.27922720 11.27904512 -0.00018208 0.00000000 -11.27922720 11.27907197 -0.00015523 0.00000000 -11.27922720 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 14.77119360 14.77120709 0.00001349 14.77120699 0.00001339 14.77154171 0.00034811 14.77106808 -0.00012552 bond 3.15389920 3.15407080 0.00017160 3.15407079 0.00017159 3.15299618 -0.00090302 3.15406656 0.00016736 bonded 133.08467200 133.08475987 0.00008787 133.08476911 0.00009711 133.08402964 -0.00064236 133.08463016 -0.00004184 dihedral 115.15957920 115.15948197 -0.00009723 115.15949134 -0.00008786 115.15949175 -0.00008745 115.15949552 -0.00008368 nonbonded -30.02856800 -30.00252600 0.02604200 -30.00252553 0.02604247 -30.00271391 0.02585409 -30.02785672 0.00071128 potential 103.05610400 103.08223387 0.02612987 103.08224145 0.02613745 103.08119754 0.02509354 103.05681528 0.00071128 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 103.05610400 Difference in potential energy from amber=>gromacs conversion: 0.02612987 Difference in potential energy from amber=>lammps conversion: 0.02613745 Difference in potential energy from amber=>desmond conversion: 0.02509354 Difference in potential energy from amber=>charmm conversion: 0.00071128 ======================================================================= INFO 2017-03-19 00:53:59 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9897248.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9897248.inpcrd') INFO 2017-03-19 00:53:59 Beginning InterMol conversion INFO 2017-03-19 00:53:59 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 00:53:59 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9913368.inpcrd INFO 2017-03-19 00:53:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9913368/mobley_9913368_converted.input INFO 2017-03-19 00:53:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9913368/mobley_9913368_converted.cms INFO 2017-03-19 00:54:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9913368/mobley_9913368_converted.rst7 WARNING 2017-03-19 00:54:15 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:54:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9913368/mobley_9913368_converted.inp INFO 2017-03-19 00:54:15 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9913368/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9913368/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9913368/mobley_9913368_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_9913368/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9913368/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.14505928 0.14505928 coulomb total 0.13263280 0.13472413 0.00209133 0.13472413 0.00209133 0.13472571 0.00209291 0.13263280 0.00000000 0.14505928 0.01242648 coulomb-14 0.13263280 0.13472413 0.00209133 0.00000000 -0.13263280 0.13472571 0.00209291 0.13263280 0.00000000 0.00000000 -0.13263280 improper 0.00000000 0.00002488 0.00002488 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00004184 0.00004184 proper 0.00041840 0.00034657 -0.00007183 0.00037120 -0.00004720 0.00036959 -0.00004881 0.00041840 0.00000000 0.00033472 -0.00008368 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.29744056 -0.29744056 vdw total -0.29748240 -0.29742826 0.00005414 -0.29742826 0.00005414 -0.29741210 0.00007030 -0.29748240 0.00000000 -0.29744056 0.00004184 vdw-14 -0.29748240 -0.29742826 0.00005414 0.00000000 0.29748240 -0.29741210 0.00007030 -0.29748240 0.00000000 0.00000000 0.29748240 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.75186480 0.75167036 -0.00019444 0.75167037 -0.00019443 0.75150190 -0.00036290 0.75186480 0.00000000 0.75169744 -0.00016736 bond 0.39329600 0.39315529 -0.00014071 0.39315529 -0.00014071 0.39316776 -0.00012824 0.39329600 0.00000000 0.39317048 -0.00012552 bonded 1.14557920 1.14519710 -0.00038210 1.14519686 -0.00038234 1.14503925 -0.00053995 1.14557920 0.00000000 1.14524448 -0.00033472 dihedral 0.00041840 0.00037145 -0.00004695 0.00037120 -0.00004720 0.00036959 -0.00004881 0.00041840 0.00000000 0.00037656 -0.00004184 nonbonded -0.16484960 -0.16270413 0.00214547 -0.16270413 0.00214547 -0.16268639 0.00216321 -0.16484960 0.00000000 -0.15238128 0.01246832 potential 0.98072960 0.98249297 0.00176337 0.98249274 0.00176314 0.98233400 0.00160440 0.98072960 0.00000000 0.99286320 0.01213360 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 0.98072960 Difference in potential energy from amber=>gromacs conversion: 0.00176337 Difference in potential energy from amber=>lammps conversion: 0.00176314 Difference in potential energy from amber=>desmond conversion: 0.00160440 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.01213360 ======================================================================= INFO 2017-03-19 00:54:15 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9913368.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9913368.inpcrd') INFO 2017-03-19 00:54:15 Beginning InterMol conversion INFO 2017-03-19 00:54:15 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:54:15 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:54:15 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9942801.inpcrd INFO 2017-03-19 00:54:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9942801/mobley_9942801_converted.input INFO 2017-03-19 00:54:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9942801/mobley_9942801_converted.cms WARNING 2017-03-19 00:54:31 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:54:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9942801/mobley_9942801_converted.inp INFO 2017-03-19 00:54:31 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9942801/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9942801/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9942801/mobley_9942801_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9942801/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 2.83270446 2.83270446 0.00000000 0.00000000 0.00000000 0.00000000 -18.38206928 -18.38206928 coulomb total -18.39704800 -18.38603081 0.01101719 -18.38603069 0.01101731 -18.38605446 0.01099354 -18.38206928 0.01497872 coulomb-14 -21.21455360 -21.21873527 -0.00418167 0.00000000 21.21455360 -21.21873342 -0.00417982 0.00000000 21.21455360 improper 0.00000000 0.00006772 0.00006772 0.00000000 0.00000000 0.00000000 0.00000000 0.00008368 0.00008368 proper 0.02008320 0.02002402 -0.00005918 0.02009178 0.00000858 0.02009445 0.00001125 0.02004136 -0.00004184 vdw (SR) 0.00000000 -3.96327482 -3.96327482 0.00000000 0.00000000 0.00000000 0.00000000 17.13632512 17.13632512 vdw total 17.13640880 17.13629678 -0.00011202 17.13629667 -0.00011213 17.13634725 -0.00006155 17.13632512 -0.00008368 vdw-14 21.09949360 21.09957161 0.00007801 0.00000000 -21.09949360 21.09962694 0.00013334 0.00000000 -21.09949360 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.05604160 1.05615170 0.00011010 1.05615168 0.00011008 1.05624739 0.00020579 1.05612528 0.00008368 bond 2.46228400 2.46218911 -0.00009489 2.46218911 -0.00009489 2.46186962 -0.00041438 2.46220032 -0.00008368 bonded 3.53840880 3.53843254 0.00002374 3.53843257 0.00002377 3.53821146 -0.00019734 3.53845064 0.00004184 dihedral 0.02008320 0.02009174 0.00000854 0.02009178 0.00000858 0.02009445 0.00001125 0.02012504 0.00004184 nonbonded -1.26063920 -1.24973402 0.01090518 -1.24973381 0.01090539 -1.24970721 0.01093199 -1.24574416 0.01489504 potential 2.27776960 2.28869852 0.01092892 2.28869875 0.01092915 2.28843383 0.01066423 2.29266464 0.01489504 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 2.27776960 Difference in potential energy from amber=>gromacs conversion: 0.01092892 Difference in potential energy from amber=>lammps conversion: 0.01092915 Difference in potential energy from amber=>desmond conversion: 0.01066423 Difference in potential energy from amber=>charmm conversion: 0.01489504 ======================================================================= INFO 2017-03-19 00:54:31 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9942801.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9942801.inpcrd') INFO 2017-03-19 00:54:31 Beginning InterMol conversion INFO 2017-03-19 00:54:31 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:54:31 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:54:31 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_994483.inpcrd INFO 2017-03-19 00:54:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_994483/mobley_994483_converted.input INFO 2017-03-19 00:54:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_994483/mobley_994483_converted.cms WARNING 2017-03-19 00:54:47 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:54:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_994483/mobley_994483_converted.inp INFO 2017-03-19 00:54:47 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_994483/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_994483/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_994483/mobley_994483_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_994483/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.56948424 -0.56948424 coulomb total -0.57488160 -0.57508867 -0.00020707 -0.57508867 -0.00020707 -0.57507962 -0.00019802 -0.56948424 0.00539736 coulomb-14 -0.57488160 -0.57508867 -0.00020707 0.00000000 0.57488160 -0.57507962 -0.00019802 0.00000000 0.57488160 proper 6.90443680 6.90444929 0.00001249 6.90444935 0.00001255 6.90443015 -0.00000665 6.90443680 0.00000000 vdw (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.22572680 0.22572680 vdw total 0.22593600 0.22572020 -0.00021580 0.22572020 -0.00021580 0.22571722 -0.00021878 0.22572680 -0.00020920 vdw-14 0.22593600 0.22572020 -0.00021580 0.00000000 -0.22593600 0.22571722 -0.00021878 0.00000000 -0.22593600 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.22881680 2.22863183 -0.00018497 2.22863183 -0.00018497 2.22872781 -0.00008899 2.22869128 -0.00012552 bond 1.26691520 1.26696688 0.00005168 1.26696687 0.00005167 1.26694841 0.00003321 1.26695704 0.00004184 bonded 10.40016880 10.40004800 -0.00012080 10.40004805 -0.00012075 10.40010637 -0.00006243 10.40008512 -0.00008368 dihedral 6.90443680 6.90444929 0.00001249 6.90444935 0.00001255 6.90443015 -0.00000665 6.90443680 0.00000000 nonbonded -0.34894560 -0.34936847 -0.00042287 -0.34936846 -0.00042286 -0.34936239 -0.00041679 -0.34375744 0.00518816 potential 10.05122320 10.05067953 -0.00054367 10.05067970 -0.00054350 10.05072635 -0.00049685 10.05636952 0.00514632 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 10.05122320 Difference in potential energy from amber=>gromacs conversion: -0.00054367 Difference in potential energy from amber=>lammps conversion: -0.00054350 Difference in potential energy from amber=>desmond conversion: -0.00049685 Difference in potential energy from amber=>charmm conversion: 0.00514632 ======================================================================= INFO 2017-03-19 00:54:47 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_994483.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_994483.inpcrd') INFO 2017-03-19 00:54:47 Beginning InterMol conversion INFO 2017-03-19 00:54:47 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:54:48 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:54:48 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9974966.inpcrd INFO 2017-03-19 00:54:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9974966/mobley_9974966_converted.input INFO 2017-03-19 00:54:48 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9974966/mobley_9974966_converted.cms WARNING 2017-03-19 00:55:03 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:55:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9974966/mobley_9974966_converted.inp INFO 2017-03-19 00:55:03 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9974966/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9974966/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9974966/mobley_9974966_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9974966/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 25.11455927 25.11455927 0.00000000 0.00000000 0.00000000 0.00000000 -43.90405088 -43.90405088 coulomb total -43.91526400 -43.90179076 0.01347324 -43.90179152 0.01347248 -43.90181478 0.01344922 -43.90405088 0.01121312 coulomb-14 -68.99541520 -69.01635003 -0.02093483 0.00000000 68.99541520 -69.01631930 -0.02090410 0.00000000 68.99541520 proper 4.78649600 4.78659170 0.00009570 4.78659181 0.00009581 4.78656123 0.00006523 4.78611944 -0.00037656 vdw (SR) 0.00000000 0.27400058 0.27400058 0.00000000 0.00000000 0.00000000 0.00000000 5.35075024 5.35075024 vdw total 5.35091760 5.35057901 -0.00033859 5.35057911 -0.00033849 5.35059762 -0.00031998 5.35075024 -0.00016736 vdw-14 5.07686560 5.07657843 -0.00028717 0.00000000 -5.07686560 5.07654799 -0.00031761 0.00000000 -5.07686560 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.60867600 4.60885931 0.00018331 4.60885926 0.00018326 4.60907549 0.00039949 4.60875968 0.00008368 bond 0.91085680 0.91088746 0.00003066 0.91088747 0.00003067 0.91062532 -0.00023148 0.91089864 0.00004184 bonded 10.30602880 10.30633847 0.00030967 10.30633854 0.00030974 10.30626204 0.00023324 10.30577776 -0.00025104 dihedral 4.78649600 4.78659170 0.00009570 4.78659181 0.00009581 4.78656123 0.00006523 4.78611944 -0.00037656 nonbonded -38.56434640 -38.55121175 0.01313465 -38.55121115 0.01313525 -38.55121716 0.01312924 -38.55330064 0.01104576 potential -28.25831760 -28.24487328 0.01344432 -28.24487273 0.01344487 -28.24502160 0.01329600 -28.24752288 0.01079472 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: -28.25831760 Difference in potential energy from amber=>gromacs conversion: 0.01344432 Difference in potential energy from amber=>lammps conversion: 0.01344487 Difference in potential energy from amber=>desmond conversion: 0.01329600 Difference in potential energy from amber=>charmm conversion: 0.01079472 ======================================================================= INFO 2017-03-19 00:55:03 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9974966.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9974966.inpcrd') INFO 2017-03-19 00:55:03 Beginning InterMol conversion INFO 2017-03-19 00:55:03 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 ERROR 2017-03-19 00:55:04 AmberParm does not support all of the parameters defined in the input Structure TypeError: AmberParm does not support all of the parameters defined in the input Structure INFO 2017-03-19 00:55:04 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9979854.inpcrd INFO 2017-03-19 00:55:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9979854/mobley_9979854_converted.input INFO 2017-03-19 00:55:04 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9979854/mobley_9979854_converted.cms WARNING 2017-03-19 00:55:19 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 00:55:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9979854/mobley_9979854_converted.inp INFO 2017-03-19 00:55:19 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9979854/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9979854/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9979854/mobley_9979854_converted.enegrp.dat charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9979854/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 -119.92027413 -119.92027413 0.00000000 0.00000000 0.00000000 0.00000000 144.61765880 144.61765880 coulomb total 144.61535760 144.61758741 0.00222981 144.61758767 0.00223007 144.61754332 0.00218572 144.61765880 0.00230120 coulomb-14 264.53632880 264.53786154 0.00153274 0.00000000 -264.53632880 264.53797228 0.00164348 0.00000000 -264.53632880 proper 7.16635520 7.16650026 0.00014506 7.16650038 0.00014518 7.16648946 0.00013426 7.16652256 0.00016736 vdw (SR) 0.00000000 0.74591675 0.74591675 0.00000000 0.00000000 0.00000000 0.00000000 7.91633720 7.91633720 vdw total 7.91654640 7.91635499 -0.00019141 7.91635519 -0.00019121 7.91635822 -0.00018818 7.91633720 -0.00020920 vdw-14 7.17053920 7.17043824 -0.00010096 0.00000000 -7.17053920 7.17042540 -0.00011380 0.00000000 -7.17053920 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.89995440 1.89994631 -0.00000809 1.89994632 -0.00000808 1.89983424 -0.00012016 1.89999624 0.00004184 bond 1.07026720 1.07023747 -0.00002973 1.07023749 -0.00002971 1.07029705 0.00002985 1.07022536 -0.00004184 bonded 10.13657680 10.13668405 0.00010725 10.13668420 0.00010740 10.13662075 0.00004395 10.13674416 0.00016736 dihedral 7.16635520 7.16650026 0.00014506 7.16650038 0.00014518 7.16648946 0.00013426 7.16652256 0.00016736 nonbonded 152.53190400 152.53394240 0.00203840 152.53394161 0.00203761 152.53390155 0.00199755 152.53399600 0.00209200 potential 162.66848080 162.67062645 0.00214565 162.67062301 0.00214221 162.67048703 0.00200623 162.67069832 0.00221752 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 162.66848080 Difference in potential energy from amber=>gromacs conversion: 0.00214565 Difference in potential energy from amber=>lammps conversion: 0.00214221 Difference in potential energy from amber=>desmond conversion: 0.00200623 Difference in potential energy from amber=>charmm conversion: 0.00221752 ======================================================================= INFO 2017-03-19 00:55:19 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9979854.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9979854.inpcrd') Directory ./converted/mobley_1017962 already exists Directory ./converted/mobley_1019269 already exists Directory ./converted/mobley_1034539 already exists Directory ./converted/mobley_1036761 already exists Directory ./converted/mobley_1046331 already exists Directory ./converted/mobley_1075836 already exists Directory ./converted/mobley_1079207 already exists Directory ./converted/mobley_1107178 already exists Directory ./converted/mobley_1139153 already exists Directory ./converted/mobley_1144156 already exists Directory ./converted/mobley_1160109 already exists Directory ./converted/mobley_1178614 already exists Directory ./converted/mobley_1189457 already exists Directory ./converted/mobley_1199854 already exists Directory ./converted/mobley_1231151 already exists Directory ./converted/mobley_1235151 already exists Directory ./converted/mobley_1244778 already exists Directory ./converted/mobley_1261349 already exists Directory ./converted/mobley_1278715 already exists Directory ./converted/mobley_129464 already exists Directory ./converted/mobley_1323538 already exists Directory ./converted/mobley_1328465 already exists Directory ./converted/mobley_1328936 already exists Directory ./converted/mobley_1352110 already exists Directory ./converted/mobley_1363784 already exists Directory ./converted/mobley_1396156 already exists Directory ./converted/mobley_1417007 already exists Directory ./converted/mobley_1424265 already exists Directory ./converted/mobley_1449384 already exists Directory ./converted/mobley_1469079 already exists Directory ./converted/mobley_1502181 already exists Directory ./converted/mobley_1520842 already exists Directory ./converted/mobley_1527293 already exists Directory ./converted/mobley_1563176 already exists Directory ./converted/mobley_1571523 already exists Directory ./converted/mobley_1592519 already exists Directory ./converted/mobley_1615431 already exists Directory ./converted/mobley_1636752 already exists Directory ./converted/mobley_1650157 already exists Directory ./converted/mobley_1659169 already exists Directory ./converted/mobley_1662128 already exists Directory ./converted/mobley_1674094 already exists Directory ./converted/mobley_1708457 already exists Directory ./converted/mobley_1717215 already exists Directory ./converted/mobley_1722522 already exists Directory ./converted/mobley_1723043 already exists Directory ./converted/mobley_1728386 already exists Directory ./converted/mobley_172879 already exists Directory ./converted/mobley_1733799 already exists Directory ./converted/mobley_1735893 already exists Directory ./converted/mobley_1743409 already exists Directory ./converted/mobley_1755375 already exists Directory ./converted/mobley_1760914 already exists Directory ./converted/mobley_1770205 already exists Directory ./converted/mobley_1781152 already exists Directory ./converted/mobley_1792062 already exists Directory ./converted/mobley_1800170 already exists Directory ./converted/mobley_1803862 already exists Directory ./converted/mobley_1821184 already exists Directory ./converted/mobley_1827204 already exists Directory ./converted/mobley_1838110 already exists Directory ./converted/mobley_1849020 already exists Directory ./converted/mobley_1855337 already exists Directory ./converted/mobley_1857976 already exists Directory ./converted/mobley_1858644 already exists Directory ./converted/mobley_186894 already exists Directory ./converted/mobley_1873346 already exists Directory ./converted/mobley_1875719 already exists Directory ./converted/mobley_1881249 already exists Directory ./converted/mobley_1893815 already exists Directory ./converted/mobley_1893937 already exists Directory ./converted/mobley_1896013 already exists Directory ./converted/mobley_1899443 already exists Directory ./converted/mobley_1903702 already exists Directory ./converted/mobley_1905088 already exists Directory ./converted/mobley_1922649 already exists Directory ./converted/mobley_1923244 already exists INFO 2017-03-19 14:06:11 Beginning InterMol conversion INFO 2017-03-19 14:06:11 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 14:06:11 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_1929982.inpcrd INFO 2017-03-19 14:06:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1929982/mobley_1929982_converted.input INFO 2017-03-19 14:06:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1929982/mobley_1929982_converted.cms INFO 2017-03-19 14:06:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1929982/mobley_1929982_converted.rst7 WARNING 2017-03-19 14:06:26 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 14:06:26 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_1929982/mobley_1929982_converted.inp INFO 2017-03-19 14:06:26 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_1929982/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_1929982/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_1929982/mobley_1929982_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_1929982/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_1929982/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00217568 0.00217568 coulomb total 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00217568 0.00217568 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.00376560 0.00394345 0.00017785 0.00394345 0.00017785 0.00394421 0.00017861 0.00376560 0.00000000 0.00393296 0.00016736 bond 0.02928800 0.02931791 0.00002991 0.02931791 0.00002991 0.02933320 0.00004520 0.02928800 0.00000000 0.02932984 0.00004184 bonded 0.03305360 0.03326136 0.00020776 0.03326136 0.00020776 0.03327741 0.00022381 0.03305360 0.00000000 0.03326280 0.00020920 nonbonded 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00217568 0.00217568 potential 0.03305360 0.03326136 0.00020776 0.03326136 0.00020776 0.03327532 0.00022172 0.03305360 0.00000000 0.03543848 0.00238488 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 0.03305360 Difference in potential energy from amber=>gromacs conversion: 0.00020776 Difference in potential energy from amber=>lammps conversion: 0.00020776 Difference in potential energy from amber=>desmond conversion: 0.00022172 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00238488 ======================================================================= INFO 2017-03-19 14:06:26 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_1929982.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_1929982.inpcrd') INFO 2017-03-19 14:06:27 Beginning InterMol conversion INFO 2017-03-19 14:06:27 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 14:06:27 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2146331.inpcrd INFO 2017-03-19 14:06:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2146331/mobley_2146331_converted.input INFO 2017-03-19 14:06:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2146331/mobley_2146331_converted.cms INFO 2017-03-19 14:06:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2146331/mobley_2146331_converted.rst7 WARNING 2017-03-19 14:06:42 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 14:06:42 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2146331/mobley_2146331_converted.inp INFO 2017-03-19 14:06:42 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2146331/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2146331/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2146331/mobley_2146331_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_2146331/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2146331/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00184096 -0.00184096 coulomb total 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00184096 -0.00184096 improper 0.00000000 0.00002055 0.00002055 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 proper 0.00000000 0.00000000 0.00000000 0.00002053 0.00002053 0.00002095 0.00002095 0.00000000 0.00000000 0.00000000 0.00000000 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.22886480 0.22906347 0.00019867 0.22906347 0.00019867 0.22913695 0.00027215 0.22886480 0.00000000 0.22907400 0.00020920 bond 0.58994400 0.59010819 0.00016419 0.59010818 0.00016418 0.58970696 -0.00023704 0.58994400 0.00000000 0.59011136 0.00016736 bonded 0.81880880 0.81919221 0.00038341 0.81919218 0.00038338 0.81886485 0.00005605 0.81880880 0.00000000 0.81918536 0.00037656 dihedral 0.00000000 0.00002055 0.00002055 0.00002053 0.00002053 0.00002095 0.00002095 0.00000000 0.00000000 0.00000000 0.00000000 nonbonded 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00184096 -0.00184096 potential 0.81880880 0.81919221 0.00038341 0.81919218 0.00038338 0.81886197 0.00005317 0.81880880 0.00000000 0.81734440 -0.00146440 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 0.81880880 Difference in potential energy from amber=>gromacs conversion: 0.00038341 Difference in potential energy from amber=>lammps conversion: 0.00038338 Difference in potential energy from amber=>desmond conversion: 0.00005317 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.00146440 ======================================================================= INFO 2017-03-19 14:06:42 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2146331.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2146331.inpcrd') INFO 2017-03-19 14:06:43 Beginning InterMol conversion INFO 2017-03-19 14:06:43 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 14:06:43 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_2996632.inpcrd INFO 2017-03-19 14:06:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2996632/mobley_2996632_converted.input INFO 2017-03-19 14:06:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2996632/mobley_2996632_converted.cms INFO 2017-03-19 14:06:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2996632/mobley_2996632_converted.rst7 WARNING 2017-03-19 14:06:58 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 14:06:58 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_2996632/mobley_2996632_converted.inp INFO 2017-03-19 14:06:58 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_2996632/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_2996632/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_2996632/mobley_2996632_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_2996632/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_2996632/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00163176 -0.00163176 coulomb total 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00163176 -0.00163176 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.26401040 0.26397146 -0.00003894 0.26397146 -0.00003894 0.26384463 -0.00016577 0.26401040 0.00000000 0.26396856 -0.00004184 bond 0.67948160 0.67955337 0.00007177 0.67955336 0.00007176 0.67977119 0.00028959 0.67948160 0.00000000 0.67956528 0.00008368 bonded 0.94349200 0.94352483 0.00003283 0.94352482 0.00003282 0.94361582 0.00012382 0.94349200 0.00000000 0.94353384 0.00004184 nonbonded 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00163176 -0.00163176 potential 0.94349200 0.94352483 0.00003283 0.94352484 0.00003284 0.94359216 0.00010016 0.94349200 0.00000000 0.94190208 -0.00158992 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 0.94349200 Difference in potential energy from amber=>gromacs conversion: 0.00003283 Difference in potential energy from amber=>lammps conversion: 0.00003284 Difference in potential energy from amber=>desmond conversion: 0.00010016 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.00158992 ======================================================================= INFO 2017-03-19 14:06:58 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_2996632.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_2996632.inpcrd') INFO 2017-03-19 14:06:59 Beginning InterMol conversion INFO 2017-03-19 14:06:59 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 14:06:59 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3425174.inpcrd INFO 2017-03-19 14:06:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3425174/mobley_3425174_converted.input INFO 2017-03-19 14:06:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3425174/mobley_3425174_converted.cms INFO 2017-03-19 14:07:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3425174/mobley_3425174_converted.rst7 WARNING 2017-03-19 14:07:14 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 14:07:14 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3425174/mobley_3425174_converted.inp INFO 2017-03-19 14:07:14 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3425174/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3425174/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3425174/mobley_3425174_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_3425174/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3425174/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00979056 0.00979056 coulomb total 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00979056 0.00979056 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.70542240 0.70531282 -0.00010958 0.70531282 -0.00010958 0.70540304 -0.00001936 0.70542240 0.00000000 0.70533872 -0.00008368 bond 0.91462240 0.91477893 0.00015653 0.91477892 0.00015652 0.91498699 0.00036459 0.91462240 0.00000000 0.91478976 0.00016736 bonded 1.62004480 1.62009175 0.00004695 1.62009174 0.00004694 1.62039002 0.00034522 1.62004480 0.00000000 1.62012848 0.00008368 nonbonded 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00979056 0.00979056 potential 1.62004480 1.62009175 0.00004695 1.62009174 0.00004694 1.62038226 0.00033746 1.62004480 0.00000000 1.62991904 0.00987424 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 1.62004480 Difference in potential energy from amber=>gromacs conversion: 0.00004695 Difference in potential energy from amber=>lammps conversion: 0.00004694 Difference in potential energy from amber=>desmond conversion: 0.00033746 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00987424 ======================================================================= INFO 2017-03-19 14:07:14 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3425174.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3425174.inpcrd') INFO 2017-03-19 14:07:15 Beginning InterMol conversion INFO 2017-03-19 14:07:15 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 14:07:15 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_3762186.inpcrd INFO 2017-03-19 14:07:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3762186/mobley_3762186_converted.input INFO 2017-03-19 14:07:15 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3762186/mobley_3762186_converted.cms INFO 2017-03-19 14:07:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3762186/mobley_3762186_converted.rst7 WARNING 2017-03-19 14:07:30 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 14:07:30 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_3762186/mobley_3762186_converted.inp INFO 2017-03-19 14:07:30 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_3762186/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_3762186/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_3762186/mobley_3762186_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_3762186/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_3762186/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00066944 -0.00066944 coulomb total 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00066944 -0.00066944 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.72843440 0.72858498 0.00015058 0.72858498 0.00015058 0.72855126 0.00011686 0.72843440 0.00000000 0.72864360 0.00020920 bond 0.99872080 0.99853920 -0.00018160 0.99853921 -0.00018159 0.99887759 0.00015679 0.99872080 0.00000000 0.99855344 -0.00016736 bonded 1.72715520 1.72712418 -0.00003102 1.72712420 -0.00003100 1.72742885 0.00027365 1.72715520 0.00000000 1.72719704 0.00004184 nonbonded 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00066944 -0.00066944 potential 1.72715520 1.72712418 -0.00003102 1.72712420 -0.00003100 1.72741549 0.00026029 1.72715520 0.00000000 1.72648576 -0.00066944 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 1.72715520 Difference in potential energy from amber=>gromacs conversion: -0.00003102 Difference in potential energy from amber=>lammps conversion: -0.00003100 Difference in potential energy from amber=>desmond conversion: 0.00026029 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.00066944 ======================================================================= INFO 2017-03-19 14:07:30 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_3762186.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_3762186.inpcrd') INFO 2017-03-19 14:07:31 Beginning InterMol conversion INFO 2017-03-19 14:07:31 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 14:07:31 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4364398.inpcrd INFO 2017-03-19 14:07:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4364398/mobley_4364398_converted.input INFO 2017-03-19 14:07:31 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4364398/mobley_4364398_converted.cms INFO 2017-03-19 14:07:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4364398/mobley_4364398_converted.rst7 WARNING 2017-03-19 14:07:46 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 14:07:46 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4364398/mobley_4364398_converted.inp INFO 2017-03-19 14:07:46 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4364398/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4364398/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4364398/mobley_4364398_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_4364398/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4364398/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00292880 -0.00292880 coulomb total 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00292880 -0.00292880 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 5.97642560 5.97636955 -0.00005605 5.97636953 -0.00005607 5.97661823 0.00019263 5.97642560 0.00000000 5.97642560 0.00000000 bond 2.29617920 2.29601855 -0.00016065 2.29601853 -0.00016067 2.29681639 0.00063719 2.29617920 0.00000000 2.29601184 -0.00016736 bonded 8.27260480 8.27238809 -0.00021671 8.27238807 -0.00021673 8.27343462 0.00082982 8.27260480 0.00000000 8.27243744 -0.00016736 nonbonded 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00292880 -0.00292880 potential 8.27260480 8.27238809 -0.00021671 8.27238807 -0.00021673 8.27342173 0.00081693 8.27260480 0.00000000 8.26955048 -0.00305432 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 8.27260480 Difference in potential energy from amber=>gromacs conversion: -0.00021671 Difference in potential energy from amber=>lammps conversion: -0.00021673 Difference in potential energy from amber=>desmond conversion: 0.00081693 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.00305432 ======================================================================= INFO 2017-03-19 14:07:46 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4364398.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4364398.inpcrd') INFO 2017-03-19 14:07:47 Beginning InterMol conversion INFO 2017-03-19 14:07:47 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 14:07:47 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_4434915.inpcrd INFO 2017-03-19 14:07:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4434915/mobley_4434915_converted.input INFO 2017-03-19 14:07:47 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4434915/mobley_4434915_converted.cms INFO 2017-03-19 14:08:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4434915/mobley_4434915_converted.rst7 WARNING 2017-03-19 14:08:02 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 14:08:02 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_4434915/mobley_4434915_converted.inp INFO 2017-03-19 14:08:03 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_4434915/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_4434915/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_4434915/mobley_4434915_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_4434915/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_4434915/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00142256 0.00142256 coulomb total 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00142256 0.00142256 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.57109200 1.57089471 -0.00019729 1.57089472 -0.00019728 1.57117536 0.00008336 1.57109200 0.00000000 1.57096648 -0.00012552 bond 0.42132880 0.42126192 -0.00006688 0.42126194 -0.00006686 0.42147255 0.00014375 0.42132880 0.00000000 0.42124512 -0.00008368 bonded 1.99242080 1.99215663 -0.00026417 1.99215666 -0.00026414 1.99264791 0.00022711 1.99242080 0.00000000 1.99221160 -0.00020920 nonbonded 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00142256 0.00142256 potential 1.99242080 1.99215663 -0.00026417 1.99215662 -0.00026418 1.99264173 0.00022093 1.99242080 0.00000000 1.99363416 0.00121336 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 1.99242080 Difference in potential energy from amber=>gromacs conversion: -0.00026417 Difference in potential energy from amber=>lammps conversion: -0.00026418 Difference in potential energy from amber=>desmond conversion: 0.00022093 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00121336 ======================================================================= INFO 2017-03-19 14:08:03 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_4434915.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_4434915.inpcrd') INFO 2017-03-19 14:08:03 Beginning InterMol conversion INFO 2017-03-19 14:08:03 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 14:08:03 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_5631798.inpcrd INFO 2017-03-19 14:08:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5631798/mobley_5631798_converted.input INFO 2017-03-19 14:08:03 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5631798/mobley_5631798_converted.cms INFO 2017-03-19 14:08:18 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5631798/mobley_5631798_converted.rst7 WARNING 2017-03-19 14:08:19 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 14:08:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_5631798/mobley_5631798_converted.inp INFO 2017-03-19 14:08:19 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_5631798/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_5631798/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_5631798/mobley_5631798_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_5631798/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_5631798/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.01974848 -0.01974848 coulomb total 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.01974848 -0.01974848 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.20166880 0.20146914 -0.00019966 0.20146914 -0.00019966 0.20147255 -0.00019625 0.20166880 0.00000000 0.20145960 -0.00020920 bond 0.00878640 0.00891897 0.00013257 0.00891897 0.00013257 0.00891241 0.00012601 0.00878640 0.00000000 0.00891192 0.00012552 bonded 0.21045520 0.21038811 -0.00006709 0.21038811 -0.00006709 0.21038497 -0.00007023 0.21045520 0.00000000 0.21037152 -0.00008368 nonbonded 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.01974848 -0.01974848 potential 0.21045520 0.21038811 -0.00006709 0.21038811 -0.00006709 0.21038409 -0.00007111 0.21045520 0.00000000 0.19062304 -0.01983216 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 0.21045520 Difference in potential energy from amber=>gromacs conversion: -0.00006709 Difference in potential energy from amber=>lammps conversion: -0.00006709 Difference in potential energy from amber=>desmond conversion: -0.00007111 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.01983216 ======================================================================= INFO 2017-03-19 14:08:19 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_5631798.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_5631798.inpcrd') INFO 2017-03-19 14:08:19 Beginning InterMol conversion INFO 2017-03-19 14:08:19 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 14:08:19 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_6359135.inpcrd INFO 2017-03-19 14:08:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6359135/mobley_6359135_converted.input INFO 2017-03-19 14:08:19 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6359135/mobley_6359135_converted.cms INFO 2017-03-19 14:08:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6359135/mobley_6359135_converted.rst7 WARNING 2017-03-19 14:08:35 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 14:08:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_6359135/mobley_6359135_converted.inp INFO 2017-03-19 14:08:35 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_6359135/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_6359135/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_6359135/mobley_6359135_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_6359135/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_6359135/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 coulomb total 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.00792560 1.00789704 -0.00002856 1.00789702 -0.00002858 1.00790418 -0.00002142 1.00792560 0.00000000 1.00784192 -0.00008368 bond 0.08326160 0.08346535 0.00020375 0.08346535 0.00020375 0.08344639 0.00018479 0.08326160 0.00000000 0.08347080 0.00020920 bonded 1.09118720 1.09136239 0.00017519 1.09136237 0.00017517 1.09135057 0.00016337 1.09118720 0.00000000 1.09131272 0.00012552 nonbonded 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00012552 0.00012552 potential 1.09118720 1.09136239 0.00017519 1.09136238 0.00017518 1.09131336 0.00012616 1.09118720 0.00000000 1.09139640 0.00020920 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 1.09118720 Difference in potential energy from amber=>gromacs conversion: 0.00017519 Difference in potential energy from amber=>lammps conversion: 0.00017518 Difference in potential energy from amber=>desmond conversion: 0.00012616 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00020920 ======================================================================= INFO 2017-03-19 14:08:35 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_6359135.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_6359135.inpcrd') INFO 2017-03-19 14:08:35 Beginning InterMol conversion INFO 2017-03-19 14:08:35 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 14:08:35 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_664966.inpcrd INFO 2017-03-19 14:08:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_664966/mobley_664966_converted.input INFO 2017-03-19 14:08:35 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_664966/mobley_664966_converted.cms INFO 2017-03-19 14:08:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_664966/mobley_664966_converted.rst7 WARNING 2017-03-19 14:08:51 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 14:08:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_664966/mobley_664966_converted.inp INFO 2017-03-19 14:08:51 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_664966/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_664966/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_664966/mobley_664966_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_664966/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_664966/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00263592 0.00263592 coulomb total 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00263592 0.00263592 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 9.51441600 9.51433568 -0.00008032 9.51433567 -0.00008033 9.51455010 0.00013410 9.51441600 0.00000000 9.51437416 -0.00004184 bond 3.24678400 3.24688657 0.00010257 3.24688655 0.00010255 3.24662282 -0.00016118 3.24678400 0.00000000 3.24686768 0.00008368 bonded 12.76120000 12.76122225 0.00002225 12.76122222 0.00002222 12.76117292 -0.00002708 12.76120000 0.00000000 12.76124184 0.00004184 nonbonded 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00263592 0.00263592 potential 12.76120000 12.76122225 0.00002225 12.76122218 0.00002218 12.76113870 -0.00006130 12.76120000 0.00000000 12.76391960 0.00271960 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 12.76120000 Difference in potential energy from amber=>gromacs conversion: 0.00002225 Difference in potential energy from amber=>lammps conversion: 0.00002218 Difference in potential energy from amber=>desmond conversion: -0.00006130 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00271960 ======================================================================= INFO 2017-03-19 14:08:51 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_664966.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_664966.inpcrd') INFO 2017-03-19 14:08:51 Beginning InterMol conversion INFO 2017-03-19 14:08:51 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 14:08:51 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_676247.inpcrd INFO 2017-03-19 14:08:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_676247/mobley_676247_converted.input INFO 2017-03-19 14:08:51 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_676247/mobley_676247_converted.cms INFO 2017-03-19 14:09:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_676247/mobley_676247_converted.rst7 WARNING 2017-03-19 14:09:07 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 14:09:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_676247/mobley_676247_converted.inp INFO 2017-03-19 14:09:07 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_676247/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_676247/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_676247/mobley_676247_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_676247/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_676247/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00305432 -0.00305432 coulomb total 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00305432 -0.00305432 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.91080880 2.91085434 0.00004554 2.91085436 0.00004556 2.91086072 0.00005192 2.91080880 0.00000000 2.91097616 0.00016736 bond 0.00125520 0.00142126 0.00016606 0.00142126 0.00016606 0.00143585 0.00018065 0.00125520 0.00000000 0.00142256 0.00016736 bonded 2.91206400 2.91227561 0.00021161 2.91227563 0.00021163 2.91229657 0.00023257 2.91206400 0.00000000 2.91239872 0.00033472 nonbonded 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00305432 -0.00305432 potential 2.91206400 2.91227561 0.00021161 2.91227563 0.00021163 2.91228960 0.00022560 2.91206400 0.00000000 2.90934440 -0.00271960 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 2.91206400 Difference in potential energy from amber=>gromacs conversion: 0.00021161 Difference in potential energy from amber=>lammps conversion: 0.00021163 Difference in potential energy from amber=>desmond conversion: 0.00022560 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.00271960 ======================================================================= INFO 2017-03-19 14:09:07 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_676247.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_676247.inpcrd') INFO 2017-03-19 14:09:07 Beginning InterMol conversion INFO 2017-03-19 14:09:07 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 14:09:07 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7578802.inpcrd INFO 2017-03-19 14:09:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7578802/mobley_7578802_converted.input INFO 2017-03-19 14:09:07 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7578802/mobley_7578802_converted.cms INFO 2017-03-19 14:09:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7578802/mobley_7578802_converted.rst7 WARNING 2017-03-19 14:09:23 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 14:09:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7578802/mobley_7578802_converted.inp INFO 2017-03-19 14:09:23 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7578802/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7578802/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7578802/mobley_7578802_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_7578802/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7578802/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00188280 -0.00188280 coulomb total 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00188280 -0.00188280 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.59659040 2.59654890 -0.00004150 2.59654889 -0.00004151 2.59648883 -0.00010157 2.59659040 0.00000000 2.59663224 0.00004184 bond 1.36565760 1.36557464 -0.00008296 1.36557463 -0.00008297 1.36571448 0.00005688 1.36565760 0.00000000 1.36557392 -0.00008368 bonded 3.96224800 3.96212354 -0.00012446 3.96212353 -0.00012447 3.96220330 -0.00004470 3.96224800 0.00000000 3.96220616 -0.00004184 nonbonded 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00188280 -0.00188280 potential 3.96224800 3.96212354 -0.00012446 3.96212353 -0.00012447 3.96216140 -0.00008660 3.96224800 0.00000000 3.96032336 -0.00192464 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 3.96224800 Difference in potential energy from amber=>gromacs conversion: -0.00012446 Difference in potential energy from amber=>lammps conversion: -0.00012447 Difference in potential energy from amber=>desmond conversion: -0.00008660 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.00192464 ======================================================================= INFO 2017-03-19 14:09:23 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7578802.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7578802.inpcrd') INFO 2017-03-19 14:09:23 Beginning InterMol conversion INFO 2017-03-19 14:09:23 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 14:09:23 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_7732703.inpcrd INFO 2017-03-19 14:09:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7732703/mobley_7732703_converted.input INFO 2017-03-19 14:09:23 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7732703/mobley_7732703_converted.cms INFO 2017-03-19 14:09:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7732703/mobley_7732703_converted.rst7 WARNING 2017-03-19 14:09:39 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 14:09:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_7732703/mobley_7732703_converted.inp INFO 2017-03-19 14:09:39 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_7732703/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_7732703/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_7732703/mobley_7732703_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_7732703/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_7732703/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00150624 -0.00150624 coulomb total 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00150624 -0.00150624 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 1.23386160 1.23400135 0.00013975 1.23400135 0.00013975 1.23392499 0.00006339 1.23386160 0.00000000 1.23407080 0.00020920 bond 1.96857200 1.96871932 0.00014732 1.96871932 0.00014732 1.96856498 -0.00000702 1.96857200 0.00000000 1.96873936 0.00016736 bonded 3.20243360 3.20272067 0.00028707 3.20272066 0.00028706 3.20248997 0.00005637 3.20243360 0.00000000 3.20281016 0.00037656 nonbonded 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00150624 -0.00150624 potential 3.20243360 3.20272067 0.00028707 3.20272066 0.00028706 3.20247357 0.00003997 3.20243360 0.00000000 3.20126208 -0.00117152 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 3.20243360 Difference in potential energy from amber=>gromacs conversion: 0.00028707 Difference in potential energy from amber=>lammps conversion: 0.00028706 Difference in potential energy from amber=>desmond conversion: 0.00003997 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.00117152 ======================================================================= INFO 2017-03-19 14:09:39 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_7732703.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_7732703.inpcrd') INFO 2017-03-19 14:09:39 Beginning InterMol conversion INFO 2017-03-19 14:09:39 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 14:09:39 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8311321.inpcrd INFO 2017-03-19 14:09:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8311321/mobley_8311321_converted.input INFO 2017-03-19 14:09:39 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8311321/mobley_8311321_converted.cms INFO 2017-03-19 14:09:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8311321/mobley_8311321_converted.rst7 WARNING 2017-03-19 14:09:55 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 14:09:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8311321/mobley_8311321_converted.inp INFO 2017-03-19 14:09:55 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8311321/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8311321/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8311321/mobley_8311321_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_8311321/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8311321/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00673624 0.00673624 coulomb total 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00673624 0.00673624 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.83136080 0.83115721 -0.00020359 0.83115721 -0.00020359 0.83104964 -0.00031116 0.83136080 0.00000000 0.83119344 -0.00016736 bond 1.15896800 1.15895749 -0.00001051 1.15895750 -0.00001050 1.15853728 -0.00043072 1.15896800 0.00000000 1.15896800 0.00000000 bonded 1.99032880 1.99011470 -0.00021410 1.99011470 -0.00021410 1.98958692 -0.00074188 1.99032880 0.00000000 1.99016144 -0.00016736 nonbonded 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00673624 0.00673624 potential 1.99032880 1.99011470 -0.00021410 1.99011470 -0.00021410 1.98957710 -0.00075170 1.99032880 0.00000000 1.99685584 0.00652704 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 1.99032880 Difference in potential energy from amber=>gromacs conversion: -0.00021410 Difference in potential energy from amber=>lammps conversion: -0.00021410 Difference in potential energy from amber=>desmond conversion: -0.00075170 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00652704 ======================================================================= INFO 2017-03-19 14:09:55 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8311321.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8311321.inpcrd') INFO 2017-03-19 14:09:55 Beginning InterMol conversion INFO 2017-03-19 14:09:55 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 14:09:55 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_8983100.inpcrd INFO 2017-03-19 14:09:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8983100/mobley_8983100_converted.input INFO 2017-03-19 14:09:55 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8983100/mobley_8983100_converted.cms INFO 2017-03-19 14:10:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8983100/mobley_8983100_converted.rst7 WARNING 2017-03-19 14:10:11 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 14:10:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_8983100/mobley_8983100_converted.inp INFO 2017-03-19 14:10:11 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_8983100/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_8983100/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_8983100/mobley_8983100_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_8983100/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_8983100/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00004184 -0.00004184 coulomb total 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00004184 -0.00004184 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 4.43127440 4.43148362 0.00020922 4.43148360 0.00020920 4.43137724 0.00010284 4.43127440 0.00000000 4.43156728 0.00029288 bond 0.91336720 0.91339297 0.00002577 0.91339297 0.00002577 0.91336167 -0.00000553 0.91336720 0.00000000 0.91340904 0.00004184 bonded 5.34464160 5.34487659 0.00023499 5.34487657 0.00023497 5.34473892 0.00009732 5.34464160 0.00000000 5.34497632 0.00033472 nonbonded 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00004184 -0.00004184 potential 5.34464160 5.34487659 0.00023499 5.34487674 0.00023514 5.34472967 0.00008807 5.34464160 0.00000000 5.34493448 0.00029288 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 5.34464160 Difference in potential energy from amber=>gromacs conversion: 0.00023499 Difference in potential energy from amber=>lammps conversion: 0.00023514 Difference in potential energy from amber=>desmond conversion: 0.00008807 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00029288 ======================================================================= INFO 2017-03-19 14:10:11 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_8983100.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_8983100.inpcrd') INFO 2017-03-19 14:10:11 Beginning InterMol conversion INFO 2017-03-19 14:10:11 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 14:10:11 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9029594.inpcrd INFO 2017-03-19 14:10:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9029594/mobley_9029594_converted.input INFO 2017-03-19 14:10:11 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9029594/mobley_9029594_converted.cms INFO 2017-03-19 14:10:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9029594/mobley_9029594_converted.rst7 WARNING 2017-03-19 14:10:27 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 14:10:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9029594/mobley_9029594_converted.inp INFO 2017-03-19 14:10:27 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9029594/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9029594/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9029594/mobley_9029594_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_9029594/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9029594/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00317984 -0.00317984 coulomb total 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00317984 -0.00317984 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.22175200 0.22194821 0.00019621 0.22194821 0.00019621 0.22197396 0.00022196 0.22175200 0.00000000 0.22196120 0.00020920 bond 0.23932480 0.23913083 -0.00019397 0.23913083 -0.00019397 0.23917486 -0.00014994 0.23932480 0.00000000 0.23911560 -0.00020920 bonded 0.46107680 0.46107904 0.00000224 0.46107904 0.00000224 0.46114882 0.00007202 0.46107680 0.00000000 0.46107680 0.00000000 nonbonded 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00317984 -0.00317984 potential 0.46107680 0.46107904 0.00000224 0.46107906 0.00000226 0.46114616 0.00006936 0.46107680 0.00000000 0.45789696 -0.00317984 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 0.46107680 Difference in potential energy from amber=>gromacs conversion: 0.00000224 Difference in potential energy from amber=>lammps conversion: 0.00000226 Difference in potential energy from amber=>desmond conversion: 0.00006936 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.00317984 ======================================================================= INFO 2017-03-19 14:10:27 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9029594.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9029594.inpcrd') INFO 2017-03-19 14:10:27 Beginning InterMol conversion INFO 2017-03-19 14:10:27 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 14:10:27 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9055303.inpcrd INFO 2017-03-19 14:10:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9055303/mobley_9055303_converted.input INFO 2017-03-19 14:10:27 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9055303/mobley_9055303_converted.cms INFO 2017-03-19 14:10:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9055303/mobley_9055303_converted.rst7 WARNING 2017-03-19 14:10:43 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 14:10:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9055303/mobley_9055303_converted.inp INFO 2017-03-19 14:10:43 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9055303/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9055303/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9055303/mobley_9055303_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_9055303/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9055303/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 0.37907040 0.37925901 0.00018861 0.37925901 0.00018861 0.37925997 0.00018957 0.37907040 0.00000000 0.37927960 0.00020920 bond 0.00041840 0.00022847 -0.00018993 0.00022847 -0.00018993 0.00022858 -0.00018982 0.00041840 0.00000000 0.00020920 -0.00020920 bonded 0.37948880 0.37948747 -0.00000133 0.37948747 -0.00000133 0.37948855 -0.00000025 0.37948880 0.00000000 0.37948880 0.00000000 potential 0.37948880 0.37948747 -0.00000133 0.37948747 -0.00000133 0.37948661 -0.00000219 0.37948880 0.00000000 0.37953064 0.00004184 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 0.37948880 Difference in potential energy from amber=>gromacs conversion: -0.00000133 Difference in potential energy from amber=>lammps conversion: -0.00000133 Difference in potential energy from amber=>desmond conversion: -0.00000219 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: 0.00004184 ======================================================================= INFO 2017-03-19 14:10:43 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9055303.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9055303.inpcrd') INFO 2017-03-19 14:10:43 Beginning InterMol conversion INFO 2017-03-19 14:10:43 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference: Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1 INFO 2017-03-19 14:10:43 Evaluating energy of $RUNPATH/FreeSolv/prmcrd/mobley_9246351.inpcrd INFO 2017-03-19 14:10:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9246351/mobley_9246351_converted.input INFO 2017-03-19 14:10:43 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9246351/mobley_9246351_converted.cms INFO 2017-03-19 14:10:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9246351/mobley_9246351_converted.rst7 WARNING 2017-03-19 14:10:59 CHARMM energy input file not used, information recreated from command line options INFO 2017-03-19 14:10:59 Evaluating energy of $RUNPATH/FreeSolv/converted/mobley_9246351/mobley_9246351_converted.inp INFO 2017-03-19 14:10:59 InterMol Conversion Energy Comparison Results amber input energy file: $RUNPATH/FreeSolv/prmcrd/amber.out gromacs output energy file: $RUNPATH/FreeSolv/converted/mobley_9246351/energy.xvg lammps output energy file: $RUNPATH/FreeSolv/converted/mobley_9246351/lammps_stdout.txt desmond output energy file: $RUNPATH/FreeSolv/converted/mobley_9246351/mobley_9246351_converted.enegrp.dat amber output energy file: $RUNPATH/FreeSolv/converted/mobley_9246351/amber.out charmm output energy file: $RUNPATH/FreeSolv/converted/mobley_9246351/charmm_stdout.txt Energy group summary ======================================================================= type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm) ----------------------------------------------------------------------- Not comparable energies: are likely not to be the same ----------------------------------------------------------------------- coulomb (SR) 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00322168 -0.00322168 coulomb total 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00322168 -0.00322168 ----------------------------------------------------------------------- Comparable energy terms: these should be very close ----------------------------------------------------------------------- angle 2.01585120 2.01583872 -0.00001248 2.01583873 -0.00001247 2.01593766 0.00008646 2.01585120 0.00000000 2.01589304 0.00004184 bond 2.22839840 2.22826059 -0.00013781 2.22826058 -0.00013782 2.22781587 -0.00058253 2.22839840 0.00000000 2.22827288 -0.00012552 bonded 4.24424960 4.24409931 -0.00015029 4.24409931 -0.00015029 4.24375353 -0.00049607 4.24424960 0.00000000 4.24416592 -0.00008368 nonbonded 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -0.00322168 -0.00322168 potential 4.24424960 4.24409931 -0.00015029 4.24409939 -0.00015021 4.24373124 -0.00051836 4.24424960 0.00000000 4.24094424 -0.00330536 ---------------- Total Potential Energy Comparison -------------------- Input amber potential energy: 4.24424960 Difference in potential energy from amber=>gromacs conversion: -0.00015029 Difference in potential energy from amber=>lammps conversion: -0.00015021 Difference in potential energy from amber=>desmond conversion: -0.00051836 Difference in potential energy from amber=>amber conversion: 0.00000000 Difference in potential energy from amber=>charmm conversion: -0.00330536 ======================================================================= INFO 2017-03-19 14:10:59 Finished! ('$RUNPATH/FreeSolv/prmcrd/mobley_9246351.prmtop', '$RUNPATH/FreeSolv/prmcrd/mobley_9246351.inpcrd') Directory ./converted/mobley_1929982 already exists