A Comparative Test for ACEPYPE

Running a testing routine, I used pymol to generate 22 pdb files. They are tripeptides of every usual amino acid residue including 2 variants for HIS. All peptides have N- and T- termini.

I used GROMACS 4.5 with all these tripeptides to generate topology files with AMBER99SB forcefield as reference.

OBS: peptides JJJ.pdb (Hip-Hip-Hip) and RRR.pdb (Arg-Arg-Arg): their net charge should be +3, but gasteiger method (the way how ACPYPE try to guess the net charge of the molecule if not given) failed to get the right value, instead it says it is 'Zero', for which SQM programme will fail to calculate the atomic partial charges. So be aware that ACPYPE may guess a wrong net charge when running it on your own molecule.

Next, I used ACPYPE to generate the topologies and parameters for these 22 entries and compare theirs results with the ones from GROMACS reference.

By using ACPYPE with option '-a amber' (which means parm99.dat + gaff.dat + frcmod.ff99SB + frcmod.parmbsc0), it seems to give better results than using just GAFF (the default option in ACPYPE) when comparing with GROMACS outputs, i.e., the former basically got almost all atom types and parameters identical to the GROMACS with AMBER99SB reference, while the latter missed just a few more.

A more detailed comparison between ACPYPE with option '-a amber' against GROMACS' AMBER99SB (including a Single Point Energy minimisation with GROMACS) results and it can be seen that they match except by:

in terms of topology

• • entries HHH (Hie-Hie-Hie), JJJ (Hip-Hip-Hip), OOO (Hid-Hid-Hid), RRR (Arg-Arg-Arg) and WWW (Trp-Trp-Trp) have some improper dihedrals inverted;

  • WWW which has 3 extra improper dihedrals related to atoms sharing in the 5-ring and 6-ring of the TRP. These improper dihedrals would be there in order to keep the planarity between 5-ring and 6-ring;

  • YYY (Tyr-Tyr-Tyr) for which atom CZ (id 15, 36 and 57) got atom type CA instead of C in GROMACS.

in terms of parameters

• • charges (can be either gasteiger or bcc with ACPYPE);

  • YYY: 6 bonds and 9 dihedrals, all involving atom CZ (id 15, 36 and 57), because of atom type changing mentioned above;

When we look the bonded potential energies for all entries, the difference is no bigger than 0.002% (even for the entries with inverted improper dihedrals) with one solely exception: YYY with 1.9%, because of the atom type change seen above.

The source code for these tests can be seen here.

See detailed output here.

usePymol: True, ffType: amber, cType: gas  File AAA.pdb : residue ALA Compare ACPYPE x GMX AMBER99SB topol & param     ==> Comparing atomtypes AC x AMBER         atomtypes OK     ==> Comparing pairs         pairs OK     ==> Comparing bonds         bonds OK     ==> Comparing angles         angles OK     ==> Comparing dihedrals         dihedrals OK Compare ACPYPE x GMX AMBER99SB Pot. Energy (|ERROR|%)           LJ-14   0.000         LJ_(SR)   0.000      Coulomb-14   76.981   215.415000 x 935.821000    Coulomb_(SR)   62.786   -387.017000 x -1039.970000  TotalNonBonded   42.492   -158.744190 x -91.291190       Potential   63.728   38.393100 x 105.849000           Angle   0.000            Bond   0.000     Proper_Dih.   0.000   Improper_Dih.   0.000    Dihedral P+I   0.000    Total_Bonded   0.001  File CCC.pdb : residue CYS Compare ACPYPE x GMX AMBER99SB topol & param     ==> Comparing atomtypes AC x AMBER         atomtypes OK     ==> Comparing pairs         pairs OK     ==> Comparing bonds         bonds OK     ==> Comparing angles         angles OK     ==> Comparing dihedrals         dihedrals OK Compare ACPYPE x GMX AMBER99SB Pot. Energy (|ERROR|%)           LJ-14   0.000         LJ_(SR)   0.000      Coulomb-14   76.949   188.291000 x 816.834000    Coulomb_(SR)   59.574   -342.955000 x -848.355000  TotalNonBonded   80.193   -153.559000 x -30.416000       Potential   72.553   46.585300 x 169.729000           Angle   0.000            Bond   0.000     Proper_Dih.   0.000   Improper_Dih.   0.000    Dihedral P+I   0.000    Total_Bonded   0.000  File DDD.pdb : residue ASP Compare ACPYPE x GMX AMBER99SB topol & param     ==> Comparing atomtypes AC x AMBER         atomtypes OK     ==> Comparing pairs         pairs OK     ==> Comparing bonds         bonds OK     ==> Comparing angles         angles OK     ==> Comparing dihedrals         dihedrals OK Compare ACPYPE x GMX AMBER99SB Pot. Energy (|ERROR|%)           LJ-14   0.000         LJ_(SR)   0.000      Coulomb-14   98.557   20.689000 x 1434.240000    Coulomb_(SR)   152.312   413.830000 x -791.079000  TotalNonBonded   32.568   432.001700 x 640.643700       Potential   24.480   643.643000 x 852.282000           Angle   0.000            Bond   0.000     Proper_Dih.   0.000   Improper_Dih.   0.000    Dihedral P+I   0.000    Total_Bonded   0.001  File EEE.pdb : residue GLU Compare ACPYPE x GMX AMBER99SB topol & param     ==> Comparing atomtypes AC x AMBER         atomtypes OK     ==> Comparing pairs         pairs OK     ==> Comparing bonds         bonds OK     ==> Comparing angles         angles OK     ==> Comparing dihedrals         dihedrals OK Compare ACPYPE x GMX AMBER99SB Pot. Energy (|ERROR|%)           LJ-14   0.000         LJ_(SR)   0.000      Coulomb-14   84.382   146.496000 x 937.969000    Coulomb_(SR)   113.598   54.962600 x -404.192000  TotalNonBonded   61.892   204.617700 x 536.936100       Potential   42.278   453.717000 x 786.037000           Angle   0.000            Bond   0.000     Proper_Dih.   0.000   Improper_Dih.   0.000    Dihedral P+I   0.000    Total_Bonded   0.001  File FFF.pdb : residue PHE Compare ACPYPE x GMX AMBER99SB topol & param     ==> Comparing atomtypes AC x AMBER         atomtypes OK     ==> Comparing pairs         pairs OK     ==> Comparing bonds         bonds OK     ==> Comparing angles         angles OK     ==> Comparing dihedrals         dihedrals OK Compare ACPYPE x GMX AMBER99SB Pot. Energy (|ERROR|%)           LJ-14   0.000         LJ_(SR)   0.000      Coulomb-14   78.357   182.820000 x 844.711000    Coulomb_(SR)   63.253   -377.329000 x -1026.840000  TotalNonBonded   7.267   -170.350100 x -157.970100       Potential   16.913   60.805000 x 73.182000           Angle   0.000            Bond   0.000     Proper_Dih.   0.000   Improper_Dih.   0.000    Dihedral P+I   0.000    Total_Bonded   0.001  File GGG.pdb : residue GLY Compare ACPYPE x GMX AMBER99SB topol & param     ==> Comparing atomtypes AC x AMBER         atomtypes OK     ==> Comparing pairs         pairs OK     ==> Comparing bonds         bonds OK     ==> Comparing angles         angles OK     ==> Comparing dihedrals         dihedrals OK Compare ACPYPE x GMX AMBER99SB Pot. Energy (|ERROR|%)           LJ-14   0.000         LJ_(SR)   0.000      Coulomb-14   73.451   173.346000 x 652.926000    Coulomb_(SR)   61.248   -357.586000 x -922.746000  TotalNonBonded   34.100   -165.389450 x -250.969450       Potential   58.507   146.272000 x 60.692400           Angle   0.000            Bond   0.000     Proper_Dih.   0.000   Improper_Dih.   0.000    Dihedral P+I   0.000    Total_Bonded   0.000  File HHH.pdb : residue HIE Compare ACPYPE x GMX AMBER99SB topol & param     ==> Comparing atomtypes AC x AMBER         atomtypes OK     ==> Comparing pairs         pairs OK     ==> Comparing bonds         bonds OK     ==> Comparing angles         angles OK     ==> Comparing dihedrals         dihedrals OK Compare ACPYPE x GMX AMBER99SB Pot. Energy (|ERROR|%)           LJ-14   0.000         LJ_(SR)   0.000      Coulomb-14   81.888   173.302000 x 956.861000    Coulomb_(SR)   69.494   -348.907000 x -1143.720000  TotalNonBonded   5.514   -192.836000 x -204.090000       Potential   3.084   365.312000 x 354.047000           Angle   0.000            Bond   0.001     Proper_Dih.   0.000   Improper_Dih.   1.532   0.898273 x 0.884509    Dihedral P+I   0.014    Total_Bonded   0.002 ('IDIH: Amb diff Acp', ['10 13 11 12', '23 26 32 27', '26 30 32 33', '27 30 28 29', '40 43 49 44', '43 47 49 50', '44 47 45 46', '6 9 15 10', '9 13 15 16']) ('IDIH: Acp diff Amb', ['12 13 11 10', '23 32 26 27', '26 33 32 30', '29 30 28 27', '40 49 43 44', '43 50 49 47', '46 47 45 44', '6 15 9 10', '9 16 15 13'])  File III.pdb : residue ILE Compare ACPYPE x GMX AMBER99SB topol & param     ==> Comparing atomtypes AC x AMBER         atomtypes OK     ==> Comparing pairs         pairs OK     ==> Comparing bonds         bonds OK     ==> Comparing angles         angles OK     ==> Comparing dihedrals         dihedrals OK Compare ACPYPE x GMX AMBER99SB Pot. Energy (|ERROR|%)           LJ-14   0.000         LJ_(SR)   0.000      Coulomb-14   69.230   199.075000 x 646.988000    Coulomb_(SR)   58.412   -354.812000 x -853.159000  TotalNonBonded   24.390   -156.344000 x -206.778000       Potential   35.203   143.271000 x 92.835900           Angle   0.000            Bond   0.000     Proper_Dih.   0.000   Improper_Dih.   0.000    Dihedral P+I   0.000    Total_Bonded   0.000  File JJJ.pdb : residue HIP Compare ACPYPE x GMX AMBER99SB topol & param     ==> Comparing atomtypes AC x AMBER         atomtypes OK     ==> Comparing pairs         pairs OK     ==> Comparing bonds         bonds OK     ==> Comparing angles         angles OK     ==> Comparing dihedrals         dihedrals OK Compare ACPYPE x GMX AMBER99SB Pot. Energy (|ERROR|%)           LJ-14   0.000         LJ_(SR)   0.000      Coulomb-14   90.527   101.523000 x 1071.690000    Coulomb_(SR)   69.386   -309.479000 x -94.742400  TotalNonBonded   123.848   -228.163800 x 956.739800       Potential   73.287   431.906000 x 1616.810000           Angle   0.000            Bond   0.000     Proper_Dih.   0.000   Improper_Dih.   0.461   1.165150 x 1.159780    Dihedral P+I   0.006    Total_Bonded   0.000 ('IDIH: Amb diff Acp', ['10 14 12 13', '24 27 34 28', '27 32 34 35', '28 32 30 31', '42 45 52 46', '45 50 52 53', '46 50 48 49', '6 9 16 10', '9 14 16 17']) ('IDIH: Acp diff Amb', ['13 10 12 14', '24 34 27 28', '27 35 34 32', '31 28 30 32', '42 52 45 46', '45 53 52 50', '49 46 48 50', '6 16 9 10', '9 17 16 14'])  File KKK.pdb : residue LYS Compare ACPYPE x GMX AMBER99SB topol & param     ==> Comparing atomtypes AC x AMBER         atomtypes OK     ==> Comparing pairs         pairs OK     ==> Comparing bonds         bonds OK     ==> Comparing angles         angles OK     ==> Comparing dihedrals         dihedrals OK Compare ACPYPE x GMX AMBER99SB Pot. Energy (|ERROR|%)           LJ-14   0.000         LJ_(SR)   0.000      Coulomb-14   74.108   339.525000 x 1311.310000    Coulomb_(SR)   103.779   23.481500 x -621.413000  TotalNonBonded   47.224   365.320900 x 692.211400       Potential   34.840   611.384000 x 938.277000           Angle   0.000            Bond   0.000     Proper_Dih.   0.000   Improper_Dih.   0.000    Dihedral P+I   0.000    Total_Bonded   0.001  File LLL.pdb : residue LEU Compare ACPYPE x GMX AMBER99SB topol & param     ==> Comparing atomtypes AC x AMBER         atomtypes OK     ==> Comparing pairs         pairs OK     ==> Comparing bonds         bonds OK     ==> Comparing angles         angles OK     ==> Comparing dihedrals         dihedrals OK Compare ACPYPE x GMX AMBER99SB Pot. Energy (|ERROR|%)           LJ-14   0.000         LJ_(SR)   0.000      Coulomb-14   74.848   186.743000 x 742.452000    Coulomb_(SR)   69.131   -349.887000 x -1133.470000  TotalNonBonded   58.805   -159.631700 x -387.505700       Potential   173.384   96.444700 x -131.425000           Angle   0.000            Bond   0.000     Proper_Dih.   0.000   Improper_Dih.   0.000    Dihedral P+I   0.000    Total_Bonded   0.002  File MMM.pdb : residue MET Compare ACPYPE x GMX AMBER99SB topol & param     ==> Comparing atomtypes AC x AMBER         atomtypes OK     ==> Comparing pairs         pairs OK     ==> Comparing bonds         bonds OK     ==> Comparing angles         angles OK     ==> Comparing dihedrals         dihedrals OK Compare ACPYPE x GMX AMBER99SB Pot. Energy (|ERROR|%)           LJ-14   0.000         LJ_(SR)   0.000      Coulomb-14   76.769   198.587000 x 854.851000    Coulomb_(SR)   65.492   -351.183000 x -1017.690000  TotalNonBonded   6.061   -158.745400 x -168.988400       Potential   15.269   67.102100 x 56.856000           Angle   0.000            Bond   0.001     Proper_Dih.   0.000   Improper_Dih.   0.000    Dihedral P+I   0.000    Total_Bonded   0.001  File NNN.pdb : residue ASN Compare ACPYPE x GMX AMBER99SB topol & param     ==> Comparing atomtypes AC x AMBER         atomtypes OK     ==> Comparing pairs         pairs OK     ==> Comparing bonds         bonds OK     ==> Comparing angles         angles OK     ==> Comparing dihedrals         dihedrals OK Compare ACPYPE x GMX AMBER99SB Pot. Energy (|ERROR|%)           LJ-14   0.000         LJ_(SR)   0.000      Coulomb-14   91.472   23.449900 x 274.966000    Coulomb_(SR)   70.875   -405.220000 x -1391.320000  TotalNonBonded   65.275   -390.779400 x -1125.363300       Potential   93.657   -49.749900 x -784.336000           Angle   0.001            Bond   0.000     Proper_Dih.   0.000   Improper_Dih.   0.000    Dihedral P+I   0.000    Total_Bonded   0.001  File OOO.pdb : residue HID Compare ACPYPE x GMX AMBER99SB topol & param     ==> Comparing atomtypes AC x AMBER         atomtypes OK     ==> Comparing pairs         pairs OK     ==> Comparing bonds         bonds OK     ==> Comparing angles         angles OK     ==> Comparing dihedrals         dihedrals OK Compare ACPYPE x GMX AMBER99SB Pot. Energy (|ERROR|%)           LJ-14   0.000         LJ_(SR)   0.000      Coulomb-14   79.204   141.251000 x 679.208000    Coulomb_(SR)   67.748   -314.460000 x -975.015000  TotalNonBonded   40.869   -177.377900 x -299.975900       Potential   24.679   496.783000 x 374.182000           Angle   0.000            Bond   0.000     Proper_Dih.   0.000   Improper_Dih.   0.209   1.048090 x 1.045900    Dihedral P+I   0.002    Total_Bonded   0.000 ('IDIH: Amb diff Acp', ['10 14 12 13', '23 26 32 27', '26 31 32 33', '27 31 29 30', '40 43 49 44', '43 48 49 50', '44 48 46 47', '6 9 15 10', '9 14 15 16']) ('IDIH: Acp diff Amb', ['13 10 12 14', '23 32 26 27', '26 33 32 31', '30 27 29 31', '40 49 43 44', '43 50 49 48', '47 44 46 48', '6 15 9 10', '9 16 15 14'])  File PPP.pdb : residue PRO Compare ACPYPE x GMX AMBER99SB topol & param     ==> Comparing atomtypes AC x AMBER         atomtypes OK     ==> Comparing pairs         pairs OK     ==> Comparing bonds         bonds OK     ==> Comparing angles         angles OK     ==> Comparing dihedrals         dihedrals OK Compare ACPYPE x GMX AMBER99SB Pot. Energy (|ERROR|%)           LJ-14   0.000         LJ_(SR)   0.000      Coulomb-14   73.364   218.006000 x 818.454000    Coulomb_(SR)   55.847   -313.270000 x -709.513000  TotalNonBonded   172.715   -85.972800 x 118.232200       Potential   30.996   454.618000 x 658.824000           Angle   0.000            Bond   0.000     Proper_Dih.   0.000   Improper_Dih.   0.000    Dihedral P+I   0.000    Total_Bonded   0.000  File QQQ.pdb : residue GLN Compare ACPYPE x GMX AMBER99SB topol & param     ==> Comparing atomtypes AC x AMBER         atomtypes OK     ==> Comparing pairs         pairs OK     ==> Comparing bonds         bonds OK     ==> Comparing angles         angles OK     ==> Comparing dihedrals         dihedrals OK Compare ACPYPE x GMX AMBER99SB Pot. Energy (|ERROR|%)           LJ-14   0.000         LJ_(SR)   0.000      Coulomb-14   184.660   104.048000 x -88.087400    Coulomb_(SR)   53.699   -396.819000 x -857.046000  TotalNonBonded   69.174   -290.715400 x -943.077800       Potential   123.577   124.461000 x -527.902000           Angle   0.000            Bond   0.001     Proper_Dih.   0.000   Improper_Dih.   0.000    Dihedral P+I   0.000    Total_Bonded   0.000  File RRR.pdb : residue ARG Compare ACPYPE x GMX AMBER99SB topol & param     ==> Comparing atomtypes AC x AMBER         atomtypes OK     ==> Comparing pairs         pairs OK     ==> Comparing bonds         bonds OK     ==> Comparing angles         angles OK     ==> Comparing dihedrals         dihedrals OK Compare ACPYPE x GMX AMBER99SB Pot. Energy (|ERROR|%)           LJ-14   0.000         LJ_(SR)   0.000      Coulomb-14   82.729   -504.705000 x -2922.250000    Coulomb_(SR)   44.608   772.922000 x 1395.370000  TotalNonBonded   117.425   266.374400 x -1528.722600       Potential   145.008   557.173000 x -1237.930000           Angle   0.000            Bond   0.001     Proper_Dih.   0.000   Improper_Dih.   1.900   0.359230 x 0.352406    Dihedral P+I   0.012    Total_Bonded   0.002 ('IDIH: Amb diff Acp', ['12 17 15 16', '36 41 39 40', '60 65 63 64']) ('IDIH: Acp diff Amb', ['17 12 15 16', '41 36 39 40', '65 60 63 64'])  File SSS.pdb : residue SER Compare ACPYPE x GMX AMBER99SB topol & param     ==> Comparing atomtypes AC x AMBER         atomtypes OK     ==> Comparing pairs         pairs OK     ==> Comparing bonds         bonds OK     ==> Comparing angles         angles OK     ==> Comparing dihedrals         dihedrals OK Compare ACPYPE x GMX AMBER99SB Pot. Energy (|ERROR|%)           LJ-14   0.000         LJ_(SR)   0.000      Coulomb-14   49.075   193.833000 x 380.621000    Coulomb_(SR)   51.509   -278.751000 x -574.856000  TotalNonBonded   58.465   -77.661300 x -186.978300       Potential   88.782   123.129000 x 13.812000           Angle   0.000            Bond   0.001     Proper_Dih.   0.000   Improper_Dih.   0.000    Dihedral P+I   0.000    Total_Bonded   0.000  File TTT.pdb : residue THR Compare ACPYPE x GMX AMBER99SB topol & param     ==> Comparing atomtypes AC x AMBER         atomtypes OK     ==> Comparing pairs         pairs OK     ==> Comparing bonds         bonds OK     ==> Comparing angles         angles OK     ==> Comparing dihedrals         dihedrals OK Compare ACPYPE x GMX AMBER99SB Pot. Energy (|ERROR|%)           LJ-14   0.000         LJ_(SR)   0.000      Coulomb-14   166.024   135.605000 x -205.387000    Coulomb_(SR)   29.208   -339.284000 x -479.267000  TotalNonBonded   70.431   -201.923900 x -682.898900       Potential   105.054   23.138000 x -457.837000           Angle   0.000            Bond   0.001     Proper_Dih.   0.000   Improper_Dih.   0.000    Dihedral P+I   0.000    Total_Bonded   0.000  File VVV.pdb : residue VAL Compare ACPYPE x GMX AMBER99SB topol & param     ==> Comparing atomtypes AC x AMBER         atomtypes OK     ==> Comparing pairs         pairs OK     ==> Comparing bonds         bonds OK     ==> Comparing angles         angles OK     ==> Comparing dihedrals         dihedrals OK Compare ACPYPE x GMX AMBER99SB Pot. Energy (|ERROR|%)           LJ-14   0.000         LJ_(SR)   0.000      Coulomb-14   6.013   195.043000 x 207.522000    Coulomb_(SR)   46.468   -353.881000 x -661.068000  TotalNonBonded   65.080   -158.129200 x -452.837200       Potential   142.174   87.421000 x -207.287000           Angle   0.000            Bond   0.000     Proper_Dih.   0.000   Improper_Dih.   0.000    Dihedral P+I   0.000    Total_Bonded   0.000  File WWW.pdb : residue TRP Compare ACPYPE x GMX AMBER99SB topol & param     ==> Comparing atomtypes AC x AMBER         atomtypes OK     ==> Comparing pairs         pairs OK     ==> Comparing bonds         bonds OK     ==> Comparing angles         angles OK     ==> Comparing dihedrals ('    ac: ', [[16, 24, 15, 13, 4, 180.0, 4.602, 2.0], [40, 48, 39, 37, 4, 180.0, 4.602, 2.0], [64, 72, 63, 61, 4, 180.0, 4.602, 2.0]]) Compare ACPYPE x GMX AMBER99SB Pot. Energy (|ERROR|%)           LJ-14   0.000         LJ_(SR)   0.000      Coulomb-14   77.500   227.454000 x 1010.900000    Coulomb_(SR)   60.345   -430.220000 x -1084.920000  TotalNonBonded   61.207   -210.345000 x -81.599000       Potential   52.058   118.566000 x 247.309000           Angle   0.000            Bond   0.000     Proper_Dih.   0.000   Improper_Dih.   0.598   0.190516 x 0.189376    Dihedral P+I   0.002    Total_Bonded   0.001 ('IDIH: Amb diff Acp', ['10 14 12 13', '14 17 15 16', '33 36 34 35', '34 38 36 37', '38 41 39 40', '57 60 58 59', '58 62 60 61', '62 65 63 64', '9 12 10 11']) ('IDIH: Acp diff Amb', ['14 10 12 13', '15 23 14 12', '17 14 15 16', '33 35 34 36', '38 34 36 37', '39 47 38 36', '41 38 39 40', '57 59 58 60', '62 58 60 61', '63 71 62 60', '65 62 63 64', '9 11 10 12'])  File YYY.pdb : residue TYR Compare ACPYPE x GMX AMBER99SB topol & param     ==> Comparing atomtypes AC x AMBER     15 CZ AC: CA   x   AMB: C     36 CZ AC: CA   x   AMB: C     57 CZ AC: CA   x   AMB: C     ==> Comparing pairs         pairs OK     ==> Comparing bonds ('    ac: ', [[13, 15, 1, 0.14, 392460.0], [13, 15, 1, 0.141, 392460.0], [15, 18, 1, 0.14, 392460.0], [15, 18, 1, 0.141, 392460.0], [34, 36, 1, 0.14, 392460.0], [34, 36, 1, 0.141, 392460.0], [36, 39, 1, 0.14, 392460.0], [36, 39, 1, 0.141, 392460.0], [55, 57, 1, 0.14, 392460.0], [55, 57, 1, 0.141, 392460.0], [57, 60, 1, 0.14, 392460.0], [57, 60, 1, 0.141, 392460.0]])     ==> Comparing angles         angles OK     ==> Comparing dihedrals ('    ac: ', [[13, 15, 16, 17, 9, 180.0, 9.623, 2.0], [17, 16, 15, 18, 9, 180.0, 3.766, 2.0], [18, 15, 16, 17, 9, 180.0, 9.623, 2.0], [34, 36, 37, 38, 9, 180.0, 9.623, 2.0], [38, 37, 36, 39, 9, 180.0, 3.766, 2.0], [39, 36, 37, 38, 9, 180.0, 9.623, 2.0], [55, 57, 58, 59, 9, 180.0, 9.623, 2.0], [59, 58, 57, 60, 9, 180.0, 3.766, 2.0], [60, 57, 58, 59, 9, 180.0, 9.623, 2.0]]) Compare ACPYPE x GMX AMBER99SB Pot. Energy (|ERROR|%)           LJ-14   0.000         LJ_(SR)   0.000      Coulomb-14   78.850   146.778000 x 693.988000    Coulomb_(SR)   66.753   -367.937000 x -1106.690000  TotalNonBonded   49.296   -197.017700 x -388.560700       Potential   121.680   151.870000 x -32.925800           Angle   0.000            Bond   0.967   215.247000 x 217.349000     Proper_Dih.   7.765   55.205700 x 59.853100   Improper_Dih.   0.000    Dihedral P+I   7.749   55.323112 x 59.970512    Total_Bonded   1.897   348.887700 x 355.634900