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Force Field X - Software for Molecular Biophysics
http://ffx.biochem.uiowa.edu/
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ffxc Biotype generation #268

Open pradipchm opened 4 days ago

pradipchm commented 4 days ago

Hi, I am trying to generate the biotype from an XYZ file for FFtoXML conversion. I am using

ffxc Biotype --name ROY --writePDB ROY.xyz

here is my xyz file

27 xxx
     1  S     -1.202900   -1.366136   -0.334602      401   15    18
     2  O      0.829206    1.293421   -1.770546      402    5
     3  O      2.860304    2.108980   -1.498071      402    5
     4  N      0.121997    0.664083    0.884464      403    9    15    19
     5  N      1.954630    1.294270   -1.242367      404    2     3    10
     6  N     -2.589823    3.171789    1.547201      405    7
     7  C     -2.482501    2.096627    1.060140      406    6    16
     8  C     -3.717386   -2.267154   -1.239056      407   18    20    21    22
     9  C      1.327059   -0.061053    0.735308      408    4    10    14
    10  C      2.252888    0.246548   -0.272914     409    5     9    11
    11  C      3.472479   -0.414307   -0.392133     410   10    12    23
    12  C      3.756735   -1.456534    0.490317     411   11    13    24
    13  C      2.844352   -1.799304    1.492733     412   12    14    25
    14  C      1.645358   -1.096823    1.622060     413    9    13    26
    15  C     -1.078377    0.184176    0.432699     414    1     4    16
    16  C     -2.318350    0.808732    0.488860     415    7    15    17
    17  C     -3.362593    0.018366   -0.093628     416   16    18    27
    18  C     -2.924487   -1.182274   -0.581077     417    1     8    17
    19  H      0.148809    1.609778    1.255676     418    4
    20  H     -4.763570   -1.955955   -1.297914     419    8
    21  H     -3.671487   -3.202893   -0.673553     419    8
    22  H     -3.363923   -2.469876   -2.254595     419    8
    23  H      4.166416   -0.128446   -1.176765     420   11
    24  H      4.695595   -1.994828    0.397647     421   12
    25  H      3.073505   -2.604712    2.184927     422   13
    26  H      0.945609   -1.325897    2.421689     423   14
    27  H     -4.399323    0.338804   -0.139483     424   17

I am getting an error like

Executing internal script: ffx.potential.groovy.Biotype

 Parsing: Internal force field (amoeba-bio-2018).
 Parsing: JVM system properties (i.e. command line -Dkey=value pairs).

 Opening ROY.xyz with 27 atoms

Nov 23, 2024 4:13:31 PM ffx.potential.parsers.XYZFilter readFile
WARNING: Check atom type 401 for Atom 1 in ROY.xyz

Nov 23, 2024 4:13:31 PM ffx.ui.UIFileOpener open
WARNING:  Failed to read file ROY.xyz

Exception in thread "Thread-8" java.lang.NullPointerException: Cannot invoke "ffx.ui.FFXSystem.toString()" because "ffxSystem" is null
        at ffx.ui.UIFileOpener.stopTimer(UIFileOpener.java:257)
        at ffx.ui.UIFileOpener.open(UIFileOpener.java:236)
        at ffx.ui.UIFileOpener.run(UIFileOpener.java:158)
        at java.base/java.lang.Thread.run(Thread.java:1575)
Nov 23, 2024 4:13:31 PM ffx.ui.ModelingShell runFFXScript
SEVERE:  Uncaught error: FFX is shutting down.

java.lang.NullPointerException: Cannot read the array length because "allSystems" is null
        at ffx.ui.MainPanel.openWait(MainPanel.java:1589)
        at ffx.ui.UIUtils.open(UIUtils.java:163)
        at ffx.ui.UIUtils.open(UIUtils.java:73)
        at ffx.potential.cli.PotentialScript.getActiveAssembly(PotentialScript.java:211)
        at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:336)
        at ffx.potential.groovy.Biotype.run(Biotype.groovy:135)
        at ffx.potential.groovy.Biotype.run(Biotype.groovy)
        at ffx.utilities.FFXScript.run(FFXScript.java:72)
        at ffx.ui.ModelingShell.runFFXScript(ModelingShell.java:724)
        at ffx.Main.runScript(Main.java:641)
        at ffx.Main.startCommandLineInterface(Main.java:458)
        at ffx.Main.main(Main.java:235)

 java.lang.NullPointerException: Cannot read the array length because "allSystems" is null
 Force Field X will not continue.
 Shutting down...
mjschnie commented 3 days ago

For the Biotype command to succeed we need to make sure the ROY force field from PolType is read in. To achieve this, create a file called "ROY.properties" (or ROY.key) and add the property "parameters ROY.prm" (where the string ROY.prm is replaced with the actual name of the PolType parameter file). We usually rename PolType parameters to the name "molecule.patch" (where the patch implies "patching" an existing force field).

pradipchm commented 3 days ago

Thanks, I couldn't understand the last line. Also, to make sure I am doing it correctly. After generating the biotype, I copied the lines into the polytype2 prm file. then ran

ffxc FFtoXML ROY_new.prm
pradipchm commented 3 days ago

Hello, I converted the polytype file to XML using FFtoXML. However, in the residue section, the list of bonds is not correct. if you compare my XYZ file and bonds, they are different.

27 xxx
     1  S     -1.202900   -1.366136   -0.334602      401   15    18
     2  O      0.829206    1.293421   -1.770546      402    5
     3  O      2.860304    2.108980   -1.498071      402    5
     4  N      0.121997    0.664083    0.884464      403    9    15    19
     5  N      1.954630    1.294270   -1.242367      404    2     3    10
     6  N     -2.589823    3.171789    1.547201      405    7
     7  C     -2.482501    2.096627    1.060140      406    6    16
     8  C     -3.717386   -2.267154   -1.239056      407   18    20    21    22
     9  C      1.327059   -0.061053    0.735308      408    4    10    14
    10  C      2.252888    0.246548   -0.272914     409    5     9    11
    11  C      3.472479   -0.414307   -0.392133     410   10    12    23
    12  C      3.756735   -1.456534    0.490317     411   11    13    24
    13  C      2.844352   -1.799304    1.492733     412   12    14    25
    14  C      1.645358   -1.096823    1.622060     413    9    13    26
    15  C     -1.078377    0.184176    0.432699     414    1     4    16
    16  C     -2.318350    0.808732    0.488860     415    7    15    17
    17  C     -3.362593    0.018366   -0.093628     416   16    18    27
    18  C     -2.924487   -1.182274   -0.581077     417    1     8    17
    19  H      0.148809    1.609778    1.255676     418    4
    20  H     -4.763570   -1.955955   -1.297914     419    8
    21  H     -3.671487   -3.202893   -0.673553     419    8
    22  H     -3.363923   -2.469876   -2.254595     419    8
    23  H      4.166416   -0.128446   -1.176765     420   11
    24  H      4.695595   -1.994828    0.397647     421   12
    25  H      3.073505   -2.604712    2.184927     422   13
    26  H      0.945609   -1.325897    2.421689     423   14
    27  H     -4.399323    0.338804   -0.139483     424   17
<Residues>
        <Residue name="ROY">
            <Atom name="O0" type="402"/>
            <Atom name="O1" type="402"/>
            <Atom name="C0" type="406"/>
            <Atom name="C1" type="407"/>
            <Atom name="C2" type="408"/>
            <Atom name="C3" type="409"/>
            <Atom name="C4" type="410"/>
            <Atom name="C5" type="411"/>
            <Atom name="C6" type="412"/>
            <Atom name="C7" type="413"/>
            <Atom name="C8" type="414"/>
            <Atom name="C9" type="415"/>
            <Atom name="N0" type="403"/>
            <Atom name="C11" type="417"/>
            <Atom name="N1" type="404"/>
            <Atom name="C10" type="416"/>
            <Atom name="N2" type="405"/>
            <Atom name="H0" type="418"/>
            <Atom name="H1" type="419"/>
            <Atom name="H2" type="419"/>
            <Atom name="H3" type="419"/>
            <Atom name="H4" type="420"/>
            <Atom name="H5" type="421"/>
            <Atom name="H6" type="422"/>
            <Atom name="H7" type="423"/>
            <Atom name="H8" type="424"/>
            <Atom name="S0" type="401"/>
            <Bond from="0" to="14"/>
            <Bond from="1" to="14"/>
            <Bond from="2" to="16"/>
            <Bond from="2" to="11"/>
            <Bond from="3" to="13"/>
            <Bond from="3" to="18"/>
            <Bond from="3" to="19"/>
            <Bond from="3" to="20"/>
            <Bond from="4" to="12"/>
            <Bond from="4" to="5"/>
            <Bond from="4" to="9"/>
            <Bond from="5" to="14"/>
            <Bond from="5" to="6"/>
            <Bond from="6" to="7"/>
            <Bond from="6" to="21"/>
            <Bond from="7" to="8"/>
            <Bond from="7" to="22"/>
            <Bond from="8" to="9"/>
            <Bond from="8" to="23"/>
            <Bond from="9" to="24"/>
            <Bond from="10" to="26"/>
            <Bond from="10" to="12"/>
            <Bond from="10" to="11"/>
            <Bond from="11" to="15"/>
            <Bond from="12" to="17"/>
            <Bond from="13" to="26"/>
            <Bond from="13" to="15"/>
            <Bond from="15" to="25"/>
        </Residue>
    </Residues>

Here the prm file

biotype      1  S0    "ROY"    401  C8    C11
biotype      2  O0    "ROY"    402  N1
biotype      3  O1    "ROY"    402  N1
biotype      4  N0    "ROY"    403  C2    C8    H0
biotype      5  N1    "ROY"    404  O0    O1    C3
biotype      6  N2    "ROY"    405  C0
biotype      7  C0    "ROY"    406  N2    C9
biotype      8  C1    "ROY"    407  C11   H1    H2    H3
biotype      9  C2    "ROY"    408  N0    C3    C7
biotype     10  C3    "ROY"    409  N1    C2    C4
biotype     11  C4    "ROY"    410  C3    C5    H4
biotype     12  C5    "ROY"    411  C4    C6    H5
biotype     13  C6    "ROY"    412  C5    C7    H6
biotype     14  C7    "ROY"    413  C2    C6    H7
biotype     15  C8    "ROY"    414  S0    N0    C9
biotype     16  C9    "ROY"    415  C0    C8    C10
biotype     17  C10   "ROY"    416  C9    C11   H8
biotype     18  C11   "ROY"    417  S0    C1    C10
biotype     19  H0    "ROY"    418  N0
biotype     20  H1    "ROY"    419  C1
biotype     21  H2    "ROY"    419  C1
biotype     22  H3    "ROY"    419  C1
biotype     23  H4    "ROY"    420  C4
biotype     24  H5    "ROY"    421  C5
biotype     25  H6    "ROY"    422  C6
biotype     26  H7    "ROY"    423  C7
biotype     27  H8    "ROY"    424  C10

      ##############################
      ##                          ##
      ##  Force Field Definition  ##
      ##                          ##
      ##############################

forcefield              AMOEBA-BIO-2018

bond-cubic              -2.55
bond-quartic            3.793125
angle-cubic             -0.014
angle-quartic           0.000056
angle-pentic            -0.0000007
angle-sextic            0.000000022
opbendtype              ALLINGER
opbend-cubic            -0.014
opbend-quartic          0.000056
opbend-pentic           -0.0000007
opbend-sextic           0.000000022
torsionunit             0.5
vdwtype                 BUFFERED-14-7
radiusrule              CUBIC-MEAN
radiustype              R-MIN
radiussize              DIAMETER
epsilonrule             HHG
dielectric              1.0
polarization            MUTUAL
vdw-12-scale            0.0
vdw-13-scale            0.0
vdw-14-scale            1.0
vdw-15-scale            1.0
mpole-12-scale          0.0
mpole-13-scale          0.0
mpole-14-scale          0.4
mpole-15-scale          0.8
polar-12-scale          0.0
polar-13-scale          0.0
polar-14-scale          1.0
polar-15-scale          1.0
polar-12-intra          0.0
polar-13-intra          0.0
polar-14-intra          0.5
polar-15-intra          1.0
direct-11-scale         0.0
direct-12-scale         1.0
direct-13-scale         1.0
direct-14-scale         1.0
mutual-11-scale         1.0
mutual-12-scale         1.0
mutual-13-scale         1.0
mutual-14-scale         1.0

#############################
##                         ##
##  Literature References  ##
##                         ##
#############################

Walker, B., Liu, C., Wait, E., Ren, P., J. Comput. Chem. 2022, 1. https://doi.org/10.1002/jcc.26954

Wu, J.C.; Chattree, G.; Ren, P.Y.; Automation of AMOEBA polarizable force field
parameterization for small molecules. Theor Chem Acc.

atom          401    401    S     "ROY                 "        16    32.066    2
atom          402    402    O     "ROY                 "         8    15.999    1
atom          403    403    N     "ROY                 "         7    14.007    3
atom          404    404    N     "ROY                 "         7    14.007    3
atom          405    405    N     "ROY                 "         7    14.007    1
atom          406    406    C     "ROY                 "         6    12.011    2
atom          407    407    C     "ROY                 "         6    12.011    4
atom          408    408    C     "ROY                 "         6    12.011    3
atom         409   409    C     "ROY                 "         6    12.011    3
atom         410   410    C     "ROY                 "         6    12.011    3
atom         411   411    C     "ROY                 "         6    12.011    3
atom         412   412    C     "ROY                 "         6    12.011    3
atom         413   413    C     "ROY                 "         6    12.011    3
atom         414   414    C     "ROY                 "         6    12.011    3
atom         415   415    C     "ROY                 "         6    12.011    3
atom         416   416    C     "ROY                 "         6    12.011    3
atom         417   417    C     "ROY                 "         6    12.011    3
atom         418   418    H     "ROY                 "         1     1.008    1
atom         419   419    H     "ROY                 "         1     1.008    1
atom         420   420    H     "ROY                 "         1     1.008    1
atom         421   421    H     "ROY                 "         1     1.008    1
atom         422   422    H     "ROY                 "         1     1.008    1
atom         423   423    H     "ROY                 "         1     1.008    1
atom         424   424    H     "ROY                 "         1     1.008    1

# Double bond detected for missing torsion
# Transferring from ['Benzene C', 'Benzene C', 'Benzene C', 'Benzene C']
# Missing torsion parameters, will attempt to fit parameters
# [408, 403, 414, 401] = [[9], [4], [15], [1]]
torsion 408 403 414 401 -0.67 0.0 1 6.287 180.0 2 0 0.0 3

# Double bond detected for missing torsion
# Transferring hydrogen torsion to reduce fit parameters
# Transferring from ['Benzene HC', 'Benzene C', 'Benzene C', 'Benzene C']
# [418, 403, 414, 401] = [[19], [4], [15], [1]]
torsion 418 403 414 401 0.55 0.0 1 6.187 180.0 2 -0.55 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene C', 'Benzene C', 'Benzene C', 'Benzene C']
# [406, 415, 414, 401] = [[7], [16], [15], [1]]
torsion 406 415 414 401 -0.67 0.0 1 6.287 180.0 2 0 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene C', 'Benzene C', 'Benzene C', 'Benzene C']
# [416, 415, 414, 401] = [[17], [16], [15], [1]]
torsion 416 415 414 401 -0.67 0.0 1 6.287 180.0 2 0 0.0 3

# Missing torsion parameters, will attempt to fit parameters
# [419, 407, 417, 401] = [[20, 21, 22], [8], [18], [1]]
# Fitted torsion
# Torsion 419 407 417 401 RMSD(MM2,QM) 0.030100774840618252 RelativeRMSD(MM2,QM) 0.01336788256101466 
 torsion     419  407  417  401      0.001 0.0 1   0.001 180.0 2   0.367 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene C', 'Benzene C', 'Benzene C', 'Benzene C']
# [415, 416, 417, 401] = [[16], [17], [18], [1]]
torsion 415 416 417 401 -0.67 0.0 1 6.287 180.0 2 0 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene HC', 'Benzene C', 'Benzene C', 'Benzene C']
# [424, 416, 417, 401] = [[27], [17], [18], [1]]
torsion 424 416 417 401 0.55 0.0 1 6.187 180.0 2 -0.55 0.0 3

# Missing torsion parameters, will attempt to fit parameters
# [408, 409, 404, 402] = [[9], [10], [5], [2, 3]]
# Fitted torsion
# Torsion 402 404 409 408 RMSD(MM2,QM) 0.4755917760701987 RelativeRMSD(MM2,QM) 0.26080797483513063 
 torsion     408  409  404  402     -0.785 0.0 1   0.972 180.0 2  -0.781 0.0 3

# Missing torsion parameters, will attempt to fit parameters
# [410, 409, 404, 402] = [[11], [10], [5], [2, 3]]
# Fitted torsion
# Torsion 402 404 409 410 RMSD(MM2,QM) 0.4755917760701987 RelativeRMSD(MM2,QM) 0.26080797483513063 
 torsion     410  409  404  402     -0.791 0.0 1   0.972 180.0 2  -0.795 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene C', 'Benzene C', 'Benzene C', 'Benzene C']
# [404, 409, 408, 403] = [[5], [10], [9], [4]]
torsion 404 409 408 403 -0.67 0.0 1 6.287 180.0 2 0 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene C', 'Benzene C', 'Benzene C', 'Benzene C']
# [410, 409, 408, 403] = [[11], [10], [9], [4]]
torsion 410 409 408 403 -0.67 0.0 1 6.287 180.0 2 0 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene C', 'Benzene C', 'Benzene C', 'Benzene C']
# [412, 413, 408, 403] = [[13], [14], [9], [4]]
torsion 412 413 408 403 -0.67 0.0 1 6.287 180.0 2 0 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene HC', 'Benzene C', 'Benzene C', 'Benzene C']
# [423, 413, 408, 403] = [[26], [14], [9], [4]]
torsion 423 413 408 403 0.55 0.0 1 6.187 180.0 2 -0.55 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Alkane -CH2-', 'Alkane -CH2-', 'Alkane -CH2-', 'Alkane -CH2-']
# [417, 401, 414, 403] = [[18], [1], [15], [4]]
torsion 417 401 414 403 0.854 0.0 1 -0.374 180.0 2 0.108 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene C', 'Benzene C', 'Benzene C', 'Benzene C']
# [406, 415, 414, 403] = [[7], [16], [15], [4]]
torsion 406 415 414 403 -0.67 0.0 1 6.287 180.0 2 0 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene C', 'Benzene C', 'Benzene C', 'Benzene C']
# [416, 415, 414, 403] = [[17], [16], [15], [4]]
torsion 416 415 414 403 -0.67 0.0 1 6.287 180.0 2 0 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene C', 'Benzene C', 'Benzene C', 'Benzene C']
# [413, 408, 409, 404] = [[14], [9], [10], [5]]
torsion 413 408 409 404 -0.67 0.0 1 6.287 180.0 2 0 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene C', 'Benzene C', 'Benzene C', 'Benzene C']
# [411, 410, 409, 404] = [[12], [11], [10], [5]]
torsion 411 410 409 404 -0.67 0.0 1 6.287 180.0 2 0 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene HC', 'Benzene C', 'Benzene C', 'Benzene C']
# [420, 410, 409, 404] = [[23], [11], [10], [5]]
torsion 420 410 409 404 0.55 0.0 1 6.187 180.0 2 -0.55 0.0 3

# [414, 415, 406, 405] = [[15], [16], [7], [6]]
torsion 414 415 406 405 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3

# [416, 415, 406, 405] = [[17], [16], [7], [6]]
torsion 416 415 406 405 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene C', 'Benzene C', 'Benzene C', 'Benzene C']
# [417, 416, 415, 406] = [[18], [17], [16], [7]]
torsion 417 416 415 406 -0.67 0.0 1 6.287 180.0 2 0 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene HC', 'Benzene C', 'Benzene C', 'Benzene C']
# [424, 416, 415, 406] = [[27], [17], [16], [7]]
torsion 424 416 415 406 0.55 0.0 1 6.187 180.0 2 -0.55 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Alkane -CH2-', 'Alkane -CH2-', 'Alkane -CH2-', 'Alkane -CH2-']
# [414, 401, 417, 407] = [[15], [1], [18], [8]]
torsion 414 401 417 407 0.854 0.0 1 -0.374 180.0 2 0.108 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene C', 'Benzene C', 'Benzene C', 'Benzene C']
# [415, 416, 417, 407] = [[16], [17], [18], [8]]
torsion 415 416 417 407 -0.67 0.0 1 6.287 180.0 2 0 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene HC', 'Benzene C', 'Benzene C', 'Benzene C']
# [424, 416, 417, 407] = [[27], [17], [18], [8]]
torsion 424 416 417 407 0.55 0.0 1 6.187 180.0 2 -0.55 0.0 3

# Double bond detected for missing torsion
# Transferring from ['Benzene C', 'Benzene C', 'Benzene C', 'Benzene C']
# Missing torsion parameters, will attempt to fit parameters
# [415, 414, 403, 408] = [[16], [15], [4], [9]]
torsion 415 414 403 408 -0.67 0.0 1 6.287 180.0 2 0 0.0 3

# Missing torsion parameters, will attempt to fit parameters
# [414, 403, 408, 409] = [[15], [4], [9], [10]]
# Fitted torsion
# Torsion 414 403 408 409 RMSD(MM2,QM) 0.11124800518185149 RelativeRMSD(MM2,QM) 0.05503793044030308 Boltzmann Fit
 torsion     414  403  408  409     -1.633 0.0 1   0.349 180.0 2  -0.859 0.0 3

# Single bond detected for missing torsion
# Transferring hydrogen torsion to reduce fit parameters
# Transferring from ['Benzene HC', 'Benzene C', 'Benzene C', 'Benzene C']
# [418, 403, 408, 409] = [[19], [4], [9], [10]]
torsion 418 403 408 409 0.55 0.0 1 6.187 180.0 2 -0.55 0.0 3

# Missing torsion parameters, will attempt to fit parameters
# [414, 403, 408, 413] = [[15], [4], [9], [14]]
# Fitted torsion
# Torsion 414 403 408 413 RMSD(MM2,QM) 0.11124800518185149 RelativeRMSD(MM2,QM) 0.05503793044030308 Boltzmann Fit
 torsion     414  403  408  413      0.000 0.0 1   0.281 180.0 2  -0.554 0.0 3

# Single bond detected for missing torsion
# Transferring hydrogen torsion to reduce fit parameters
# Transferring from ['Benzene HC', 'Benzene C', 'Benzene C', 'Benzene C']
# [418, 403, 408, 413] = [[19], [4], [9], [14]]
torsion 418 403 408 413 0.55 0.0 1 6.187 180.0 2 -0.55 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Alkane -CH2-', 'Alkane -CH2-', 'Alkane -CH2-', 'Alkane -CH2-']
# [416, 417, 401, 414] = [[17], [18], [1], [15]]
torsion 416 417 401 414 0.854 0.0 1 -0.374 180.0 2 0.108 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene C', 'Benzene C', 'Benzene C', 'Benzene C']
# [417, 416, 415, 414] = [[18], [17], [16], [15]]
torsion 417 416 415 414 -0.67 0.0 1 6.287 180.0 2 0 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene HC', 'Benzene C', 'Benzene C', 'Benzene C']
# [424, 416, 415, 414] = [[27], [17], [16], [15]]
torsion 424 416 415 414 0.55 0.0 1 6.187 180.0 2 -0.55 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Alkane -CH2-', 'Alkane -CH2-', 'Alkane -CH2-', 'Alkane -CH2-']
# [417, 401, 414, 415] = [[18], [1], [15], [16]]
torsion 417 401 414 415 0.854 0.0 1 -0.374 180.0 2 0.108 0.0 3

# Double bond detected for missing torsion
# Transferring hydrogen torsion to reduce fit parameters
# Transferring from ['Benzene HC', 'Benzene C', 'Benzene C', 'Benzene C']
# [418, 403, 414, 415] = [[19], [4], [15], [16]]
torsion 418 403 414 415 0.55 0.0 1 6.187 180.0 2 -0.55 0.0 3

# Missing torsion parameters, will attempt to fit parameters
# [419, 407, 417, 416] = [[20, 21, 22], [8], [18], [17]]
# Fitted torsion
# Torsion 419 407 417 416 RMSD(MM2,QM) 0.030100774840618252 RelativeRMSD(MM2,QM) 0.01336788256101466 
 torsion     419  407  417  416      0.001 0.0 1   0.001 180.0 2   0.000 0.0 3

# [421, 411, 412, 413] = [[24], [12], [13], [14]]
torsion 421 411 412 413 0.550 0.0 1 11.384 180.0 2 -0.550 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene C', 'Benzene C', 'Benzene C', 'Benzene C']
# [411, 410, 409, 408] = [[12], [11], [10], [9]]
torsion 411 410 409 408 -0.67 0.0 1 6.287 180.0 2 0 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene C', 'Benzene C', 'Benzene C', 'Benzene C']
# [411, 412, 413, 408] = [[12], [13], [14], [9]]
torsion 411 412 413 408 -0.67 0.0 1 6.287 180.0 2 0 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene C', 'Benzene C', 'Benzene C', 'Benzene C']
# [413, 408, 409, 410] = [[14], [9], [10], [11]]
torsion 413 408 409 410 -0.67 0.0 1 6.287 180.0 2 0 0.0 3

# [413, 412, 411, 410] = [[14], [13], [12], [11]]
torsion 413 412 411 410 -0.670 0.0 1 6.287333333333333 180.0 2 0.000 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene HC', 'Benzene C', 'Benzene C', 'Benzene C']
# [422, 412, 413, 408] = [[25], [13], [14], [9]]
torsion 422 412 413 408 0.55 0.0 1 6.187 180.0 2 -0.55 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene HC', 'Benzene C', 'Benzene C', 'Benzene C']
# [421, 411, 410, 409] = [[24], [12], [11], [10]]
torsion 421 411 410 409 0.55 0.0 1 6.187 180.0 2 -0.55 0.0 3

# [422, 412, 411, 410] = [[25], [13], [12], [11]]
torsion 422 412 411 410 0.550 0.0 1 6.817333333333333 180.0 2 -0.550 0.0 3

# [423, 413, 412, 411] = [[26], [14], [13], [12]]
torsion 423 413 412 411 0.550 0.0 1 7.959 180.0 2 -0.550 0.0 3

# [420, 410, 411, 412] = [[23], [11], [12], [13]]
torsion 420 410 411 412 0.550 0.0 1 11.384 180.0 2 -0.550 0.0 3

# [421, 411, 410, 420] = [[24], [12], [11], [23]]
torsion 421 411 410 420 0.000 0.0 1 7.497 180.0 2 0.000 0.0 3

# [422, 412, 411, 421] = [[25], [13], [12], [24]]
torsion 422 412 411 421 0.000 0.0 1 6.355333333333333 180.0 2 0.000 0.0 3

# [423, 413, 412, 422] = [[26], [14], [13], [25]]
torsion 423 413 412 422 0.000 0.0 1 7.497 180.0 2 0.000 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene HC', 'Benzene C', 'Benzene C', 'Benzene C']
# [408, 409, 410, 420] = [[9], [10], [11], [23]]
torsion 408 409 410 420 0.55 0.0 1 6.187 180.0 2 -0.55 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene HC', 'Benzene C', 'Benzene C', 'Benzene C']
# [409, 408, 413, 423] = [[10], [9], [14], [26]]
torsion 409 408 413 423 0.55 0.0 1 6.187 180.0 2 -0.55 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene C', 'Benzene C', 'Benzene C', 'Benzene C']
# [412, 413, 408, 409] = [[13], [14], [9], [10]]
torsion 412 413 408 409 -0.67 0.0 1 6.287 180.0 2 0 0.0 3

# Ring bond detected for missing torsion
# Transferring from ['Benzene C', 'Benzene C', 'Benzene C', 'Benzene C']
# [412, 411, 410, 409] = [[13], [12], [11], [10]]
torsion 412 411 410 409 -0.67 0.0 1 6.287 180.0 2 0 0.0 3

# [401] = [[1]]
polarize           401          3.4060     0.3900 414 417
# [402] = [[2, 3]]
polarize           402          0.8580     0.3900 404
# [403] = [[4]]
polarize           403          1.7020     0.3900 418
# [404] = [[5]]
polarize           404          1.1850     0.3900 402
# [405] = [[6]]
polarize           405          1.1580     0.3900 406
# [406] = [[7]]
polarize           406          2.2020     0.3900 405 415
# [407] = [[8]]
polarize           407          1.4150     0.3900 419
# [408] = [[9]]
polarize           408          1.6000     0.3900 409 413
# [409] = [[10]]
polarize          409          1.6000     0.3900 408 410
# [410] = [[11]]
polarize          410          1.6000     0.3900 409 411 420
# [411] = [[12]]
polarize          411          1.6000     0.3900 410 412 421
# [412] = [[13]]
polarize          412          1.6000     0.3900 411 413 422
# [413] = [[14]]
polarize          413          1.6000     0.3900 408 412 423
# [414] = [[15]]
polarize          414          1.6200     0.3900 401 415
# [415] = [[16]]
polarize          415          1.6000     0.3900 406 414 416
# [416] = [[17]]
polarize          416          1.6000     0.3900 415 417 424
# [417] = [[18]]
polarize          417          1.4150     0.3900 401 416
# [418] = [[19]]
polarize          418          0.4570     0.3900 403
# [419] = [[20, 21, 22]]
polarize          419          0.4800     0.3900 407
# [420] = [[23]]
polarize          420          0.4320     0.3900 410
# [421] = [[24]]
polarize          421          0.4320     0.3900 411
# [422] = [[25]]
polarize          422          0.4320     0.3900 412
# [423] = [[26]]
polarize          423          0.4320     0.3900 413
# [424] = [[27]]
polarize          424          0.4320     0.3900 416

#
# Multipoles from Electrostatic Potential Fitting
#

# [401] = [[1]]
multipole   401  414  417               0.57864
                                        1.03081    0.00000    0.79002
                                        1.28164
                                        0.00000   -2.20999
                                        0.93591    0.00000    0.92835
# [402] = [[2, 3]]
multipole   402  404  402              -0.37782
                                        0.00065    0.00000    0.08809
                                       -0.50984
                                        0.00000    0.08093
                                       -0.05434    0.00000    0.42891
# [403] = [[4]]
multipole   403  414  408              -0.14279
                                        0.10481    0.00000    0.05711
                                        0.51835
                                        0.00000   -0.48900
                                        0.45890    0.00000   -0.02935
# [404] = [[5]]
multipole   404 -402 -402               0.64219
                                        0.00000    0.00000    0.12308
                                        0.16383
                                        0.00000    0.00295
                                        0.00000    0.00000   -0.16678
# [405] = [[6]]
multipole   405  406                   -0.73577
                                        0.00000    0.00000   -0.75769
                                        0.70656
                                        0.00000    0.70656
                                        0.00000    0.00000   -1.41312
# [406] = [[7]]
multipole   406  405                    0.50670
                                        0.00000    0.00000    0.13788
                                        0.55354
                                        0.00000    0.55354
                                        0.00000    0.00000   -1.10708
# [407] = [[8]]
multipole   407  417  401              -0.14418
                                        0.03235    0.00000    0.15851
                                       -0.12079
                                        0.00000   -0.16191
                                        0.05107    0.00000    0.28270
# [408] = [[9]]
multipole   408  403  409              -0.06461
                                        0.20461    0.00000    0.32788
                                        0.07742
                                        0.00000    0.12674
                                        0.09127    0.00000   -0.20416
# [409] = [[10]]
multipole   409  404  408               0.26892
                                        0.00273    0.00000   -0.60511
                                       -1.67181
                                        0.00000   -1.01959
                                        0.25958    0.00000    2.69140
# [410] = [[11]]
multipole   410  409  411              -0.05952
                                       -0.21801    0.00000    0.06924
                                       -0.15710
                                        0.00000    0.04070
                                       -0.29385    0.00000    0.11640
# [411] = [[12]]
multipole   411  410  412              -0.05244
                                       -0.13283    0.00000   -0.09557
                                       -0.11257
                                        0.00000   -0.03075
                                       -0.18940    0.00000    0.14332
# [412] = [[13]]
multipole   412  413  411               0.01888
                                        0.01950    0.00000   -0.01011
                                        0.19675
                                        0.00000   -0.26910
                                        0.06349    0.00000    0.07235
# [413] = [[14]]
multipole   413  408  412              -0.08245
                                       -0.15783    0.00000   -0.09790
                                       -0.05521
                                        0.00000    0.12614
                                       -0.23845    0.00000   -0.07093
# [414] = [[15]]
multipole   414  401  403              -0.06124
                                        0.17166    0.00000   -0.21778
                                        0.35323
                                        0.00000   -0.32251
                                       -0.35554    0.00000   -0.03072
# [415] = [[16]]
multipole   415  406  414              -0.07833
                                       -0.07497    0.00000    0.34403
                                        0.45069
                                        0.00000   -0.03112
                                       -0.01886    0.00000   -0.41957
# [416] = [[17]]
multipole   416  417  415              -0.11585
                                       -0.13394    0.00000   -0.10248
                                        0.13266
                                        0.00000   -0.14666
                                        0.19796    0.00000    0.01400
# [417] = [[18]]
multipole   417  401  416              -0.20257
                                       -0.09156    0.00000   -0.21088
                                        0.57129
                                        0.00000   -0.65355
                                        0.07587    0.00000    0.08226
# [418] = [[19]]
multipole   418  403  414               0.10628
                                       -0.00346    0.00000   -0.13318
                                        0.15850
                                        0.00000   -0.09655
                                        0.03979    0.00000   -0.06195
# [419] = [[20, 21, 22]]
multipole   419  407  417               0.07491
                                        0.02149    0.00000   -0.07041
                                        0.05000
                                        0.00000    0.00226
                                       -0.02046    0.00000   -0.05226
# [420] = [[23]]
multipole   420  410  409               0.04321
                                        0.00804    0.00000   -0.17867
                                        0.05353
                                        0.00000    0.05164
                                        0.05998    0.00000   -0.10517
# [421] = [[24]]
multipole   421  411  410               0.02285
                                        0.01241    0.00000   -0.17057
                                        0.09278
                                        0.00000    0.00684
                                       -0.00708    0.00000   -0.09962
# [422] = [[25]]
multipole   422  412  413               0.02106
                                        0.00328    0.00000   -0.14992
                                        0.06580
                                        0.00000    0.02376
                                       -0.00431    0.00000   -0.08956
# [423] = [[26]]
multipole   423  413  408               0.05755
                                       -0.03048    0.00000   -0.11507
                                        0.00154
                                        0.00000    0.01809
                                        0.03137    0.00000   -0.01963
# [424] = [[27]]
multipole   424  416  417               0.00438
                                       -0.01141    0.00000   -0.17365
                                        0.10860
                                        0.00000   -0.01232
                                       -0.02622    0.00000   -0.09628

#
# Charge Penetration from Electrostatic Potential Fitting
#

chgpen           401          0.0000    0.00000
chgpen           402          0.0000    0.00000
chgpen           403          0.0000    0.00000
chgpen           404          0.0000    0.00000
chgpen           405          0.0000    0.00000
chgpen           406          0.0000    0.00000
chgpen           407          0.0000    0.00000
chgpen           408          0.0000    0.00000
chgpen           409          0.0000    0.00000
chgpen           410          0.0000    0.00000
chgpen           411          0.0000    0.00000
chgpen           412          0.0000    0.00000
chgpen           413          0.0000    0.00000
chgpen           414          0.0000    0.00000
chgpen           415          0.0000    0.00000
chgpen           416          0.0000    0.00000
chgpen           417          0.0000    0.00000
chgpen           418          0.0000    0.00000
chgpen           419          0.0000    0.00000
chgpen           420          0.0000    0.00000
chgpen           421          0.0000    0.00000
chgpen           422          0.0000    0.00000
chgpen           423          0.0000    0.00000
chgpen           424          0.0000    0.00000
# [401, 414] = [[1], [15]]
bond   401   414   657.2676   1.7343
# [401, 417] = [[1], [18]]
bond   401   417   609.2913   1.7488
# [402, 404] = [[2, 3], [5]]
bond   402   404   274.3661   1.2440
# [403, 408] = [[4], [9]]
bond   403   408   312.6977   1.3871

# [403, 414] = [[4], [15]]
bond   403   414   349.1162   1.3479

# [403, 418] = [[4], [19]]
bond   403   418   451.4284   1.0163
# [404, 409] = [[5], [10]]
bond   404   409   361.7223   1.4427

# [405, 406] = [[6], [7]]
bond   405   406   996.9348   1.1852
# [406, 415] = [[7], [16]]
bond   406   415   746.0230   1.4184
# [407, 417] = [[8], [18]]
bond   407   417   332.7929   1.4962
# [407, 419] = [[8], [20, 21, 22]]
bond   407   419   345.9789   1.0939
# [408, 409] = [[9], [10]]
bond   408   409   379.0943   1.3737

# [408, 413] = [[9], [14]]
bond   408   413   379.0943   1.3789

# [409, 410] = [[10], [11]]
bond   409   410   379.0943   1.3742

# [410, 411] = [[11], [12]]
bond   410   411   379.0943   1.3859

# [410, 420] = [[11], [23]]
bond   410   420   368.0934   1.0858
# [411, 412] = [[12], [13]]
bond   411   412   379.0943   1.3898

# [411, 421] = [[12], [24]]
bond   411   421   368.0934   1.0862
# [412, 413] = [[13], [14]]
bond   412   413   379.0943   1.3842

# [412, 422] = [[13], [25]]
bond   412   422   368.0934   1.0864
# [413, 423] = [[14], [26]]
bond   413   423   368.0934   1.0870
# [414, 415] = [[15], [16]]
bond   414   415   607.1513   1.3895
# [415, 416] = [[16], [17]]
bond   415   416   485.3892   1.4333
# [416, 417] = [[17], [18]]
bond   416   417   402.4135   1.3679
# [416, 424] = [[17], [27]]
bond   416   424   365.1617   1.0861
# [414, 401, 417] = [[15], [1], [18]]
angle   414   401   417   54.6300   90.241
anglep   408   403   414   51.8597   116.035
anglep   408   403   418   40.0459   122.372
anglep   414   403   418   51.5407   121.057
anglep   402   404   402   67.7318   125.649
anglep   402   404   409   67.7318   117.5527
# [405, 406, 415] = [[6], [7], [16]]
angle   405   406   415   44.2965   178.4823
# [417, 407, 419] = [[18], [8], [20, 21, 22]]
angle   417   407   419   78.6275   110.8256
# [419, 407, 419] = [[20, 21, 22], [8], [20, 21, 22]]
angle   419   407   419   36.4069   108.0791
anglep   403   408   409   78.0230   121.7125
anglep   403   408   413   78.0230   119.110
anglep   409   408   413   74.6307   118.805
anglep   404   409   408   93.4081   119.199
anglep   404   409   410   93.4081   117.5987
anglep   408   409   410   74.6307   122.3807
anglep   409   410   411   74.6307   118.6198
anglep   409   410   420   36.7702   119.7865
anglep   411   410   420   36.7702   121.5764
anglep   410   411   412   74.6307   120.2495
anglep   410   411   421   36.7702   119.5017
anglep   412   411   421   36.7702   120.2471
anglep   411   412   413   74.6307   120.2428
anglep   411   412   422   36.7702   120.0600
anglep   413   412   422   36.7702   119.6903
anglep   408   413   412   74.6307   119.959
anglep   408   413   423   36.7702   117.105
anglep   412   413   423   36.7702   122.915
anglep   401   414   403   65.7159   119.361
anglep   401   414   415   65.7159   112.897
anglep   403   414   415   67.4827   127.6886
anglep   406   415   414   45.9142   121.8474
anglep   406   415   416   43.7002   126.777
anglep   414   415   416   47.2504   111.731
anglep   415   416   417   45.9142   112.689
anglep   415   416   424   57.3007   123.3604
anglep   417   416   424   44.3867   123.3429
anglep   401   417   407   33.1270   120.4932
anglep   401   417   416   53.8723   112.499
anglep   407   417   416   53.8723   127.425
# [414, 401, 417] = [[15], [1], [18]]
strbnd   414   401   417   -3.4389   -3.4389
# [408, 403, 414] = [[9], [4], [15]]
strbnd   408   403   414   11.1412   11.1412
# [408, 403, 418] = [[9], [4], [19]]
strbnd   408   403   418   22.6877   22.6877
# [414, 403, 418] = [[15], [4], [19]]
strbnd   414   403   418   10.8801   10.8801
# [402, 404, 402] = [[2, 3], [5], [2, 3]]
strbnd   402   404   402   20.0049   20.0049
# [402, 404, 409] = [[2, 3], [5], [10]]
strbnd   402   404   409   20.0049   20.0049
# [405, 406, 415] = [[6], [7], [16]]
strbnd   405   406   415   11.9518   11.9518
# [417, 407, 419] = [[18], [8], [20, 21, 22]]
strbnd   417   407   419   20.4528   20.4528
# [419, 407, 419] = [[20, 21, 22], [8], [20, 21, 22]]
strbnd   419   407   419   5.7126   5.7126
# [403, 408, 409] = [[4], [9], [10]]
strbnd   403   408   409   20.4528   20.4528
# [403, 408, 413] = [[4], [9], [14]]
strbnd   403   408   413   20.4528   20.4528
# [409, 408, 413] = [[10], [9], [14]]
strbnd   409   408   413   20.4528   20.4528
# [404, 409, 408] = [[5], [10], [9]]
strbnd   404   409   408   20.4528   20.4528
# [404, 409, 410] = [[5], [10], [11]]
strbnd   404   409   410   20.4528   20.4528
# [408, 409, 410] = [[9], [10], [11]]
strbnd   408   409   410   20.4528   20.4528
# [409, 410, 411] = [[10], [11], [12]]
strbnd   409   410   411   20.4528   20.4528
# [409, 410, 420] = [[10], [11], [23]]
strbnd   409   410   420   20.4528   20.4528
# [411, 410, 420] = [[12], [11], [23]]
strbnd   411   410   420   20.4528   20.4528
# [410, 411, 412] = [[11], [12], [13]]
strbnd   410   411   412   20.4528   20.4528
# [410, 411, 421] = [[11], [12], [24]]
strbnd   410   411   421   20.4528   20.4528
# [412, 411, 421] = [[13], [12], [24]]
strbnd   412   411   421   20.4528   20.4528
# [411, 412, 413] = [[12], [13], [14]]
strbnd   411   412   413   20.4528   20.4528
# [411, 412, 422] = [[12], [13], [25]]
strbnd   411   412   422   20.4528   20.4528
# [413, 412, 422] = [[14], [13], [25]]
strbnd   413   412   422   20.4528   20.4528
# [408, 413, 412] = [[9], [14], [13]]
strbnd   408   413   412   20.4528   20.4528
# [408, 413, 423] = [[9], [14], [26]]
strbnd   408   413   423   20.4528   20.4528
# [412, 413, 423] = [[13], [14], [26]]
strbnd   412   413   423   20.4528   20.4528
# [401, 414, 403] = [[1], [15], [4]]
strbnd   401   414   403   7.6289   7.6289
# [401, 414, 415] = [[1], [15], [16]]
strbnd   401   414   415   7.6289   7.6289
# [403, 414, 415] = [[4], [15], [16]]
strbnd   403   414   415   7.6289   7.6289
# [406, 415, 414] = [[7], [16], [15]]
strbnd   406   415   414   5.7126   5.7126
# [406, 415, 416] = [[7], [16], [17]]
strbnd   406   415   416   5.7126   5.7126
# [414, 415, 416] = [[15], [16], [17]]
strbnd   414   415   416   5.7126   5.7126
# [415, 416, 417] = [[16], [17], [18]]
strbnd   415   416   417   5.7126   5.7126
# [415, 416, 424] = [[16], [17], [27]]
strbnd   415   416   424   34.2002   34.2002
# [417, 416, 424] = [[18], [17], [27]]
strbnd   417   416   424   5.7126   5.7126
# [401, 417, 407] = [[1], [18], [8]]
strbnd   401   417   407   9.9539   9.9539
# [401, 417, 416] = [[1], [18], [17]]
strbnd   401   417   416   12.7158   12.7158
# [407, 417, 416] = [[8], [18], [17]]
strbnd   407   417   416   12.7158   12.7158
# [408, 403] = [[9], [4]]
opbend   408   403   414   418   45.4009
# [414, 403] = [[15], [4]]
opbend   414   403   408   418   42.8145
# [418, 403] = [[19], [4]]
opbend   418   403   408   414   47.7090
# [402, 404] = [[2, 3], [5]]
opbend   402   404   402   409   14.0000
# [409, 404] = [[10], [5]]
opbend   409   404   402   402   22.6501
# [403, 408] = [[4], [9]]
opbend   403   408   409   413   47.7090
# [409, 408] = [[10], [9]]
opbend   409   408   403   413   92.0233
# [413, 408] = [[14], [9]]
opbend   413   408   403   409   92.0233
# [404, 409] = [[5], [10]]
opbend   404   409   408   410   22.6501
# [408, 409] = [[9], [10]]
opbend   408   409   404   410   92.0233
# [410, 409] = [[11], [10]]
opbend   410   409   404   408   92.0233
# [409, 410] = [[10], [11]]
opbend   409   410   411   420   92.0233
# [411, 410] = [[12], [11]]
opbend   411   410   409   420   92.0233
# [420, 410] = [[23], [11]]
opbend   420   410   409   411   79.0289
# [410, 411] = [[11], [12]]
opbend   410   411   412   421   92.0233
# [412, 411] = [[13], [12]]
opbend   412   411   410   421   92.0233
# [421, 411] = [[24], [12]]
opbend   421   411   410   412   79.0289
# [411, 412] = [[12], [13]]
opbend   411   412   413   422   92.0233
# [413, 412] = [[14], [13]]
opbend   413   412   411   422   92.0233
# [422, 412] = [[25], [13]]
opbend   422   412   411   413   79.0289
# [408, 413] = [[9], [14]]
opbend   408   413   412   423   92.0233
# [412, 413] = [[13], [14]]
opbend   412   413   408   423   92.0233
# [423, 413] = [[26], [14]]
opbend   423   413   408   412   79.0289
# [401, 414] = [[1], [15]]
opbend   401   414   403   415   41.4183
# [403, 414] = [[4], [15]]
opbend   403   414   401   415   42.8145
# [415, 414] = [[16], [15]]
opbend   415   414   401   403   15.0917
# [406, 415] = [[7], [16]]
opbend   406   415   414   416   15.0111
# [414, 415] = [[15], [16]]
opbend   414   415   406   416   15.0917
# [416, 415] = [[17], [16]]
opbend   416   415   406   414   14.0000
# [415, 416] = [[16], [17]]
opbend   415   416   417   424   14.0000
# [417, 416] = [[18], [17]]
opbend   417   416   415   424   14.3997
# [424, 416] = [[27], [17]]
opbend   424   416   415   417   14.0000
# [401, 417] = [[1], [18]]
opbend   401   417   407   416   51.1922
# [407, 417] = [[8], [18]]
opbend   407   417   401   416   14.5995
# [416, 417] = [[17], [18]]
opbend   416   417   401   407   14.3997
# [401] = [[1]]
vdw 401 3.9100  0.3850  0.0000
# [402] = [[2, 3]]
vdw 402 3.5500  0.0950  0.0000
# [403] = [[4]]
vdw 403 3.7100  0.1100  0.0000
# [404] = [[5]]
vdw 404 3.7100  0.1100  0.0000
# [405] = [[6]]
vdw 405 3.5800  0.1100  0.0000
# [406] = [[7]]
vdw 406 3.8200  0.1010  0.0000
# [407] = [[8]]
vdw 407 3.8200  0.1010  0.0000
# [408] = [[9]]
vdw 408 3.8000  0.0890  0.0000
# [409] = [[10]]
vdw 409 3.8000  0.0890  0.0000
# [410] = [[11]]
vdw 410 3.8000  0.0890  0.0000
# [411] = [[12]]
vdw 411 3.8000  0.0890  0.0000
# [412] = [[13]]
vdw 412 3.8000  0.0890  0.0000
# [413] = [[14]]
vdw 413 3.8000  0.0890  0.0000
# [414] = [[15]]
vdw 414 3.8200  0.1010  0.0000
# [415] = [[16]]
vdw 415 3.8200  0.1010  0.0000
# [416] = [[17]]
vdw 416 3.8200  0.1010  0.0000
# [417] = [[18]]
vdw 417 3.8200  0.1010  0.0000
# [418] = [[19]]
vdw 418 2.7000  0.0200  0.9100
# [419] = [[20, 21, 22]]
vdw 419 2.9000  0.0220  0.9000
# [420] = [[23]]
vdw 420 2.9800  0.0260  0.9200
# [421] = [[24]]
vdw 421 2.9800  0.0260  0.9200
# [422] = [[25]]
vdw 422 2.9800  0.0260  0.9200
# [423] = [[26]]
vdw 423 2.9800  0.0260  0.9200
# [424] = [[27]]
vdw 424 2.9800  0.0240  0.9200
# AMOEBA GK parameter matched from [#1]([N+;D3])
solute 418 3.6491   3.404   2.9894   0.1350
# AMOEBA GK parameter matched from [#1][CH3]
solute 419 3.143   3.374   4.144   0.1350
# AMOEBA GK parameter matched from [#1](c)
solute 420 3.002   2.635   3.3763   0.1350
# AMOEBA GK parameter matched from [#1](c)
solute 421 3.002   2.635   3.3763   0.1350
# AMOEBA GK parameter matched from [#1](c)
solute 422 3.002   2.635   3.3763   0.1350
# AMOEBA GK parameter matched from [#1](c)
solute 423 3.002   2.635   3.3763   0.1350
# AMOEBA GK parameter matched from [#1][#6;D3]
solute 424 2.574   2.758   2.9054   0.1350
# AMOEBA GK parameter matched from [#6]
solute 406 3.3025   2.854   4.9016   0.1350
# AMOEBA GK parameter matched from [CH3]
solute 407 3.5062   3.309   4.536   0.1350
# AMOEBA GK parameter matched from c([cH0])
solute 408 3.8585   3.766   3.8448   0.1350
# AMOEBA GK parameter matched from [cH0]
solute 409 3.6909   3.766   4.4258   0.1350
# AMOEBA GK parameter matched from c(c([cH0]))
solute 410 3.8286   3.893   4.5084   0.1350
# AMOEBA GK parameter matched from c(c(c([cH0])))
solute 411 3.8286   3.893   4.5084   0.1350
# AMOEBA GK parameter matched from c(c(c([cH0])))
solute 412 3.8286   3.893   4.5084   0.1350
# AMOEBA GK parameter matched from c(c([cH0]))
solute 413 3.8286   3.893   4.5084   0.1350
# AMOEBA GK parameter matched from C(S)
solute 414 3.3967   3.255   4.7385   0.1350
# AMOEBA GK parameter matched from [#6;D3]([*])([*])(=[*])
solute 415 2.9301   4.506   4.2118   0.1350
# AMOEBA GK parameter matched from [#6;D3]([*])([*])(=[*])
solute 416 2.9301   4.506   4.2118   0.1350
# AMOEBA GK parameter matched from [#6;D3]([*])([*])(=[*])
solute 417 2.9301   4.506   4.2118   0.1350
# AMOEBA GK parameter matched from [#7;D3]
solute 403 3.4243   3.491   4.2676   0.1350
# AMOEBA GK parameter matched from [#7;D3]
solute 404 3.4243   3.491   4.2676   0.1350
# AMOEBA GK parameter matched from [#7]
solute 405 3.710   3.710   3.710   0.1350
# AMOEBA GK parameter matched from [#8;D1][*]
solute 402 2.801   3.128   2.9814   0.1350
# AMOEBA GK parameter matched from [#16]
solute 401 4.4346   4.194   4.5431   0.1350
mjschnie commented 2 days ago

Are the differences in the XML Bonds you're noticing just due to the atom ordering changing? In the XML file, the atom with index 0 is O0 and the atom with index 1 is O1. They both bond to the N1 atom at index 14, which matches the XYZ file. The best check is to compare the FFX (or Tinker) potential energy with the OpenMM potential energy.

pradipchm commented 2 days ago

I think the order has changed. The O atoms, which are 2 and 3 in the XYZ file, should be 1 and 2 in XML. The O atoms attached to the 5th N atoms should be 4 in XML.

     1  S     -1.202900   -1.366136   -0.334602      401   15    18
     2  O      0.829206    1.293421   -1.770546      402    5
     3  O      2.860304    2.108980   -1.498071      402    5
     4  N      0.121997    0.664083    0.884464      403    9    15    19
     5  N      1.954630    1.294270   -1.242367      404    2     3    10

But if you look at the XML. The bonds are not the same. Also, S has been written at the end, if that is an issue. 

<Residues>
        <Residue name="ROY">
            <Atom name="O0" type="402"/>
            <Atom name="O1" type="402"/>
            <Atom name="C0" type="406"/>
            <Atom name="C1" type="407"/>
            <Atom name="C2" type="408"/>
            <Atom name="C3" type="409"/>
            <Atom name="C4" type="410"/>
            <Atom name="C5" type="411"/>
            <Atom name="C6" type="412"/>
            <Atom name="C7" type="413"/>
            <Atom name="C8" type="414"/>
            <Atom name="C9" type="415"/>
            <Atom name="N0" type="403"/>
            <Atom name="C11" type="417"/>
            <Atom name="N1" type="404"/>
            <Atom name="C10" type="416"/>
            <Atom name="N2" type="405"/>
            <Atom name="H0" type="418"/>
            <Atom name="H1" type="419"/>
            <Atom name="H2" type="419"/>
            <Atom name="H3" type="419"/>
            <Atom name="H4" type="420"/>
            <Atom name="H5" type="421"/>
            <Atom name="H6" type="422"/>
            <Atom name="H7" type="423"/>
            <Atom name="H8" type="424"/>
            <Atom name="S0" type="401"/>
            <Bond from="0" to="14"/>
            <Bond from="1" to="14"/>
            <Bond from="2" to="16"/>
            <Bond from="2" to="11"/>
            <Bond from="3" to="13"/>
            <Bond from="3" to="18"/>
            <Bond from="3" to="19"/>
            <Bond from="3" to="20"/>
            <Bond from="4" to="12"/>
            <Bond from="4" to="5"/>
            <Bond from="4" to="9"/>
            <Bond from="5" to="14"/>
            <Bond from="5" to="6"/>
            <Bond from="6" to="7"/>
            <Bond from="6" to="21"/>
            <Bond from="7" to="8"/>
            <Bond from="7" to="22"/>
            <Bond from="8" to="9"/>
            <Bond from="8" to="23"/>
            <Bond from="9" to="24"/>
            <Bond from="10" to="26"/>
            <Bond from="10" to="12"/>
            <Bond from="10" to="11"/>
            <Bond from="11" to="15"/>
            <Bond from="12" to="17"/>
            <Bond from="13" to="26"/>
            <Bond from="13" to="15"/>
            <Bond from="15" to="25"/>
        </Residue>
    </Residues>

I tried to run the energy calculation for Tinker and openMM. Tinker works but openMM is showing an error for ffxc MinimizeOpenMM, do I need to install openMM separately? 

Plugin Directory:  /tmp/openmm17234683147377483412/linux_x64/plugins
 Number of Plugins: 9
  Plugin: /tmp/openmm17234683147377483412/linux_x64/plugins/libOpenMMPME.so
  Plugin: /tmp/openmm17234683147377483412/linux_x64/plugins/libOpenMMCPU.so
  Plugin: /tmp/openmm17234683147377483412/linux_x64/plugins/libOpenMMOpenCL.so
  Plugin: /tmp/openmm17234683147377483412/linux_x64/plugins/libOpenMMRPMDOpenCL.so
  Plugin: /tmp/openmm17234683147377483412/linux_x64/plugins/libOpenMMDrudeOpenCL.so
  Plugin: /tmp/openmm17234683147377483412/linux_x64/plugins/libOpenMMAmoebaOpenCL.so
  Plugin: /tmp/openmm17234683147377483412/linux_x64/plugins/libOpenMMRPMDReference.so
  Plugin: /tmp/openmm17234683147377483412/linux_x64/plugins/libOpenMMDrudeReference.so
  Plugin: /tmp/openmm17234683147377483412/linux_x64/plugins/libOpenMMAmoebaReference.so
 Number of Platforms: 2
 Precision level: mixed
 Available devices: 1.
terminate called after throwing an instance of 'OpenMM::OpenMMException'
  what():  There is no registered Platform called "OpenCL"

I tried in openMM separately with the XML file but because of the wrong bond, it shows an error.