view alchemical_run/test-data/morph.top @ 0:19d1d4c30402 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
author chemteam
date Mon, 11 Nov 2019 13:20:39 -0500
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; Gromacs Topology File written by Sire
; File written 05/01/19  13:21:14
[ defaults ]
; nbfunc      comb-rule       gen-pairs      fudgeLJ     fudgeQQ
  1           2               yes            0.5         0.833333

[ atomtypes ]
; name      at.num        mass      charge   ptype       sigma     epsilon
   Cl-          17   35.453000    0.000000       A    0.447766    0.148913
    HW           1    1.007940    0.000000       A    0.000000    0.000000
   Na+          11   22.989770    0.000000       A    0.243928    0.365846
    OW           8   15.999400    0.000000       A    0.315075    0.635968
    c3           6   12.010700    0.000000       A    0.339771    0.451035
    ca           6   12.010700    0.000000       A    0.331521    0.413379
    ha           1    1.007940    0.000000       A    0.262548    0.067362
    hc           1    1.007940    0.000000       A    0.260018    0.087027
 hc_du           0    0.000000    0.000000       A    0.000000    0.000000

[ moleculetype ]
; name  nrexcl
CL  3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr     charge         mass
     1    Cl-      1      CL    CL      1  -1.000000    35.450000


[ moleculetype ]
; name  nrexcl
Merged_Molecule  3

[ atoms ]
;   nr   type0  resnr residue  atom   cgnr    charge0        mass0   type1    charge1        mass1
     1      ca      1     LIG     C      1  -0.130000    12.010000      ca  -0.075744    12.010000
     2      ca      1     LIG    C1      2  -0.130000    12.010000      ca  -0.129444    12.010000
     3      ca      1     LIG    C2      3  -0.130000    12.010000      ca  -0.131444    12.010000
     4      ca      1     LIG    C3      4  -0.130000    12.010000      ca  -0.131444    12.010000
     5      ca      1     LIG    C4      5  -0.130000    12.010000      ca  -0.129444    12.010000
     6      ca      1     LIG    C5      6  -0.130000    12.010000      ca  -0.075744    12.010000
     7      ha      1     LIG     H      7   0.130000     1.008000      c3  -0.053744    12.010000
     8      ha      1     LIG    H1      8   0.130000     1.008000      ha   0.129056     1.008000
     9      ha      1     LIG    H2      9   0.130000     1.008000      ha   0.130056     1.008000
    10      ha      1     LIG    H3     10   0.130000     1.008000      ha   0.130056     1.008000
    11      ha      1     LIG    H4     11   0.130000     1.008000      ha   0.129056     1.008000
    12      ha      1     LIG    H5     12   0.130000     1.008000      c3  -0.053744    12.010000
    13   hc_du      1     LIG     H     13   0.000000     1.008000      hc   0.043756     1.008000
    14   hc_du      1     LIG    H1     14   0.000000     1.008000      hc   0.043756     1.008000
    15   hc_du      1     LIG    H2     15   0.000000     1.008000      hc   0.043756     1.008000
    16   hc_du      1     LIG    H7     16   0.000000     1.008000      hc   0.043756     1.008000
    17   hc_du      1     LIG    H8     17   0.000000     1.008000      hc   0.043756     1.008000
    18   hc_du      1     LIG    H9     18   0.000000     1.008000      hc   0.043756     1.008000

[ bonds ]
;   ai     aj  funct  parameters
     1      2      1  0.1398  316812  0.1398  316812
     1      6      1  0.1398  316812  0.1398  316812
     1      7      1  0.1086  331122  0.1516  209451
     2      3      1  0.1398  316812  0.1398  316812
     2      8      1  0.1086  331122  0.1086  331122
     3      4      1  0.1398  316812  0.1398  316812
     3      9      1  0.1086  331122  0.1086  331122
     4      5      1  0.1398  316812  0.1398  316812
     4     10      1  0.1086  331122  0.1086  331122
     5      6      1  0.1398  316812  0.1398  316812
     5     11      1  0.1086  331122  0.1086  331122
     6     12      1  0.1086  331122  0.1516  209451
     7     13      1  0.1097  314553  0.1097  314553
     7     14      1  0.1097  314553  0.1097  314553
     7     15      1  0.1097  314553  0.1097  314553
    12     16      1  0.1097  314553  0.1097  314553
    12     17      1  0.1097  314553  0.1097  314553
    12     18      1  0.1097  314553  0.1097  314553

[ pairs ]
;   ai     aj funct 
     1      4     1
     1      9     1
     1     11     1
     1     16     1
     1     17     1
     1     18     1
     2      5     1
     2     10     1
     2     12     1
     2     13     1
     2     14     1
     2     15     1
     3      6     1
     3      7     1
     3     11     1
     4      8     1
     4     12     1
     5      7     1
     5      9     1
     5     16     1
     5     17     1
     5     18     1
     6      8     1
     6     10     1
     6     13     1
     6     14     1
     6     15     1
     7      8     1
     7     12     1
     8      9     1
     9     10     1
    10     11     1
    11     12     1

[ angles ]
;   ai     aj     ak   funct   parameters
     1      2      3       1   120.02  575.718  120.02  575.718
     1      2      8       1   119.88  407.522  119.88  407.522
     1      6      5       1   120.02  575.718  120.02  575.718
     1      6     12       1   119.88  407.522  120.77  548.941
     1      7     13       1   110.47  395.806  110.47  395.806
     1      7     14       1   110.47  395.806  110.47  395.806
     1      7     15       1   110.47  395.806  110.47  395.806
     2      1      6       1   120.02  575.718  120.02  575.718
     2      1      7       1   119.88  407.522  120.77  548.941
     2      3      4       1   120.02  575.718  120.02  575.718
     2      3      9       1   119.88  407.522  119.88  407.522
     3      2      8       1   119.88  407.522  119.88  407.522
     3      4      5       1   120.02  575.718  120.02  575.718
     3      4     10       1   119.88  407.522  119.88  407.522
     4      3      9       1   119.88  407.522  119.88  407.522
     4      5      6       1   120.02  575.718  120.02  575.718
     4      5     11       1   119.88  407.522  119.88  407.522
     5      4     10       1   119.88  407.522  119.88  407.522
     5      6     12       1   119.88  407.522  120.77  548.941
     6      1      7       1   119.88  407.522  120.77  548.941
     6      5     11       1   119.88  407.522  119.88  407.522
     6     12     16       1   110.47  395.806  110.47  395.806
     6     12     17       1   110.47  395.806  110.47  395.806
     6     12     18       1   110.47  395.806  110.47  395.806
    13      7     14       1   107.58  326.352  107.58  326.352
    13      7     15       1   107.58  326.352  107.58  326.352
    14      7     15       1   107.58  326.352  107.58  326.352
    16     12     17       1   107.58  326.352  107.58  326.352
    16     12     18       1   107.58  326.352  107.58  326.352
    17     12     18       1   107.58  326.352  107.58  326.352

[ dihedrals ]
;   ai     aj     ak     al  funct  parameters
     1      2      3      4      1  180  15.167  2  180  15.167  2
     1      2      3      9      1  180  15.167  2  180  15.167  2
     1      3      2      8      4  180  4.6024  2  180  4.6024  2
     1      5      6     12      4  180  4.6024  2  0  0  2
     1      6      5      4      1  180  15.167  2  180  15.167  2
     1      6      5     11      1  180  15.167  2  180  15.167  2
     1      6     12     16      1  0  0  0  0  0  0
     1      6     12     17      1  0  0  0  0  0  0
     1      6     12     18      1  0  0  0  0  0  0
     2      1      6      5      1  180  15.167  2  180  15.167  2
     2      1      6     12      1  180  15.167  2  180  15.167  2
     2      1      7     13      1  0  0  0  0  0  0
     2      1      7     14      1  0  0  0  0  0  0
     2      1      7     15      1  0  0  0  0  0  0
     2      3      4      5      1  180  15.167  2  180  15.167  2
     2      3      4     10      1  180  15.167  2  180  15.167  2
     2      4      3      9      4  180  4.6024  2  180  4.6024  2
     2      6      1      7      4  180  4.6024  2  180  4.6024  2
     3      2      1      6      1  180  15.167  2  180  15.167  2
     3      2      1      7      1  180  15.167  2  180  15.167  2
     3      4      5      6      1  180  15.167  2  180  15.167  2
     3      4      5     11      1  180  15.167  2  180  15.167  2
     3      5      4     10      4  180  4.6024  2  180  4.6024  2
     4      3      2      8      1  180  15.167  2  180  15.167  2
     4      5      6     12      1  180  15.167  2  180  15.167  2
     4      6      5     11      4  180  4.6024  2  180  4.6024  2
     5      4      3      9      1  180  15.167  2  180  15.167  2
     5      6      1      7      1  180  15.167  2  180  15.167  2
     5      6      1     12      4  0  0  2  180  4.6024  2
     5      6     12     16      1  0  0  0  0  0  0
     5      6     12     17      1  0  0  0  0  0  0
     5      6     12     18      1  0  0  0  0  0  0
     6      1      2      8      1  180  15.167  2  180  15.167  2
     6      1      7     13      1  0  0  0  0  0  0
     6      1      7     14      1  0  0  0  0  0  0
     6      1      7     15      1  0  0  0  0  0  0
     6      5      4     10      1  180  15.167  2  180  15.167  2
     7      1      2      8      1  180  15.167  2  180  15.167  2
     7      1      6     12      1  180  15.167  2  180  15.167  2
     8      2      3      9      1  180  15.167  2  180  15.167  2
     9      3      4     10      1  180  15.167  2  180  15.167  2
    10      4      5     11      1  180  15.167  2  180  15.167  2
    11      5      6     12      1  180  15.167  2  180  15.167  2


[ moleculetype ]
; name  nrexcl
NA  3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr     charge         mass
     1    Na+      1      NA    NA      1   1.000000    22.990000


[ moleculetype ]
; name  nrexcl
WAT  3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr     charge         mass
     1     OW      1     WAT     O      1  -0.834000    16.000000
     2     HW      1     WAT    H1      2   0.417000     1.008000
     3     HW      1     WAT    H2      3   0.417000     1.008000

#ifdef FLEXIBLE
#else

[ settles ]
; OW    funct   doh dhh
1       1       0.09572 0.15136

[ exclusions ]
1   2   3
2   1   3
3   1   2

#endif

[ system ]
BioSimSpace System

[ molecules ]
;molecule name    nr.
Merged_Molecule      1
            NA      5
            CL      5
           WAT   2151