diff test-data/topol_md.top @ 8:14a7bf3e03df draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3"
author chemteam
date Wed, 29 Sep 2021 07:41:24 +0000
parents
children
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/topol_md.top	Wed Sep 29 07:41:24 2021 +0000
@@ -0,0 +1,910 @@
+;
+;	File 'topol.top' was generated
+;	By user: unknown (1000)
+;	On host: simon-notebook
+;	At date: Tue May 12 12:59:21 2020
+;
+;	This is a standalone topology file
+;
+;	Created by:
+;	                    :-) GROMACS - gmx pdb2gmx, 2019.1 (-:
+;	
+;	Executable:   /home/simon/miniconda3/envs/__gromacs@2019.1/bin/gmx
+;	Data prefix:  /home/simon/miniconda3/envs/__gromacs@2019.1
+;	Working dir:  /tmp/tmpg0ncnt9q/job_working_directory/000/10/working
+;	Command line:
+;	  gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water spce -ff oplsaa -noignh -merge all
+;	Force field was read from the standard GROMACS share directory.
+;
+
+; Include forcefield parameters
+#include "oplsaa.ff/forcefield.itp"
+
+[ moleculetype ]
+; Name            nrexcl
+Protein             3
+
+[ atoms ]
+;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
+; residue   1 LYS rtp LYSH q +2.0
+     1   opls_287      1    LYS      N      1       -0.3    14.0027
+     2   opls_290      1    LYS     H1      1       0.33      1.008
+     3   opls_290      1    LYS     H2      1       0.33      1.008
+     4   opls_290      1    LYS     H3      1       0.33      1.008
+     5  opls_293B      1    LYS     CA      1       0.25     12.011
+     6   opls_140      1    LYS     HA      1       0.06      1.008
+     7   opls_136      1    LYS     CB      2      -0.12     12.011
+     8   opls_140      1    LYS    HB1      2       0.06      1.008
+     9   opls_140      1    LYS    HB2      2       0.06      1.008
+    10   opls_136      1    LYS     CG      3      -0.12     12.011
+    11   opls_140      1    LYS    HG1      3       0.06      1.008
+    12   opls_140      1    LYS    HG2      3       0.06      1.008
+    13   opls_136      1    LYS     CD      4      -0.12     12.011
+    14   opls_140      1    LYS    HD1      4       0.06      1.008
+    15   opls_140      1    LYS    HD2      4       0.06      1.008
+    16   opls_292      1    LYS     CE      5       0.19     12.011
+    17   opls_140      1    LYS    HE1      5       0.06      1.008
+    18   opls_140      1    LYS    HE2      5       0.06      1.008
+    19   opls_287      1    LYS     NZ      6       -0.3    14.0067
+    20   opls_290      1    LYS    HZ1      6       0.33      1.008
+    21   opls_290      1    LYS    HZ2      6       0.33      1.008
+    22   opls_290      1    LYS    HZ3      6       0.33      1.008
+    23   opls_235      1    LYS      C      7        0.5     12.011
+    24   opls_236      1    LYS      O      7       -0.5    15.9994   ; qtot 2
+; residue   2 VAL rtp VAL  q  0.0
+    25   opls_238      2    VAL      N      8       -0.5    14.0067
+    26   opls_241      2    VAL      H      8        0.3      1.008
+    27  opls_224B      2    VAL     CA      8       0.14     12.011
+    28   opls_140      2    VAL     HA      8       0.06      1.008
+    29   opls_137      2    VAL     CB      9      -0.06     12.011
+    30   opls_140      2    VAL     HB      9       0.06      1.008
+    31   opls_135      2    VAL    CG1     10      -0.18     12.011
+    32   opls_140      2    VAL   HG11     10       0.06      1.008
+    33   opls_140      2    VAL   HG12     10       0.06      1.008
+    34   opls_140      2    VAL   HG13     10       0.06      1.008
+    35   opls_135      2    VAL    CG2     11      -0.18     12.011
+    36   opls_140      2    VAL   HG21     11       0.06      1.008
+    37   opls_140      2    VAL   HG22     11       0.06      1.008
+    38   opls_140      2    VAL   HG23     11       0.06      1.008
+    39   opls_235      2    VAL      C     12        0.5     12.011
+    40   opls_236      2    VAL      O     12       -0.5    15.9994   ; qtot 2
+; residue   3 PHE rtp PHE  q  0.0
+    41   opls_238      3    PHE      N     13       -0.5    14.0067
+    42   opls_241      3    PHE      H     13        0.3      1.008
+    43  opls_224B      3    PHE     CA     13       0.14     12.011
+    44   opls_140      3    PHE     HA     13       0.06      1.008
+    45   opls_149      3    PHE     CB     14     -0.005     12.011
+    46   opls_140      3    PHE    HB1     14       0.06      1.008
+    47   opls_140      3    PHE    HB2     14       0.06      1.008
+    48   opls_145      3    PHE     CG     14     -0.115     12.011
+    49   opls_145      3    PHE    CD1     15     -0.115     12.011
+    50   opls_146      3    PHE    HD1     15      0.115      1.008
+    51   opls_145      3    PHE    CD2     16     -0.115     12.011
+    52   opls_146      3    PHE    HD2     16      0.115      1.008
+    53   opls_145      3    PHE    CE1     17     -0.115     12.011
+    54   opls_146      3    PHE    HE1     17      0.115      1.008
+    55   opls_145      3    PHE    CE2     18     -0.115     12.011
+    56   opls_146      3    PHE    HE2     18      0.115      1.008
+    57   opls_145      3    PHE     CZ     19     -0.115     12.011
+    58   opls_146      3    PHE     HZ     19      0.115      1.008
+    59   opls_235      3    PHE      C     20        0.5     12.011
+    60   opls_236      3    PHE      O     20       -0.5    15.9994   ; qtot 2
+; residue   4 GLY rtp GLY  q  0.0
+    61   opls_238      4    GLY      N     21       -0.5    14.0067
+    62   opls_241      4    GLY      H     21        0.3      1.008
+    63  opls_223B      4    GLY     CA     21       0.08     12.011
+    64   opls_140      4    GLY    HA1     21       0.06      1.008
+    65   opls_140      4    GLY    HA2     21       0.06      1.008
+    66   opls_235      4    GLY      C     22        0.5     12.011
+    67   opls_236      4    GLY      O     22       -0.5    15.9994   ; qtot 2
+; residue   5 ARG rtp ARG  q  0.0
+    68   opls_238      5    ARG      N     23       -0.5    14.0067
+    69   opls_241      5    ARG      H     23        0.3      1.008
+    70   opls_283      5    ARG     CA     23       0.04     12.011
+    71   opls_140      5    ARG     HA     23       0.06      1.008
+    72   opls_136      5    ARG     CB     24      -0.12     12.011
+    73   opls_140      5    ARG    HB1     24       0.06      1.008
+    74   opls_140      5    ARG    HB2     24       0.06      1.008
+    75   opls_308      5    ARG     CG     25      -0.05     12.011
+    76   opls_140      5    ARG    HG1     25       0.06      1.008
+    77   opls_140      5    ARG    HG2     25       0.06      1.008
+    78   opls_307      5    ARG     CD     26       0.19     12.011
+    79   opls_140      5    ARG    HD1     26       0.06      1.008
+    80   opls_140      5    ARG    HD2     26       0.06      1.008
+    81   opls_303      5    ARG     NE     27       -0.7    14.0067
+    82   opls_304      5    ARG     HE     27       0.44      1.008
+    83   opls_302      5    ARG     CZ     27       0.64     12.011
+    84   opls_300      5    ARG    NH1     28       -0.8    14.0067
+    85   opls_301      5    ARG   HH11     28       0.46      1.008
+    86   opls_301      5    ARG   HH12     28       0.46      1.008
+    87   opls_300      5    ARG    NH2     29       -0.8    14.0067
+    88   opls_301      5    ARG   HH21     29       0.46      1.008
+    89   opls_301      5    ARG   HH22     29       0.46      1.008
+    90   opls_271      5    ARG      C     30        0.7     12.011
+    91   opls_272      5    ARG     O1     30       -0.8    15.9994
+    92   opls_272      5    ARG     O2     30       -0.8    15.9994   ; qtot 2
+
+[ bonds ]
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+
+[ pairs ]
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+
+[ angles ]
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+
+[ dihedrals ]
+;  ai    aj    ak    al funct            c0            c1            c2            c3            c4            c5
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+    3     1     5     6     3 
+    3     1     5     7     3 
+    3     1     5    23     3 
+    4     1     5     6     3 
+    4     1     5     7     3 
+    4     1     5    23     3 
+    1     5     7    10     3    dih_LYS_chi1_N_C_C_C
+   23     5     7    10     3    dih_LYS_chi1_C_C_C_CO
+    1     5     7     8     3 
+    1     5     7     9     3 
+    6     5     7     8     3 
+    6     5     7     9     3 
+    6     5     7    10     3 
+   23     5     7     8     3 
+   23     5     7     9     3 
+    1     5    23    24     3 
+    1     5    23    25     3 
+    6     5    23    24     3 
+    6     5    23    25     3 
+    7     5    23    24     3 
+    7     5    23    25     3 
+    5     7    10    11     3 
+    5     7    10    12     3 
+    5     7    10    13     3 
+    8     7    10    11     3 
+    8     7    10    12     3 
+    8     7    10    13     3 
+    9     7    10    11     3 
+    9     7    10    12     3 
+    9     7    10    13     3 
+    7    10    13    14     3 
+    7    10    13    15     3 
+    7    10    13    16     3 
+   11    10    13    14     3 
+   11    10    13    15     3 
+   11    10    13    16     3 
+   12    10    13    14     3 
+   12    10    13    15     3 
+   12    10    13    16     3 
+   10    13    16    17     3 
+   10    13    16    18     3 
+   10    13    16    19     3 
+   14    13    16    17     3 
+   14    13    16    18     3 
+   14    13    16    19     3 
+   15    13    16    17     3 
+   15    13    16    18     3 
+   15    13    16    19     3 
+   13    16    19    20     3    dih_LYS_chi5_C_C_N_H
+   13    16    19    21     3    dih_LYS_chi5_C_C_N_H
+   13    16    19    22     3    dih_LYS_chi5_C_C_N_H
+   17    16    19    20     3 
+   17    16    19    21     3 
+   17    16    19    22     3 
+   18    16    19    20     3 
+   18    16    19    21     3 
+   18    16    19    22     3 
+    5    23    25    26     3 
+    5    23    25    27     3 
+   24    23    25    26     3 
+   24    23    25    27     3 
+   23    25    27    28     3 
+   23    25    27    29     3 
+   23    25    27    39     3 
+   26    25    27    28     3 
+   26    25    27    29     3 
+   26    25    27    39     3 
+   25    27    29    31     3    dih_VAL_chi1_N_C_C_C
+   25    27    29    35     3    dih_VAL_chi1_N_C_C_C
+   39    27    29    31     3    dih_VAL_chi1_C_C_C_CO
+   39    27    29    35     3    dih_VAL_chi1_C_C_C_CO
+   25    27    29    30     3 
+   28    27    29    30     3 
+   28    27    29    31     3 
+   28    27    29    35     3 
+   39    27    29    30     3 
+   25    27    39    40     3 
+   25    27    39    41     3 
+   28    27    39    40     3 
+   28    27    39    41     3 
+   29    27    39    40     3 
+   29    27    39    41     3 
+   27    29    31    32     3 
+   27    29    31    33     3 
+   27    29    31    34     3 
+   30    29    31    32     3 
+   30    29    31    33     3 
+   30    29    31    34     3 
+   35    29    31    32     3 
+   35    29    31    33     3 
+   35    29    31    34     3 
+   27    29    35    36     3 
+   27    29    35    37     3 
+   27    29    35    38     3 
+   30    29    35    36     3 
+   30    29    35    37     3 
+   30    29    35    38     3 
+   31    29    35    36     3 
+   31    29    35    37     3 
+   31    29    35    38     3 
+   27    39    41    42     3 
+   27    39    41    43     3 
+   40    39    41    42     3 
+   40    39    41    43     3 
+   39    41    43    44     3 
+   39    41    43    45     3 
+   39    41    43    59     3 
+   42    41    43    44     3 
+   42    41    43    45     3 
+   42    41    43    59     3 
+   41    43    45    46     3 
+   41    43    45    47     3 
+   41    43    45    48     3 
+   44    43    45    46     3 
+   44    43    45    47     3 
+   44    43    45    48     3 
+   59    43    45    46     3 
+   59    43    45    47     3 
+   59    43    45    48     3 
+   41    43    59    60     3 
+   41    43    59    61     3 
+   44    43    59    60     3 
+   44    43    59    61     3 
+   45    43    59    60     3 
+   45    43    59    61     3 
+   43    45    48    49     3 
+   43    45    48    51     3 
+   46    45    48    49     3 
+   46    45    48    51     3 
+   47    45    48    49     3 
+   47    45    48    51     3 
+   45    48    49    50     3 
+   45    48    49    53     3 
+   51    48    49    50     3 
+   51    48    49    53     3 
+   45    48    51    52     3 
+   45    48    51    55     3 
+   49    48    51    52     3 
+   49    48    51    55     3 
+   48    49    53    54     3 
+   48    49    53    57     3 
+   50    49    53    54     3 
+   50    49    53    57     3 
+   48    51    55    56     3 
+   48    51    55    57     3 
+   52    51    55    56     3 
+   52    51    55    57     3 
+   49    53    57    55     3 
+   49    53    57    58     3 
+   54    53    57    55     3 
+   54    53    57    58     3 
+   51    55    57    53     3 
+   51    55    57    58     3 
+   56    55    57    53     3 
+   56    55    57    58     3 
+   43    59    61    62     3 
+   43    59    61    63     3 
+   60    59    61    62     3 
+   60    59    61    63     3 
+   59    61    63    64     3 
+   59    61    63    65     3 
+   59    61    63    66     3 
+   62    61    63    64     3 
+   62    61    63    65     3 
+   62    61    63    66     3 
+   61    63    66    67     3 
+   61    63    66    68     3 
+   64    63    66    67     3 
+   64    63    66    68     3 
+   65    63    66    67     3 
+   65    63    66    68     3 
+   63    66    68    69     3 
+   63    66    68    70     3 
+   67    66    68    69     3 
+   67    66    68    70     3 
+   66    68    70    71     3 
+   66    68    70    72     3 
+   66    68    70    90     3 
+   69    68    70    71     3 
+   69    68    70    72     3 
+   69    68    70    90     3 
+   68    70    72    75     3    dih_ARG_chi1_N_C_C_C
+   90    70    72    75     3    dih_ARG_chi1_C_C_C_CO
+   68    70    72    73     3 
+   68    70    72    74     3 
+   71    70    72    73     3 
+   71    70    72    74     3 
+   71    70    72    75     3 
+   90    70    72    73     3 
+   90    70    72    74     3 
+   68    70    90    91     3 
+   68    70    90    92     3 
+   71    70    90    91     3 
+   71    70    90    92     3 
+   72    70    90    91     3 
+   72    70    90    92     3 
+   70    72    75    76     3 
+   70    72    75    77     3 
+   70    72    75    78     3 
+   73    72    75    76     3 
+   73    72    75    77     3 
+   73    72    75    78     3 
+   74    72    75    76     3 
+   74    72    75    77     3 
+   74    72    75    78     3 
+   72    75    78    79     3 
+   72    75    78    80     3 
+   72    75    78    81     3 
+   76    75    78    79     3 
+   76    75    78    80     3 
+   76    75    78    81     3 
+   77    75    78    79     3 
+   77    75    78    80     3 
+   77    75    78    81     3 
+   75    78    81    82     3 
+   75    78    81    83     3 
+   79    78    81    82     3 
+   79    78    81    83     3 
+   80    78    81    82     3 
+   80    78    81    83     3 
+   78    81    83    84     3 
+   78    81    83    87     3 
+   82    81    83    84     3 
+   82    81    83    87     3 
+   81    83    84    85     3 
+   81    83    84    86     3 
+   87    83    84    85     3 
+   87    83    84    86     3 
+   81    83    87    88     3 
+   81    83    87    89     3 
+   84    83    87    88     3 
+   84    83    87    89     3 
+
+[ dihedrals ]
+;  ai    aj    ak    al funct            c0            c1            c2            c3
+    5    25    23    24     1    improper_O_C_X_Y
+   23    27    25    26     1    improper_Z_N_X_Y
+   27    41    39    40     1    improper_O_C_X_Y
+   39    43    41    42     1    improper_Z_N_X_Y
+   43    61    59    60     1    improper_O_C_X_Y
+   45    48    51    49     1    improper_Z_CA_X_Y
+   48    53    49    50     1    improper_Z_CA_X_Y
+   48    55    51    52     1    improper_Z_CA_X_Y
+   49    57    53    54     1    improper_Z_CA_X_Y
+   51    57    55    56     1    improper_Z_CA_X_Y
+   53    55    57    58     1    improper_Z_CA_X_Y
+   59    63    61    62     1    improper_Z_N_X_Y
+   63    68    66    67     1    improper_O_C_X_Y
+   66    70    68    69     1    improper_Z_N_X_Y
+   70    91    90    92     1    improper_O_C_X_Y
+   78    83    81    82     1    improper_Z_N_X_Y
+   81    84    83    87     1    improper_O_C_X_Y
+   83    85    84    86     1    improper_Z_N_X_Y
+   83    88    87    89     1    improper_Z_N_X_Y
+
+; Include Position restraint file
+#ifdef POSRES
+#include "posres.itp"
+#endif
+
+; Include water topology
+#include "oplsaa.ff/spce.itp"
+
+#ifdef POSRES_WATER
+; Position restraint for each water oxygen
+[ position_restraints ]
+;  i funct       fcx        fcy        fcz
+   1    1       1000       1000       1000
+#endif
+
+; Include topology for ions
+#include "oplsaa.ff/ions.itp"
+
+[ system ]
+; Name
+TEST in water
+
+[ molecules ]
+; Compound        #mols
+Protein             1
+CL               2