annotate test-data/topol_md.top @ 14:593c63b5aff8 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 5536c9fbb2f680a5f296db81362099e5a68e0587"

;
;	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 ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     1 
    1     3     1 
    1     4     1 
    1     5     1 
    5     6     1 
    5     7     1 
    5    23     1 
    7     8     1 
    7     9     1 
    7    10     1 
   10    11     1 
   10    12     1 
   10    13     1 
   13    14     1 
   13    15     1 
   13    16     1 
   16    17     1 
   16    18     1 
   16    19     1 
   19    20     1 
   19    21     1 
   19    22     1 
   23    24     1 
   23    25     1 
   25    26     1 
   25    27     1 
   27    28     1 
   27    29     1 
   27    39     1 
   29    30     1 
   29    31     1 
   29    35     1 
   31    32     1 
   31    33     1 
   31    34     1 
   35    36     1 
   35    37     1 
   35    38     1 
   39    40     1 
   39    41     1 
   41    42     1 
   41    43     1 
   43    44     1 
   43    45     1 
   43    59     1 
   45    46     1 
   45    47     1 
   45    48     1 
   48    49     1 
   48    51     1 
   49    50     1 
   49    53     1 
   51    52     1 
   51    55     1 
   53    54     1 
   53    57     1 
   55    56     1 
   55    57     1 
   57    58     1 
   59    60     1 
   59    61     1 
   61    62     1 
   61    63     1 
   63    64     1 
   63    65     1 
   63    66     1 
   66    67     1 
   66    68     1 
   68    69     1 
   68    70     1 
   70    71     1 
   70    72     1 
   70    90     1 
   72    73     1 
   72    74     1 
   72    75     1 
   75    76     1 
   75    77     1 
   75    78     1 
   78    79     1 
   78    80     1 
   78    81     1 
   81    82     1 
   81    83     1 
   83    84     1 
   83    87     1 
   84    85     1 
   84    86     1 
   87    88     1 
   87    89     1 
   90    91     1 
   90    92     1 

[ pairs ]
;  ai    aj funct            c0            c1            c2            c3
    1     8     1 
    1     9     1 
    1    10     1 
    1    24     1 
    1    25     1 
    2     6     1 
    2     7     1 
    2    23     1 
    3     6     1 
    3     7     1 
    3    23     1 
    4     6     1 
    4     7     1 
    4    23     1 
    5    11     1 
    5    12     1 
    5    13     1 
    5    26     1 
    5    27     1 
    6     8     1 
    6     9     1 
    6    10     1 
    6    24     1 
    6    25     1 
    7    14     1 
    7    15     1 
    7    16     1 
    7    24     1 
    7    25     1 
    8    11     1 
    8    12     1 
    8    13     1 
    8    23     1 
    9    11     1 
    9    12     1 
    9    13     1 
    9    23     1 
   10    17     1 
   10    18     1 
   10    19     1 
   10    23     1 
   11    14     1 
   11    15     1 
   11    16     1 
   12    14     1 
   12    15     1 
   12    16     1 
   13    20     1 
   13    21     1 
   13    22     1 
   14    17     1 
   14    18     1 
   14    19     1 
   15    17     1 
   15    18     1 
   15    19     1 
   17    20     1 
   17    21     1 
   17    22     1 
   18    20     1 
   18    21     1 
   18    22     1 
   23    28     1 
   23    29     1 
   23    39     1 
   24    26     1 
   24    27     1 
   25    30     1 
   25    31     1 
   25    35     1 
   25    40     1 
   25    41     1 
   26    28     1 
   26    29     1 
   26    39     1 
   27    32     1 
   27    33     1 
   27    34     1 
   27    36     1 
   27    37     1 
   27    38     1 
   27    42     1 
   27    43     1 
   28    30     1 
   28    31     1 
   28    35     1 
   28    40     1 
   28    41     1 
   29    40     1 
   29    41     1 
   30    32     1 
   30    33     1 
   30    34     1 
   30    36     1 
   30    37     1 
   30    38     1 
   30    39     1 
   31    36     1 
   31    37     1 
   31    38     1 
   31    39     1 
   32    35     1 
   33    35     1 
   34    35     1 
   35    39     1 
   39    44     1 
   39    45     1 
   39    59     1 
   40    42     1 
   40    43     1 
   41    46     1 
   41    47     1 
   41    48     1 
   41    60     1 
   41    61     1 
   42    44     1 
   42    45     1 
   42    59     1 
   43    49     1 
   43    51     1 
   43    62     1 
   43    63     1 
   44    46     1 
   44    47     1 
   44    48     1 
   44    60     1 
   44    61     1 
   45    50     1 
   45    52     1 
   45    53     1 
   45    55     1 
   45    60     1 
   45    61     1 
   46    49     1 
   46    51     1 
   46    59     1 
   47    49     1 
   47    51     1 
   47    59     1 
   48    54     1 
   48    56     1 
   48    57     1 
   48    59     1 
   49    52     1 
   49    55     1 
   49    58     1 
   50    51     1 
   50    54     1 
   50    57     1 
   51    53     1 
   51    58     1 
   52    56     1 
   52    57     1 
   53    56     1 
   54    55     1 
   54    58     1 
   56    58     1 
   59    64     1 
   59    65     1 
   59    66     1 
   60    62     1 
   60    63     1 
   61    67     1 
   61    68     1 
   62    64     1 
   62    65     1 
   62    66     1 
   63    69     1 
   63    70     1 
   64    67     1 
   64    68     1 
   65    67     1 
   65    68     1 
   66    71     1 
   66    72     1 
   66    90     1 
   67    69     1 
   67    70     1 
   68    73     1 
   68    74     1 
   68    75     1 
   68    91     1 
   68    92     1 
   69    71     1 
   69    72     1 
   69    90     1 
   70    76     1 
   70    77     1 
   70    78     1 
   71    73     1 
   71    74     1 
   71    75     1 
   71    91     1 
   71    92     1 
   72    79     1 
   72    80     1 
   72    81     1 
   72    91     1 
   72    92     1 
   73    76     1 
   73    77     1 
   73    78     1 
   73    90     1 
   74    76     1 
   74    77     1 
   74    78     1 
   74    90     1 
   75    82     1 
   75    83     1 
   75    90     1 
   76    79     1 
   76    80     1 
   76    81     1 
   77    79     1 
   77    80     1 
   77    81     1 
   78    84     1 
   78    87     1 
   79    82     1 
   79    83     1 
   80    82     1 
   80    83     1 
   81    85     1 
   81    86     1 
   81    88     1 
   81    89     1 
   82    84     1 
   82    87     1 
   84    88     1 
   84    89     1 
   85    87     1 
   86    87     1 

[ angles ]
;  ai    aj    ak funct            c0            c1            c2            c3
    2     1     3     1 
    2     1     4     1 
    2     1     5     1 
    3     1     4     1 
    3     1     5     1 
    4     1     5     1 
    1     5     6     1 
    1     5     7     1 
    1     5    23     1 
    6     5     7     1 
    6     5    23     1 
    7     5    23     1 
    5     7     8     1 
    5     7     9     1 
    5     7    10     1 
    8     7     9     1 
    8     7    10     1 
    9     7    10     1 
    7    10    11     1 
    7    10    12     1 
    7    10    13     1 
   11    10    12     1 
   11    10    13     1 
   12    10    13     1 
   10    13    14     1 
   10    13    15     1 
   10    13    16     1 
   14    13    15     1 
   14    13    16     1 
   15    13    16     1 
   13    16    17     1 
   13    16    18     1 
   13    16    19     1 
   17    16    18     1 
   17    16    19     1 
   18    16    19     1 
   16    19    20     1 
   16    19    21     1 
   16    19    22     1 
   20    19    21     1 
   20    19    22     1 
   21    19    22     1 
    5    23    24     1 
    5    23    25     1 
   24    23    25     1 
   23    25    26     1 
   23    25    27     1 
   26    25    27     1 
   25    27    28     1 
   25    27    29     1 
   25    27    39     1 
   28    27    29     1 
   28    27    39     1 
   29    27    39     1 
   27    29    30     1 
   27    29    31     1 
   27    29    35     1 
   30    29    31     1 
   30    29    35     1 
   31    29    35     1 
   29    31    32     1 
   29    31    33     1 
   29    31    34     1 
   32    31    33     1 
   32    31    34     1 
   33    31    34     1 
   29    35    36     1 
   29    35    37     1 
   29    35    38     1 
   36    35    37     1 
   36    35    38     1 
   37    35    38     1 
   27    39    40     1 
   27    39    41     1 
   40    39    41     1 
   39    41    42     1 
   39    41    43     1 
   42    41    43     1 
   41    43    44     1 
   41    43    45     1 
   41    43    59     1 
   44    43    45     1 
   44    43    59     1 
   45    43    59     1 
   43    45    46     1 
   43    45    47     1 
   43    45    48     1 
   46    45    47     1 
   46    45    48     1 
   47    45    48     1 
   45    48    49     1 
   45    48    51     1 
   49    48    51     1 
   48    49    50     1 
   48    49    53     1 
   50    49    53     1 
   48    51    52     1 
   48    51    55     1 
   52    51    55     1 
   49    53    54     1 
   49    53    57     1 
   54    53    57     1 
   51    55    56     1 
   51    55    57     1 
   56    55    57     1 
   53    57    55     1 
   53    57    58     1 
   55    57    58     1 
   43    59    60     1 
   43    59    61     1 
   60    59    61     1 
   59    61    62     1 
   59    61    63     1 
   62    61    63     1 
   61    63    64     1 
   61    63    65     1 
   61    63    66     1 
   64    63    65     1 
   64    63    66     1 
   65    63    66     1 
   63    66    67     1 
   63    66    68     1 
   67    66    68     1 
   66    68    69     1 
   66    68    70     1 
   69    68    70     1 
   68    70    71     1 
   68    70    72     1 
   68    70    90     1 
   71    70    72     1 
   71    70    90     1 
   72    70    90     1 
   70    72    73     1 
   70    72    74     1 
   70    72    75     1 
   73    72    74     1 
   73    72    75     1 
   74    72    75     1 
   72    75    76     1 
   72    75    77     1 
   72    75    78     1 
   76    75    77     1 
   76    75    78     1 
   77    75    78     1 
   75    78    79     1 
   75    78    80     1 
   75    78    81     1 
   79    78    80     1 
   79    78    81     1 
   80    78    81     1 
   78    81    82     1 
   78    81    83     1 
   82    81    83     1 
   81    83    84     1 
   81    83    87     1 
   84    83    87     1 
   83    84    85     1 
   83    84    86     1 
   85    84    86     1 
   83    87    88     1 
   83    87    89     1 
   88    87    89     1 
   70    90    91     1 
   70    90    92     1 
   91    90    92     1 

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2            c3            c4            c5
    2     1     5     6     3 
    2     1     5     7     3 
    2     1     5    23     3 
    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