[gmx-users] add a group to an amino acid

[hengame fallah]

Thank you very much, Mark!
Now i have errors from my .top file after grompp command.
The question is that why in pdb2gmx, editconf ,genbox and make_ndx steps i
don't see these errors:

...
processing topology...
Opening library file /usr/share/gromacs/top/ffoplsaa.itp
Opening library file /usr/share/gromacs/top/ffoplsaanb.itp
Opening library file /usr/share/gromacs/top/ffoplsaabon.itp
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations

ERROR 1 [file topol.top, line 412]:
  No default Angle types


ERROR 2 [file topol.top, line 567]:
  No default Ryckaert-Bell. types


ERROR 3 [file topol.top, line 570]:
  No default Ryckaert-Bell. types


ERROR 4 [file topol.top, line 573]:
  No default Ryckaert-Bell. types


ERROR 5 [file topol.top, line 580]:
  No default Ryckaert-Bell. types


ERROR 6 [file topol.top, line 581]:
  No default Ryckaert-Bell. types


ERROR 7 [file topol.top, line 582]:
  No default Ryckaert-Bell. types

Opening library file /usr/share/gromacs/top/spc.itp
Opening library file /usr/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 1 [file topol.top, line 664]:
  System has non-zero total charge: 6.000000e-02



processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...

There was 1 note

-------------------------------------------------------
Program grompp, VERSION 4.0.7
Source code file: ../../../../src/kernel/grompp.c, line: 986

Fatal error:
There were 7 errors in input file(s)

*topol.top:*
...
    43   opls_238      3    BOC      N       17       -0.5    14.0067   ;
qtot 0.5
    44   opls_241      3    BOC      H       17        0.3      1.008   ;
qtot 0.8
    45   opls_283      3    BOC     CA      17       0.04     12.011   ;
qtot 0.84
    46   opls_140      3    BOC    HA1     17       0.06      1.008   ; qtot
0.9
    47   opls_140      3    BOC    HA2     17       0.06      1.008   ; qtot
0.96
    48   opls_149      3    BOC     CB     18      0.055     12.011   ; qtot
1.015
    49   opls_140      3    BOC     HB     18       0.06      1.008   ; qtot
1.075
    50   opls_145      3    BOC    CG1     18     -0.115     12.011   ; qtot
0.96
    51   opls_145      3    BOC    CD1     19     -0.115     12.011   ; qtot
0.845
    52   opls_146      3    BOC    HD1     19      0.115      1.008   ; qtot
0.96
    53   opls_145      3    BOC    CD2     20     -0.115     12.011   ; qtot
0.845
    54   opls_146      3    BOC    HD2     20      0.115      1.008   ; qtot
0.96
    55   opls_145      3    BOC    CE1     21     -0.115     12.011   ; qtot
0.845
    56   opls_146      3    BOC    HE1     21      0.115      1.008   ; qtot
0.96
    57   opls_145      3    BOC    CE2     22     -0.115     12.011   ; qtot
0.845
    58   opls_146      3    BOC    HE2     22      0.115      1.008   ; qtot
0.96
    59   opls_145      3    BOC     CZ      23          1     12.011   ;
qtot 1.96
    60   opls_264      3    BOC     Cl        23         -1     35.453   ;
qtot 0.96
    61  opls_224B     3    BOC    CG2     24      -0.12     12.011   ; qtot
0.84
    62   opls_140      3    BOC    HG1     24       0.06      1.008   ; qtot
0.9
    63   opls_140      3    BOC    HG2     24       0.06      1.008   ; qtot
0.96
    64   opls_271      3    BOC      C       25        0.7     12.011   ;
qtot 1.66
    65   opls_272      3    BOC     O1     25       -0.8    15.9994   ; qtot
0.86
    66   opls_272      3    BOC     O2     25       -0.8    15.9994   ; qtot
0.06
...
[ angles ]
...
line 412: 45    48    61     1
...
[ dihedrals ]
...
line 567: 43    45    48    61     3
...
line 570: 46    45    48    61     3
...
line 573: 47    45    48    61     3
...
line 580: 45    48    61    62     3
line 581: 45    48    61    63     3
line 582: 45    48    61    64     3
...

it seems that "45   48    61" is the problem. CA    CB    CG2
Where i should define angle type for it?
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