[gmx-users] Re:problem adding H atoms

[Stacey Meadley]

Hi Justin,
the gromacs version is 4.0.4.
command line: pdb2gmx -f 1B9Eostate.pdb -o 1B9Eostate.gro -p 1B9Eostate.top
-ff amber03
message: WARNING: atom H is missing in residue ILE 2 in the pdb file
         You might need to add atom H to the hydrogen database of residue
ILE
         in the file ff???.hdb (see the manual)
beginning of pdb file:
ATOM      1  N   NGLYA   1      -5.201   9.673  -2.852  1.00 21.99
N
ATOM      2  CA  NGLYA   1      -3.724   9.368  -2.711  1.00 21.30
C
ATOM      3  C   NGLYA   1      -3.320   8.030  -3.324  1.00 18.48
C
ATOM      4  O   NGLYA   1      -4.164   7.323  -3.878  1.00 24.81
O
ATOM      5  N   ILE A   2      -2.065   7.644  -3.159  1.00 13.65
N
ATOM      6  CA  ILE A   2      -1.579   6.399  -3.716  1.00 12.18
C
ATOM      7  C   ILE A   2      -2.254   5.174  -3.077  1.00 15.61
C
ATOM      8  O   ILE A   2      -2.629   4.249  -3.786  1.00 13.09
O
ATOM      9  CB  ILE A   2      -0.037   6.325  -3.601  1.00 12.48
C
ATOM     10  CG1 ILE A   2       0.494   5.122  -4.357  1.00 14.27
C
ATOM     11  CG2 ILE A   2       0.397   6.250  -2.171  1.00  7.71
C
ATOM     12  CD  ILE A   2       1.946   5.193  -4.618  1.00 11.64
C
ATOM     13  N   VAL A   3      -2.487   5.202  -1.759  1.00 19.67
N
ATOM     14  CA  VAL A   3      -3.123   4.072  -1.065  1.00 21.16
C
ATOM     15  C   VAL A   3      -4.531   3.814  -1.605  1.00 21.76
C
ATOM     16  O   VAL A   3      -4.954   2.670  -1.806  1.00 20.69
O
ATOM     17  CB  VAL A   3      -3.225   4.312   0.465  1.00 21.43
C
ATOM     18  CG1 VAL A   3      -3.687   3.033   1.165  1.00 21.34
C
ATOM     19  CG2 VAL A   3      -1.885   4.782   1.039  1.00 19.65
C
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