[gmx-users] (no subject)

[mymonii at pob.huji.ac.il]

Hello
I use the  pdb2gms command with DNA, and I get this massages:

WARNING: atom H41 is missing in residue DCYT 1 in the pdb file
         You might need to add atom H41 to the hydrogen database of residue DCYT
         in the file ff???.hdb (see the manual)


WARNING: atom H42 is missing in residue DCYT 1 in the pdb file
         You might need to add atom H42 to the hydrogen database of residue DCYT
         in the file ff???.hdb (see the manual)

Here is the pdb file which show that the atoms H41 and H42 are not missing,
then what is the real problem any one can tell me ???????????

ATOM   1003  P   DCYTB M10      60.015  44.057  39.754  1.00100.00           P
ATOM   1004  O1P DCYTB M10      59.508  45.143  40.640  1.00100.00           O
ATOM   1005  O2P DCYTB M10      60.980  44.381  38.664  1.00100.00           O
ATOM   1006  O5* DCYTB M10      60.706  42.951  40.693  1.00 85.34           O
ATOM   1007  C5* DCYTB M10      60.126  42.621  41.947  1.00 84.43           C
ATOM   1008  C4* DCYTB M10      60.572  43.572  43.042  1.00 74.92           C
ATOM   1009  O4* DCYTB M10      59.518  43.621  44.025  1.00 67.89           O
ATOM   1010  C3* DCYTB M10      61.766  43.074  43.841  1.00 75.06           C
ATOM   1011  O3* DCYTB M10      62.339  44.121  44.621  1.00 85.97           O
ATOM   1012  C2* DCYTB M10      61.118  42.021  44.734  1.00 69.18           C
ATOM   1013  C1* DCYTB M10      59.750  42.628  45.012  1.00 61.99           C
ATOM   1014  N1  DCYTB M10      58.655  41.625  44.944  1.00 50.66           N
ATOM   1015  C2  DCYTB M10      58.057  41.236  46.145  1.00 46.21           C
ATOM   1016  O2  DCYTB M10      58.462  41.735  47.194  1.00 46.53           O
ATOM   1017  N3  DCYTB M10      57.058  40.326  46.115  1.00 43.34           N
ATOM   1018  C4  DCYTB M10      56.668  39.834  44.932  1.00 46.06           C
ATOM   1019  N4  DCYTB M10      55.678  38.949  44.919  1.00 49.15           N
ATOM   1020  C5  DCYTB M10      57.266  40.218  43.697  1.00 43.69           C
ATOM   1021  C6  DCYTB M10      58.249  41.109  43.751  1.00 46.04           C
ATOM   1022 1H5* DCYTB M10      60.398  41.615  42.267  1.00  0.00           H
ATOM   1023 2H5* DCYTB M10      59.037  42.661  41.913  1.00  0.00           H
ATOM   1024  H4* DCYTB M10      60.850  44.520  42.582  1.00  0.00           H
ATOM   1025  H3* DCYTB M10      62.534  42.654  43.191  1.00  0.00           H
ATOM   1026 1H2* DCYTB M10      61.694  41.868  45.647  1.00  0.00           H
ATOM   1027 2H2* DCYTB M10      61.046  41.060  44.225  1.00  0.00           H
ATOM   1028  H1* DCYTB M10      59.764  43.106  45.991  1.00  0.00           H
ATOM   1029  H41 DCYTB M10      55.354  38.551  44.026  1.00  0.00           H
ATOM   1030  H42 DCYTB M10      55.234  38.660  45.802  1.00  0.00           H
ATOM   1031  H5  DCYTB M10      56.931  39.798  42.749  1.00  0.00           H
ATOM   1032  H6  DCYTB M10      58.736  41.431  42.831  1.00  0.00           H


I will be gratefull for help.
Ilanit Mymoni
Medicinal chemistry Jerusalem Israel

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