[gmx-users] Converting PDB to gromacs (Hydrogen problems)

[Craig Schwartz]

Hey Gromacs Users,
     I am trying to convert the zwitterionic form of glycine into a top and
gro file from the pdb, while I appear to be able to do this with some
efficiency by PRODRG is there a way to do this that keeps all my hydrogens
in the same locations?  This gets more complicated when I try and perform a
similar thing on the anion, as I can generate the # of hydrogens etc. but I
can't get it to freeze the hydrogen locations.  Is there a way to generate
the .gro and .top files directly from a PDB?
Best,
Craig

Anionic Glycine PDB
REMARK 888
REMARK 888 WRITTEN BY MAESTRO (A PRODUCT OF SCHRODINGER, LLC)
TITLE     /glab/d1/craig/.schrodinger/tmp/12031/_mmoddat2
MODEL        1
HETATM    1  C1  UNK   900       0.315  -1.043   0.000  1.00  0.00
C
HETATM    2  C2  UNK   900       0.304   0.522   0.000  1.00  0.00
C
HETATM    3  N1  UNK   900      -1.016  -1.711   0.000  1.00  0.00
N
HETATM    4  O1  UNK   900       1.456   1.075   0.000  1.00  0.00
O1-
HETATM    5  O2  UNK   900      -0.850   1.079   0.000  1.00  0.00
O
HETATM    6  H1  UNK   900       0.885  -1.385   0.880  1.00  0.00
H
HETATM    7  H2  UNK   900       0.885  -1.385  -0.880  1.00  0.00
H
HETATM    8  H3  UNK   900      -1.520  -1.279   0.789  1.00  0.00
H
HETATM    9  H4  UNK   900      -1.520  -1.279  -0.789  1.00  0.00
H
CONECT    1    2    3    6    7
CONECT    2    1    4    5
CONECT    2    5
CONECT    3    1    8    9
CONECT    4    2
CONECT    5    2
CONECT    5    2
CONECT    6    1
CONECT    7    1
CONECT    8    3
CONECT    9    3
ENDMDL
END
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