[gmx-users] Problem with adding H using amber03

Peggy Yao peggy.yao at gmail.com
Wed Feb 18 02:39:46 CET 2009

Dear all,

I am trying to use amber03 force field. I corrected the amino acid names as
described on http://chemistry.csulb.edu/ffamber/.

However, when I ran pdb2gmx on a PDB file without H-atoms, I got the
following error:

pdb2gmx -ff amber03 -f protein_without_H.pdb -o protein_amber03.pdb

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

Program pdb2gmx, VERSION 4.0.2
Source code file: pdb2top.c, line: 701

Fatal error:
There were 1 missing atoms in molecule Protein_A, if you want to use this
incomplete topology anyhow, use the option -missing

I checked the ffamber03.hdb. It is in the correct directory as other *.hdb
files. It also contains the entry for H-atom in THR:

THR     5
1       1       H       N       -C      CA
1       5       HA      CA      N       CB      C
1       5       HB      CB      CA      CG2     OG1
3       4       HG2     CG2     CB      CA
1       2       HG1     OG1     CB      CA

Can anyone tell me what might be the problem? I should be able to use
pdb2gmx and amber03 to add all H-atoms, right?


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