[gmx-users] error with pdb2gmx when using AMBER ff in GROMACS

Mon Mar 31 20:37:19 CEST 2008

Hi all, 

I am trying to use AMBER ff in GROMACS. I have followed the steps that are given in the  http://chemistry.csulb.edu/ffamber/  link. 

The first residue of the protein is GLN. I put an N prefix to this residue. The pdg2gmx works well except giving an warning of long bond between some atoms. 

In contrast, if I have not put any prefix to GLN, then, the following error appears:
WARNING: atom H is missing in residue GLN 1 in the pdb file
You might need to add atom H to the hydrogen database of residue GLN
in the file ff???.hdb (see the manual)

Program pdb2gmx, VERSION 3.3.1
Source code file: pdb2top.c, line: 697

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

I looked at both the .rtp and .hdb files, but everything seems to be correct.

Does anybody face with a similar problem?

Thanks in advance
Ozge Engin
Computational Science & Engineering
Koc University

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