[gmx-users] Bug? in version 3.1.4

Erik Lindahl lindahl at stanford.edu
Tue Sep 23 18:45:01 CEST 2003

Hi Istvan,

You're perfectly correct. The problem is that the atom is sometimes 
called CA and sometimes CH3 in pdb files, but we're working on a more 
general converter that can accept alternative names for atoms :-)



On Tuesday, September 23, 2003, at 07:44 AM, istvan at kolossvary.hu wrote:

> Hi,
> I was trying to "pdb2gmx" a simple peptide capped with ACE at the 
> N-terminus and NAC at the C-terminus, but generating the hydrogens 
> failed on NAC with an error message coming from genhydro.c "Atom CA 
> not found in residue NAC3 for while adding hydrogens". It turns out 
> that the problem is a mismatch between respective .rtp and .hdb files. 
> I specifically worked with oplsaa, but it seems that similar 
> mismatches are present in the other force field files, too. For 
> example, for oplsaa, the NAC carbon is a CH3 in the .rtp file, which 
> is correct, but the same carbon in the corresponding .hdb file is a 
> CA, which seems incorrect, because NAC does not have a CA. Changing 
> the CA to CH3 in the .hdb file solved the problem. Since I am new to 
> Gromacs, I am not sure that this is a correct fix, or I am missing 
> something.
> Thanks for your help.
>  Istvan Kolossvary _______________________________________________
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