[gmx-users] Gromacs tools mistakenly change the name of atoms in coordinate files

[David van der Spoel]

Robert Johnson wrote:
> Hello everyone,
> I'm attempting to run a simulation of a protein that contains an atom
> named OXT (for the terminal oxygen atom). We are using the amber force
> field and have already successfully built a topology for the protein.
> However, when running Grompp we consistently receive the following
> error message:
> 
> Warning: atom names in topology.top and coordinates.pdb don't match (OXT 
> - O2)
> 
> However, checking the actual files reveals that the atoms were
> initially named consistently. It seems that whenever we run various
> Gromacs programs (such as grompp or editconf), the OXT atom name is
> changed to O2. In other words, topology.top and coordinates.pdb both
> have the atom correctly named as OXT. It seems that Gromacs wants to
> substitute a "2" for the "XT".
> 
> Does anyone know why Gromacs does this? Is this due to a bug in the
> code or is there some environment variable that defines XT=2?
> 
> Thanks,
> Bob Johnson
> _______________________________________________
AFAIK only pdb2gmx renames atoms. If you have an example that proves 
otherwise it's worth a bugzilla. The pdb has to be correctly formatted 
of course.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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