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

David van der Spoel spoel at xray.bmc.uu.se
Tue Jun 12 21:40:26 CEST 2007

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 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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