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

[Robert Johnson]

These are all fine points. However, the question I'm asking is why do
Gromacs tools change atoms named OXT in PDB files to O2? Of course
there are always workarounds i.e. just simply change the atom name in
the coordinate file. However, I was wondering if anyone knew why this
happened. I suppose I will submit a bugzilla.

On 6/13/07, TJ Piggot <t.piggot at bristol.ac.uk> wrote:
> Hi,
>
> I think that the terminal oxygen atoms should not be named OXT for the
> amber forcefields but rather OC1 and OC2. To check this look in the top
> folder at the ffamberXX.rtp file.
>
> Hope this helps
>
> Tom
>
> --On Tuesday, June 12, 2007 15:30 -0400 Robert Johnson
> <bobjohnson1981 at gmail.com> 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
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>
>
> ----------------------
> TJ Piggot
> t.piggot at bristol.ac.uk
> University of Bristol, UK.
>
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