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

[TJ Piggot]

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.