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

Robert Johnson bobjohnson1981 at gmail.com
Tue Jun 12 21:30:41 CEST 2007

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?

Bob Johnson

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