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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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