[gmx-users] pdb2gmx -chainsep vs -merge

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Sep 7 11:14:04 CEST 2010


> One work-around for the -chainsep situation you've observed is to remove or rename the terminal oxygen atoms (OXT) that pdb2gmx is complaining about when it tries to merge the chains. It should be taking care of that itself, but handling it yourself might help. pdb2gmx can probably rebuild the carboxyl oxygen. Keeping (one of the) OXT atoms and renaming it to "O" (keeping the fixed-column format correct) might be needed.

There should be only one OXT per chain. Removing those seems like a good idea:

sed -i '/^ATOM.*OXT/d' file.pdb
(Remove all lines starting with ATOM and containing OXT, in the file)

Hope it helps,


Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology /
University of Groningen
The Netherlands

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