Hi, > 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology / University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
