[gmx-users] pdb2gmx -chainsep vs -merge

Mark Abraham mark.abraham at anu.edu.au
Tue Sep 7 03:41:35 CEST 2010

----- Original Message -----
From: nahren manuel <meetnahren at yahoo.com>
Date: Tuesday, September 7, 2010 7:16
Subject: [gmx-users] pdb2gmx -chainsep vs -merge
To: gromacs gromacs <gmx-users at gromacs.org>

| > Dear Gromacs Users,
> Has anybody merged all chains in a PDB file using -chainsep. because -chainsep does not
> seem to work.
> http://www.mail-archive.com/gmx-users@gromacs.org/msg33192.html
> Is there a alternate way of doing it ?, 
> One way I could think of is to add the atoms numbers in the  topologies.

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.


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