AMBER Archive (2009)
Subject: Re: [AMBER] adding chain id to ptraj pdb output
From: Joe Krahn (krahn_at_niehs.nih.gov)
Date: Mon Mar 23 2009 - 18:20:30 CDT
The simple approach is to have a "reference" PDB file with exactly the
same atom sequence, and use some simple code to combine the chain and
residue number columns from the reference file with the coordinate data
from the other file. It is a hack, but simple and fast once you have the
reference PDB file set up.
I am working on modifying the PRMTOP to include chainID and
residue-number information, which will hopefully become part of the next
AMBER release. For now, I can add chain and residue data to the PRMTOP,
and generate a properly labelled PDB file from the PRMTOP and a CRD
file, but that won't help with ptraj output.
Maybe I should write a utility to add this info to a "flat" AMBER PDB
file. It shouldn't be too hard.
Paul Brandt wrote:
> Dear amber users,
> I need to add chain IDs and renumber the pdb file output from ptraj. I need
> to do this for hundreds of files. I'm pretty sure the ptraj can't do this,
> but would love to find out that I'm wrong.
> If ptraj can't: Does anyone know of a program can do this for a batch of
> ptraj pdb output files.
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