[gmx-users] question about chain identifier

Berk Hess gmx3 at hotmail.com
Fri Sep 18 08:48:13 CEST 2009


The only program that really uses chain identifiers is pdb2gmx.
It uses chain identifiers to recognize different protein (or DNA)
molecules that appear sequentially in pdb files.
All other programs will read chain identifiers and write them out again.
Also Gromacs will add chain identifiers for multi-residue molecules,
this is to make selection in visualization software.


Date: Thu, 17 Sep 2009 19:13:04 -0700
From: kgp.amit at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] question about chain identifier

hi everyone,
I had a question about the purpose of chain identifier character in pdb. What does it mean for Gromacs, i mean what does gromacs do with it? I actually have a "bad" pdb file which has different chain identifiers for first few molecules of the same type and then there exists none for rest of the molecules (I am dealing with only one kind of molecule). The limitation is due to the fact that the chain identifier has to be a single character. Now the molecules are also distinguished by there residue sequence no. in the pdb file, which makes the purpose of chain identifier useless.

So should i get rid of all the chain identifiers in the pdb file?
I am also interested in knowing what the chain identifier really does?
Thank you,
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