Hi,
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.
Berk
Date: Thu, 17 Sep 2009 19:13:04 -0700
From: [email protected]
To: [email protected]
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,
Amit
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