[gmx-users] mdrun output conformation file loses chain identifier

Berk Hess gmx3 at hotmail.com
Mon Jan 19 11:28:19 CET 2009


Are the two chains in a single molecule definition or in two molecule definitions?

There are no chain identifiers written in the tpr file.
But mdrun of Gromacs 4.0 will automatically generate chain identifiers for each molecule.
In Gromacs 3 no chain identifiers will be written.

You can always run trjconv with for -s a pdb file with chain identifiers
and they will be copied to the pdb output.


Date: Mon, 19 Jan 2009 16:45:50 +0800
From: nomadoro at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] mdrun output conformation file loses chain identifier

I'm using GROMACS to perform a double-chain MD simulation. It surprises me that the mdrun output conformation file ( specified by -c ) contains no more chain identifier ( A or B ) that exists in the original input PDB file. So can someone tell me how to re-integrate the chain identifier into the output conformation file? 

Department of Physics
Nanjing University, China

Express yourself instantly with MSN Messenger! Download today it's FREE!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090119/1ca88b83/attachment.html>

More information about the gromacs.org_gmx-users mailing list