[gmx-users] MD for two merged chains

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Sep 23 09:06:18 CEST 2008

Hi Dimitry,

Well, you can use pdb2gmx with -merge to merge chains.

Hope it helps,


On Mon, Sep 22, 2008 at 4:12 PM, DimitryASuplatov <genesup at gmail.com> wrote:
> Hello,
> I have a two-chain protein. I want to merge N-terminal residue of chain
> A with C-terminal of chain B. I can tweak the coordinates with pymol but
> when I run energy minimization two chains split again because gromacs
> fairly treats the input as a two-chain protein.
> I could switch the ATOM entries for chains A and B in the coordinate
> file - so that they are in the right order - and then delete the chain
> identifier, this workout will not help in more complex situations like 4
> chains merge though.
> Is there any option that allows gromacs not to consider chain IDs and
> the order of aa in the coordinate?
> Thanks. I really appreciate your help.
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

More information about the gromacs.org_gmx-users mailing list