[gmx-users] Having Multiple Chains From One pdb File

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 15 04:48:34 CEST 2010

C Johnson wrote:
> Hi,
> I have a pdb file with a single short peptide chain.  I would like to 
> simulate multiple chains, in this case 5.  I've looked at:
> http://www.gromacs.org/Documentation/How-tos/Multiple_Chains
> but am still a little confused.  Is it possible to get more detail on 
> how to simulate multiple chains using a single chain pdb file?

The fundamental point is that whatever is in your coordinate file must be 
reflected in the topology as well.  Place the 5 copies of the peptide within the 
simulation cell however you need and then in your [molecules] directive, you'll 

Protein 5


> Thanks,
> Casey


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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