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

[Justin A. Lemkul]

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 
have:

Protein 5

-Justin

> Thanks,
> Casey
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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