[gmx-users] Re Multiple Chains

[Justin A. Lemkul]

C Johnson wrote:
> So the easiest way of having multiple chains would be to just have a 
> single pdb file with the multiple chains?  Would you happen to know of a 
> single pdb file with multiple chains (something I could grab off the pdb 
> site) I could use as a reference?
> 
> 

This depends entirely upon what your goal is.  Your original question implied 
you wished to build a system of multiple, identical peptides, pertaining to:

http://www.gromacs.org/Documentation/How-tos/Multiple_Chains#Identical_chains

Now you want a multimeric protein for which there are multiple, potentially 
different peptide, i.e.:

http://www.gromacs.org/Documentation/How-tos/Multiple_Chains#Non-identical_chains

The approaches are completely different, as the documentation should make quite 
clear.  Simply "having multiple chains" is a very vague statement.  Perhaps if 
you clearly stated your goal for the simulation I (or someone else) could help 
you better.

As for the PDB site, there are probably thousands of proteins in line with what 
you want.  Any heteromultimeric protein would do (assuming, of course, the 
latter case of non-identical chains).

-Justin

-- 
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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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