[gmx-users] Re Multiple Chains

Justin A. Lemkul jalemkul at vt.edu
Thu Sep 16 00:49:50 CEST 2010

C Johnson wrote:
> """
> 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
> """
> Sorry I wasn't clear.  Basically I want to have a simulation box with as many of the same polypeptide as I can cram in, essentially a simulation of the polypeptide melted.
> I would like to see how the polypeptides interact with each other with the ultimate goal of simulating block copolymers.  Since I'm new with Gromacs, I'm just trying
> to figure out how to run simulations with multiple chains where all chains are the same type.

Then I doubt anything you download from the PDB would be very helpful.  You have 
topologically identical chains that are not all going to be processed by 
pdb2gmx.  What you need to do is generate coordinates for your (identical) 
peptides in some way that makes sense.  You can do this with genconf (applying 
-nbox and/or -maxrot as necessary), editconf (manually centering and/or 
translating your peptides to obtain the desired configuration), or perhaps even 
genbox (with -ci and -nmol options).  Once you have constructed a suitable 
system, then and only then should you modify the topology (to reflect the number 
of peptides present) and proceed.

You will have to experiment a bit to decide which approach is best for your needs.

> Justin, you've been very helpful so far and I appreciate it. 

Happy to help.



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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