[gmx-users] multiple chain

Justin Lemkul jalemkul at vt.edu
Fri Sep 6 04:11:10 CEST 2013

On 9/5/13 10:09 PM, Nur Syafiqah Abdul Ghani wrote:
> Hi all,
> Need your help to explain more about this multiple chain.I would like
> to do a simulation with a multiple type identical protein. By using
> the instruction that gromacs wrote in
> 'http://www.gromacs.org/Documentation/How-tos/Multiple_Chains', seem
> that i'm a bit lost when it tells us to us the .top file for grompp
> input and need to change the coordinate..Any one had facing this time
> problem?
> Btw i already do the pdb2gmx command for single protein and only don't
> understand after i put the number of amount of protein that i want in
> .top file.

The number of molecules in the .top must correspond to a configuration you have 
built that has the same number of molecules.  You can position molecules in the 
unit cell using editconf and the various options it provides (centering, 
translation, rotation).



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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