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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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