On 9/5/13 10:31 PM, shika wrote:
Thanks Justin for the quick reply.
by the way after i solvated the protein with water and i change the
amount of the protein that i want for example 8 and the amount of
water that already in is 20453.But after i proceed with grompp the
result shows that my .top file have different number of configuration
with the solvation, .gro file. In addition when i view the file with
vmd it still show only one protein and not the exact amount that i
want.Well i'm kinda lost because after pdb2gmx for the single molecule
and i separate the topology file with the .itp protein,the itp file
still consist of 1 protein not 8 proteins right?
Changing the topology has no effect on the coordinate file. You can't magically
produce 8 proteins by manipulating the topology; you have to build a
corresponding coordinate file. If you just want replicate boxes, genconf -nbox
can do that. That may or may not be an efficient or appropriate way to deal
with the task at hand. You should build the configuration first, and modify the
topology only once you're satisfied with the configuration.
-Justin
On Fri, Sep 6, 2013 at 10:13 AM, Justin Lemkul [via GROMACS]
<ml-node+s5086n5011001...@n6.nabble.com> wrote:
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
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Baltimore, MD 21201
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==================================================
Justin A. Lemkul, Ph.D.
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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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