[gmx-users] Re: multiple chain

shika pqah123 at gmail.com
Fri Sep 6 04:31:30 CEST 2013

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?

On Fri, Sep 6, 2013 at 10:13 AM, Justin Lemkul [via GROMACS]
<ml-node+s5086n5011001h15 at 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
> --
> ==================================================
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
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> University of Maryland, Baltimore
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Best Regards,

Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400 Serdang,
alternative email : syafiqahabdulghani at gmail.com @ GS33669 at mutiara.upm.edu.my

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