[gmx-users] Re: multiple chain

[Justin Lemkul]

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+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
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> [hidden email] | (410) 706-7441
>>
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>
>

-- 
==================================================

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

==================================================