[gmx-users] Multiprotein lipid bilayer

[Justin A. Lemkul]

ram bio wrote:
> HI Justin,
> 
> Thanks for the info.
> 
> I have followed your tutorial earlier, it really works, and that was
> for 1 protein, but if 2 or more different kinds of proteins are to be
> inserted then how to generate the a single topology file for all the
> proteins using pdb2gmx and also can you please let me know the other
> ways to insert the proteins in lipid bilayers....
> 

You don't need a single topology for all the proteins.  Instead you can generate 
individual topologies for each protein with pdb2gmx, remove the unnecessary 
#includes, [system], and [molecules] directives to make them single-molecule 
.itp files, and then simply:

#include "protein_A.itp"
#include "protein_B.itp"

in your .top file.

Other ways to insert proteins might include using genbox creatively, VMD, 
g_membed, etc.  Search the list archive.

-Justin

> 
> Ram
> 
> On Thu, Mar 4, 2010 at 4:36 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> ram bio wrote:
>>> Dear Gromacs Users,
>>>
>>> I would like to run molecular dynamics by inserting multiple proteins
>>> in the same lipid bilayer using gromacs, is it possible? if so, please
>> Just about anything is possible :)
>>
>>> let me know if any tutorial is available or any kind of help is
>>> available....
>>>
>> There is a tutorial for a basic membrane protein system linked from the
>> Gromacs tutorials page.  As for inserting multiple proteins in the membrane,
>> there are several ways to do it, but if you want to use InflateGRO, you'll
>> need the latest version:
>>
>> http://www.csb.bit.uni-bonn.de/inflategro.html
>>
>> -Justin
>>
>>> Thanks in advance,
>>>
>>> Ram
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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> 

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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