[gmx-users] Topology for ready-made membrane protein system

[Justin Lemkul]

On 7/6/15 7:05 AM, anu chandra wrote:
> Dear Justin,
>
> Do I need to add lipid topology manually, if I use Charmm36 force filed
> that have protein and lipid parameters together?
>

You always need a topology for any molecule in the system.

-Justin

> Thanks
> Anu
>
> On Fri, Jul 3, 2015 at 4:47 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 7/3/15 7:56 AM, anu chandra wrote:
>>
>>> Dear Gromacs users,
>>>
>>> I am working with membrane proteins. I have generated the
>>> membrane-protein
>>> system ( contains lipids, protein, water and ions) with some
>>> specification.
>>> For eg.,  I have positioned  few ions and water molecules at particular
>>> location using some in-house programs. Now, I would like to generate
>>> topology for the my system in order to run MD using Gromacs. Since my
>>> system is ready-made, I cant follow the methodology adopt by Gromcas
>>> membrane-protein  tutorials.
>>>
>>> Hence, can anybody suggest me a way to generate Gromacs inputs files for
>>> such ready-made membrane-protein systems?
>>>
>>>
>> Process the protein with pdb2gmx and add an #include statements for the
>> lipid topology.  Then modify [molecules] to account for what's actually in
>> the system.  Water and ion topologies will automatically be #included in
>> the .top written by pdb2gmx.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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