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

[anu chandra]

Dear Justin,

Do I need to add lipid topology manually, if I use Charmm36 force filed
that have protein and lipid parameters together?

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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