[gmx-users] Regarding error after equilibration of protein in membrane using g_membed

[shalini.s at iitg.ernet.in]

I am attaching the membedded.gro which was created using g_membed...Kindly
suggest..

Thanks



>
>
> On 2/20/14, 8:46 AM, shalini.s at iitg.ernet.in wrote:
>>
>> Hello...
>>
>> Thanks justin....I have used POPC 128 for embedding protein. While
>> embedding the protein using g_membed, it was found that 123 lipids are
>> overlapping the protein and 10 of them are deleted. Should I use POPC
>> 256
>> for simulation. Or should i try placing the protein in differently in
>> POPC128a itself. Kindly suggest. What should I do to place the protein
>> symmetrically in membrane.
>>
>
> No clue.  I don't know anything about your protein.  Visualization should
> indicate very obviously whether the membrane patch is of sufficient size.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA 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
> http://mackerell.umaryland.edu/~jalemkul
>
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Shalini Singh
Research Scholar
Department of Biotechnology
IIT Guwahati
Guwahati
Assam-781039