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

Justin Lemkul jalemkul at vt.edu
Thu Feb 20 15:01:40 CET 2014

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 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


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