[gmx-users] Simulating a semi-membrane protein
jalemkul at vt.edu
Tue Jul 23 03:19:12 CEST 2013
On 7/22/13 9:13 PM, pavithrakb wrote:
> Dear Users,
> I'm not sure if the term I coined as semi-membrane protein is correct.
Either a protein is a membrane protein or it is not. Is any part of it embedded
or bound to the membrane? If yes, it is a membrane protein.
> But My protein is half (alpha subunit) in membrane and other half (beta
> subunit) outside the cell.
> is it possible to simulate such proteins? if So, how can we use membrane for
> just one half?
You need to define the position of the protein appropriately, such that the
alpha domain coincides with the membrane, using any and all available
experimental evidence to place the protein appropriately. This is where clever
use of editconf -center is necessary to position all components of the system
within the box.
Justin A. Lemkul, Ph.D.
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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