[gmx-users] Simulating a semi-membrane protein

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
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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