[gmx-users] Re: problem in g_membed

[Justin Lemkul]

On 7/29/13 4:31 AM, pavithrakb wrote:
> Thank you both of you (Justin and Albert) sir.
> Initially I was using dppc128 and now I changed to POPE 340 and still my
> protein (its a GPCR protein) protrude out of the membrane (the same region;
> two amino acids).

Out of curiosity, why have you chosen POPE?

> since you (Justin) you have mentioned that the protein must be completely
> inside the membrane to avoid any instability, what must I do to avoid this
> problem?

I did not say that.  The previous discussion was around the fact that your 
protein crossed a periodic boundary, which is very different from specifying 
that the whole protein must be inside the membrane.  It needs to fit within the 
box to avoid minimum image convention problems.  Whether or not the protein sits 
completely within the membrane is dependent upon the actual biology of the system.

> is something wrong with my protein?
> The region protruding out is a loop. is it still a problem?

Out of the membrane?  Not necessarily a problem.  Out of the box?  Possibly a 
problem, depending on the overall geometry of the system and its orientation 
within the box.

> the protein's box size is 4.49101 4.74797 7.29103 (from protein.gro).

Most membranes of 128 lipids or more are larger in the x-y plane, so that's 
fine.  The z-dimension is usually the limiting factor, and thus your membrane 
box needs to suitably accommodate the protein.

-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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