On 7/7/13 10:52 PM, pavithrakb wrote:
Dear Sir,
Thanks so much..
now what's the solution? Should I increase the box size?
Yes. If the protein protrudes "out" of the central image, then you will have an
unstable system due to atomic overlap as well as violations of the minimum image
convention.
Already I have centered the protein and fixed the POPE membrane size.
Can you tell me how to increase the box size? or is there any other
solution?
If you need more space in the x-y plane, use genconf to replicate the membrane
patch appropriately. If x-y is sufficient and only z is the problem, use
editconf to adjust the box size and (if desired) the location of the
membrane-protein complex and then solvate with genbox to fill the newly
introduced void.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Associate
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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