[gmx-users] antiparallel beta sheet
jalemkul at vt.edu
Mon Mar 3 21:30:31 CET 2014
On 3/3/14, 2:02 PM, Nidhi Katyal wrote:
> Dear users,
> I would like to analyse the time variation of antiparallel beta sheet
> formation. I am aware that dssp and stride program can calculate the beta
> sheet content but is there a tool that can distinguish between antiparallel
> and parallel beta sheet (in terms of giving numeric value as output and not
> through visual inspection)?
You can define an order parameter between 0 and 1 to discriminate between the
two. It is fairly common in simulation literature of amyloids.
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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