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 -- ================================================== 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
