On 7/22/14, 9:59 AM, Venkat Reddy wrote:
Dear Gromacs users, Can I use GROMOS53A6 ff for simulating beta-peptides? I found some articles on beta peptide simulations using GROMOS53A6 and 53A7 ff. Do I have to edit any dihedral angle info to process my beta peptide after pdb2gmx step?
You'll have to write new force field files, the .rtp at minimum, because beta-peptide connectivity is different. There may be new bonded parameters involved, but those should be described in the literature.
-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.
