On 12/7/13 8:11 AM, Shine A wrote:
Sir, I am using MD to study the folding of peptides. Now I want to modify N terminal of the peptide with acetyl group and C terminus with amide group.How Can I do this? What are the changes I should made in various files? Gromos96 53a6 is using for simulation.
You need to add the coordinates for the capping groups to your input coordinate file, with names that agree with the expected nomenclature of the force field.
-Justin -- ================================================== 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- 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.