On 6/25/14, 4:44 AM, mirko busato wrote:
Thank you very much, In my analysis ,I would like to consider Hydrogen bonds involving S atom as well. I think that g_hbond is not built to manage Hydrogen bonds with S. Do you know if there are available scripts? or Could you suggest me something to solve this problem?
g_hbond is hard-coded to deal with certain groups, so it's not very flexible. The workaround we've used in the past is to simply rename the S atoms of interest as O in the .top file, generate a .tpr with those dummy names, and run g_hbond using that .tpr file.
-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.