On 6/28/16 6:41 AM, Ming Tang wrote:
Dear list, I want to calculate hbond between backbone atoms on different chains of my protein only. but when it give me this error "nothing to be none". I used this command: gxm hbond -f traj.trr -s topol.tpr -num hbnum.xvg -a 30 -r 0.5 I can use this command to get hbond between protein and protein. Can anybody give me some suggestions?
Use Mainchain+H. Backbone considers only C+CA+N, so there can be no H-bonds in those atoms. MainChain+H is C+CA+N+H+O, which includes what you actually want.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 [email protected] | (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 [email protected].
