On 6/15/16 11:49 AM, Nikhil Maroli wrote:
Hi, Justin , thanks for your reply. Actually, my system is cyclic peptide nanotube in water,which I made using charmm-gui. Protonation option availbe in " PDB reader " but how to confirm the pH,based on protonation ? or is it possbile to make any
You don't "confirm the pH" because there is none. You don't have titratable sites and you don't have H3O+ floating around. The point of a fixed-charge simulation is to simulate the dominant protonation state that would be found at a given pH in a real, physical system. The protonation states are chosen based on pKa values of those titratable moieties and which form will dominate at a given pH.
changed after getting the out put
I wouldn't try to make post-hoc changes. Adding or deleting H atoms will change everything about the topology. Set it up properly to start.
-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 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.
