On 6/19/14, 4:58 PM, Negar Parvizi wrote:
Dear Gromacs users; I use Gromacs version 4.5.4. I finished protein-ligand complex tutorial(Dr.justin lemkul tutorial). Now i want to use my ligand. I am new in this field(charge group blocking). For getting an idea about charge group blocking, i check .rtp files. cheking aminoacides.rtp files of gromos force field , it has ATP charge group blocking, but i didn't understand it and also i didn't find many of molecules ex. : TEMP, BA, RTOL, ... It would be greatly appreciated if anyone can help me in this field?
You need to tell us what ligand you're dealing with. A few other things to consider:
1. The manual has a very good description of what charge groups are and how they're designed. 2. If you're using PME, charge groups summing to zero or an integer is not strictly necessary. 3. If you're going to use the Verlet cutoff scheme for the simulation, charge groups are totally irrelevant.
-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.
