On 6/16/17 8:03 AM, Shivangi Agarwal wrote:
Hi all When i am generating a ligand topology using PRODRG, I am getting topology file with hydrogens deleted in it. Which another server can I use for ligand topology generation?
GROMOS is a united-atom force field, so the aliphatic H atoms are not going to be explicitly represented; you should check your assumptions about force fields and which one you should be using if this comes as a surprise :) PRODRG is not of sufficient quality for MD simulations without significant manual revision. ATB is better if you want to use a GROMOS parameter set.
-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.
