On 9/11/14 6:09 AM, Lovika Moudgil wrote:
Thanks for reply Lalit , Actually my system have citrate anion and I want .itp for citrate and further I will use OPLA/SS force field!! It can't be generated be pdb2gmx!!
The OPLS-AA strategy is generally similar to GROMOS - you can piece the molecule together from existing functional groups. Since the force field already covers everything you need for citrate, assigning charges and atomtypes is straightforward. You can create an .rtp entry for it and have pdb2gmx do all the work of assigning the bonded interactions (you need to specify the [bonds], pdb2gmx does the rest).
-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.
