On 3/28/15 11:33 PM, Kamalesh Roy wrote:
Dear all, I am using gromacs latest version in Ubuntu... I am trying to simulate oleic acid in a box with some protein. Have made the .itp from prodrg server... incorporate the same still not recognizing OLA residue.
PRODRG parameters always require manual refinement, and the old(er) version of the GROMOS force field that it supports will probably have an inadequate description of the alkyl chains. Look into newer parameters, e.g. those derived from 53A6.
I have change the aminoacid.rtp also....
You shouldn't.
Can anybody suggest me the procedure ......
You haven't really said what you've done, so it's pointless to guess where the problem is. You haven't even said if there's a specific error that you're getting. If you want free and efficient help, you need to make it easy to provide it.
-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.
