On 6/22/17 9:47 AM, gozde ergin wrote:
Hey Justin, I figured out how they calculated the sigma values. Basically they just take the geometric mean of nitrogen and oxygen sigma and epsilon from ffnonbed.itp file in OPLS-AA force field and calculated the pairwise LJ for N-O interaction. Now I also try to add this information in my topol.top file. In order to do that as you have mentioned I added a section , [ nonbond_params ] ; i j func sigma epsilon opls_287 opls_272 1 0.323161248385416 0.790543521382599 after [ atoms ] section however I am facing with an error : Fatal error: Syntax error - File topol.top, line 42 Last line read: '[ nonbond_params ]' Invalid order for directive nonbond_params Any suggestion would be appreciated.
You can't declare force field parameters after you've introduced a [moleculetype]. Put it in ffnonbonded.itp or immediately after the #include statement for the force field.
-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.
