On Tue, Nov 26, 2013 at 8:08 AM, sunita gupta <sunita....@gmail.com> wrote:
> Thanks Justin, > > Its strange that some atomtypes like ha, h1, n2 etc whose parameters are > already present in the gbsa.itp are also not recognised. > I have many more ligands to deal with. Can you tell me how to overcome this > issue, or whats the possibility of doing implicit simulation of > protein-ligand complexes with gromacs You need to list all of the atomtypes you are using within [implicit_genborn_params], and I believe they are case-sensitive so h1 and H1 are not the same. If the ligand h1 is actually the same as the force field's H1, then just use H1 and save yourself the trouble. -Justin -- ========================================== Justin A. Lemkul, Ph.D. 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 ========================================== -- 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.