On Wed, Nov 20, 2013 at 4:53 PM, Ehsan Sadeghi <es...@sfu.ca> wrote: > Thanks Justin. Could you explain more? You meant that I don't need > topology file for propanol? How about g_b, g_a, g_d values? > > You need a topology, but what I'm saying is that it is very easy to do. CH3 and CH2 groups are uncharged except the CH2-O-H group, which you can take from serine. Look through common functional groups across molecules - they have the same parameters. That is the design of GROMOS and many other force fields. The bonded parameters can also be taken from similar groups. The g_* notation corresponds to the labeling defined in ffbonded.itp - b for bonds, a for angles, d for dihedrals. The functional groups to which they apply are described in ffbonded.itp.
-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.