On 8/6/14, 10:11 PM, Meenakshi Rajput wrote:
hello I have used charmm27 force field to parametrize my protein(human serum
CHARMM27 is a nucleic acid force field. The force field you're using is CHARMM22/CMAP, which is bundled (in Gromacs) in the same files.
albumin,584a.a) and swiss param to provide parameters to the ligand due to which coordinates of ligand is changed and active site of protein is also completely changed. Can anybody tell me that ligand coordinates should be changed after parametrization? or any energy minimisation problem is there.
That depends on what SwissParam is doing; maybe it does energy minimization as part of its process. You don't want it to do that because it will screw up the geometry that you need. If EM can be disabled, do so. If not, find a new way to generate parameters or otherwise just use the original coordinates, not the ones from SwissParam (unless you need H added, in which case you'll have to do that yourself, but many programs can do it).
Am i doing right or not? My energy minimization mdp file is here:- cpp = /lib/cpp include = -I../top integrator = steep emtol = 100 nsteps = 200 nstenergy = 10 nstxtcout = 10 xtc_grps = Protein energygrps = Protein nstlist = 5 ns_type = grid rlist = 1.4 coulombtype = PME rcoulomb = 1.4 rvdw = 1.4
These nonbonded settings are incorrect for CHARMM force fields. You need force-switching for van der Waals and the longest cutoffs should be 1.2.
-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.
