On 4/11/14, 7:47 AM, neha_bharty wrote:
Hello I am new user of gromacs. I am using gromacs 4.6.3 I wanted to minimize the energy of a protein. Before energy minimization the prockeck result for Ramachandran plot was 89% in allowed region but after energy minimization the result become worse i.e. 87%. I was performing energy minimization to refine the model. But the model become worse after that.
That's not a huge change, nor is energy minimization rigorous enough to fully refine a model. EM will probably optimize the side chains pretty well, but the backbone may require actual MD simulation to sample better conformations. The changes that take place during EM are typically very small.
I Model the protein using homology modeling and needed it for docking I am also doing it with different protein molecules but again the same problem occurs. I don't know that its normal or there is problem with my parameter or force field. I am also mentioning the detail of my energy minimization. The details are: Force Field Used: CHARMM27 all-atom force field Water Model: TIP3P
CHARMM36 may be a better option. The recalibration of the CMAP terms could be relevant here. See http://mackerell.umaryland.edu/CHARMM_ff_params.html to download the force field files.
-Justin
em.mdp file is: ; VARIOUS PREPROCESSING OPTIONS = title = cpp = /lib/cpp include = define = -DFLEXIBLE ; RUN CONTROL PARAMETERS = integrator = steep ; start time and timestep in ps = tinit = 0 dt = 0.002 nsteps = 15000 ; ENERGY MINIMIZATION OPTIONS = emtol = 10 emstep = 0.1 nstcgsteep = 1000 coulombtype =pme nstenergy =10 Please help me out for this. -- View this message in context: http://gromacs.5086.x6.nabble.com/Re-Energy-minimization-result-problem-tp5015793.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- ================================================== 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.
