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. 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 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. -- 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.
