I am new user of gromacs. I modeled a structure of protein with the help of Homology modeling and after that I validate the structure using Ramachandran plot with the help of procheck server. The residues present in most-favored region was 89%. To refine the model I tried to perform energy minimization and MD Using gromacs. But after energy minimization when I check my result again in procheck server the ramachandran plot become become worse and the residues present in most-favored region decreases to 87%. after MD also the result was same.
As I am new user of gromacs I don't know that is this a normal that after energy minimization result can be decreases??
Also can I use this energy minimize structure for docking?? or should I use the previous structure which is having 89% residues in most favored region.
The detail of energy minimization is as follows:
Force Field Used: CHARMM27 all-atom force field Water Model: TIP3P
I have also perform EM and MD with different force fields like AMBER, OPLS but the result was better in CHARMM27.
My 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
It would be great if any one will help me out with this.