Thank mark for comments, but I have check the structure after energy minimization through ramachandran plot and found 82% residues were lies in core region. After performed position restrained dynamics it reduced to 52% in core region also 1 bad contact was found. I have taken SPC water model then add 2 NA+ ions in the solvent, done energy minimization at emtol value of 2000 kJ/mol and steps for 250. Below is the pr.mdp file for position restraiuned dynamics, please let me know if any serious flaws. So help me by giving me the reference.
title = Position restrained of Bcl-2. integrator = md define = -DPOSRES dt = 0.002 nsteps = 100000 nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 5 xtc_grps = protein sol energygrps = protein sol ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 fourierspacing = 0.135 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes Dispcorr = no Tcoupl = v-rescale tc-grps = protein sol NA+ tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 constraints = all-bonds -- Pawan
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