hello I have used charmm27 force field to parametrize my protein(human serum 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. 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 constraints = none pbc = xyz Energy is not reached upto mentioned limit after EM run. -- Gromacs Users mailing list
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