[gmx-users] ligand binding

Meenakshi Rajput ashi.rajput39 at gmail.com
Thu Aug 7 06:11:38 CEST 2014

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.

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