Hi everybody,
I've been trying to derive free energies of binding of a ligand (organic molecule), small protein complex following the procedure given in tutorial 3
http://ambermd.org/tutorials/advanced/tutorial3/section1.htm
My question is whether during minimisation, heating and density equilibration BOTH the ligand and protein should be restrained using the SAME restraint weight. The reason I'm asking this is that on a couple of occasions where I used restraints of the same weight (restraint_wt = 2.0) on both ligand and protein the ligand failed to move much from its original position.
Many thanks on any advice on this matter
Regards
George
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Received on Mon Apr 25 2011 - 05:00:03 PDT
