Hi Amber users,
I need to calculate the binding energy for some synthesized ligands in our
lap with some artificial enzyme (which I simulate as well). the problem is
that I notice these ligands does not stick to the protein (as it appear in
X-ray structure that we developed also in our lap) in a free MD simulation.
So that I assume to put some weak restraints during MD simulation. My
question is: is it scientifically acceptable to calculate the binding
energies of these ligands to the protein with keeping some weak restraints
(and can I compare between these binding energies for these ligands if I put
the same restraint force)...Have you seen somebody doing this before???
Thanks for your help
Best wishes
Mahmoud
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Received on Mon Mar 21 2011 - 08:00:05 PDT
