[AMBER] can I calculate binding energy with some restraints

From: Mahmoud Soliman <mahmoudelkot.gmail.com>
Date: Mon, 21 Mar 2011 17:06:17 +0200

   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
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Received on Mon Mar 21 2011 - 08:00:05 PDT
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