[AMBER] energetics of displacing water molecules from protein binding sites

From: Changqing Yan <ycqchemical.gmail.com>
Date: Tue, 24 Sep 2013 12:09:51 +0800

Dear Amber experts,

Greetings. Recently I used MM_GBSA techniques to compute the binding
energies of two ligands (to the same receptor). It has some difference
between these two energies. So I want to find out the reason. One reason,
as you know, is possibly due to displacement of water molecular by the new
function group of the new ligand. As I know, there is a program called JAWS
could determine whether a displacement happens or not. But if it happens,
how can I determine this is the real reason?

During my MM_GBSA calculation, I stripped all of water molecules. Does it
necessarily mean that the binding energies I obtained has nothing to do
with the water molecules? thx.

look forward to your reply.

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Received on Mon Sep 23 2013 - 21:30:03 PDT
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