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.
Rgds,
C.Q.
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Received on Mon Sep 23 2013 - 21:30:03 PDT
