Hi Amber users,
I try to do some MM-PBSA calculation on a protein-ligand complex keeping
some of the waters in the active site. I've treated the water molecules
as part of the receptor molecule. The results however a bit strange.
When I do a binding decomposition, all the water molecules have a high
positive contribution (10-13 kcal/mol) and that is a bit more than
unrealistic. I think that the error might be due to the fact that as a
total the solute (protein complex) is given a dielectric constant of 1.
While this might be suitable for the treatment of amino acid residues is
a gross error for water. Is there any way to by pass this problem and
get realistic values for the contribution of water molecules to binding?
Looking forward to your suggestions.
Cristina
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Received on Tue Apr 27 2010 - 07:00:05 PDT
