[AMBER] explicit water MMPBSA

From: Cristina Sisu <csds2.cam.ac.uk>
Date: Tue, 27 Apr 2010 14:54:56 +0100

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.


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Received on Tue Apr 27 2010 - 07:00:05 PDT
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