I wanted to mean whether it is already parameterized in "implicit solvent model" so that post-processing with GBSA model would take care of that.
--- On Thu, 8/7/08, Swarup Gupta <swarupgupta.yahoo.com> wrote:
From: Swarup Gupta <swarupgupta.yahoo.com>
Subject: entropy of released water
To: amber.scripps.edu
Date: Thursday, August 7, 2008, 7:36 AM
I am working on a protein-protein complex. Initially explicit waster MD was run and now post-porcessing with MMGBSA model to calculate binding free energy.
�
My concern is whether the change of entropy of the system due to the release of�water molecules from the binding site of the ligand and receptor is parameterized in the available solvent models or I would need to account for them seperately? Or in fact there is any recognize methods to calculate that?
regards,
S Gupta
�
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Received on Sun Aug 10 2008 - 06:07:26 PDT
