AMBER Archive (2008)

Subject: AMBER: Re: entropy of released water

From: Swarup Gupta (swarupgupta_at_yahoo.com)
Date: Thu Aug 07 2008 - 07:40:26 CDT

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_at_yahoo.com> wrote:

From: Swarup Gupta <swarupgupta_at_yahoo.com>
Subject: entropy of released water
To: amber_at_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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