AMBER: Re: entropy of released water

From: Swarup Gupta <>
Date: Thu, 7 Aug 2008 05:40:26 -0700 (PDT)

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 <> wrote:

From: Swarup Gupta <>
Subject: entropy of released water
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?

S Gupta


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
Received on Sun Aug 10 2008 - 06:07:26 PDT
Custom Search