[AMBER] free energy contribution of water

From: Hyma vathi <hymavathi.niper.gmail.com>
Date: Wed, 31 Mar 2010 17:00:57 +0530

Dear Ross,

I want to perform Thermodynamic integration by using double decoupling
method as done by Yipin et al, in their paper " Binding free energy
contributions of interfacial waters in HIV-1 protease/inhibitor complexes"
I have some queries regarding this:
How can we take particular water molecule, Wat 301 and study its
contribution in binding free energy?
Do we need to take all the crystallographic waters or that particular water
is possible? But I think the numbering of molecules changes?
They have mentioned about turning off electrostatic interactions first and
then van der Waals interactions. Is this done on whole of the protein or
Thank you in advance.

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Received on Wed Mar 31 2010 - 05:00:02 PDT
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