[AMBER] MMPBSA.py: Factoring in the contribution of individual HOH molecules to delta G

From: George Tzotzos <gtzotzos.me.com>
Date: Tue, 15 Feb 2011 17:40:00 +0100

Hi everybody,

I understand that MMPBSA.py strips all HOH molecules (?) and ions from the original trajectory. In my case, an individual HOH molecule contributes to the binding of the ligand to the receptor. This is in accordance with the corresponding crystallographic model.

Is there a way of keeping this HOH molecule in the trajectory files? I would like to find out the contribution of this HOH molecule to delta G and delta S.

I'd be grateful for any advice on how to go about this issue.

Best regards


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Received on Tue Feb 15 2011 - 09:00:03 PST
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