Re: [AMBER] Factoring in the contribution of individual HOH molecules to delta G

From: Bill Miller III <>
Date: Tue, 15 Feb 2011 11:57:32 -0500

You will have to explicitly set the strip_mask variable in the
input file. You will have to define the mask to strip out all the water
molecules you do not want, but specifically keep the residue number of the
one water molecule you want to keep. You can read about the details of how
to define the residue masks in the manual.

Good luck!


On Tue, Feb 15, 2011 at 11:40 AM, George Tzotzos <> wrote:

> Hi everybody,
> I understand that 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
> George
> _______________________________________________
> AMBER mailing list

Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Tue Feb 15 2011 - 09:00:04 PST
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