Re: AMBER: How to add water to calculate MMPBSA

From: David A. Case <>
Date: Wed, 14 Dec 2005 15:50:13 -0800

On Wed, Dec 14, 2005, Kitiyaporn Wittayanarakul wrote:

> Due to when calculate MMPBSA, it's not include water molecule. So I'd to
> add the water molecule and then doing MMPBSA calculation. I'm wodering if
> it has the tutorial website ortherwise how to know to set up this system.
> Please help me to find out this problem.

The whole point of MM/PBSA is to treat the solvent as a continuum. So,
including water molecules would lead to some other type of theory, which would
have to be developed and tested. I am not aware of anyone who has done this.

....good luck...dac

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Received on Wed Dec 14 2005 - 23:53:00 PST
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