Re: [AMBER] binding free energy by MM_PBSA

From: Carlos Simmerling <>
Date: Mon, 22 Nov 2010 16:16:22 -0500

You can't really do this without including the bond energy.

On Nov 22, 2010 3:03 PM, "Shuang Ding" <> wrote:

Hi everyone,

There are lots of applications for calculating protein and ligand binding
free energy by MM_PBSA. I want to calculate the binding free energy of the
DNA duplex with a covalent bonded small molecule. How to use MM_PBSA to
calculate the binding free energy involving a covalent bond formation? Any
suggestion is greatly appreciated.

Many thanks,

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Received on Mon Nov 22 2010 - 13:30:04 PST
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