Re: [AMBER] binding free energy by MM_PBSA

From: Carlos Simmerling <carlos.simmerling.gmail.com>
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" <sd517.nyu.edu> 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,
Shuang

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Nov 22 2010 - 13:30:04 PST
Custom Search