Re: [AMBER] which PBRadii is best when we use PBSA method to calculate the bonding affinity

From: Jason Swails <>
Date: Mon, 18 Nov 2013 07:47:39 -0500

On Mon, 2013-11-18 at 15:32 +0800, fjliu wrote:
> Hello everyone !!
> I am using MM-PBSA approach to calculate the binding free energy of a ligand with the protein,there is a great difference of the results when I changed the PBRadii from mbondi to mbondi2 in my leapin files,at the same time I kept other parameters as the same,so I want to know which PBRadii is the best for we calculate the bonding free energy.
> Please provide valuable suggestions in this direction and if possible relevant articles based on similar concept.

This depends entirely on the solvation model you're using.

As always, if you want specific answers you need to give more specific
details about what it is you're doing. What model are you using? Which
energy terms differ the most, and in what models? etc.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Nov 18 2013 - 05:00:03 PST
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