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

From: fjliu <fjliu208.gmail.com>
Date: Mon, 18 Nov 2013 15:32:41 +0800

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.

Thanks a lot!

Sincerely yours,

Fengjiao liu

AMBER mailing list
Received on Mon Nov 18 2013 - 00:00:02 PST
Custom Search