From: David A. Case <>
Date: Wed, 2 Mar 2005 07:44:15 -0800

On Wed, Mar 02, 2005, Alessio Coi wrote:
> I'm using a MM-GBSA analysis technique to estimate free energies of
> binding for comparison with experiment. I wonder whether it's suggested
> to use explicit ions to couteract the -10 charge of the protein or if
> it's better to perform minimization and MD with a value for the total
> charge of the protein different from 0...

My personal preference is not to use explicit counterions with MM-GBSA, but
rather to set the saltcon variable to an appropriate number. But since no
technique is known to be all that reliable, you should probably treat
questions like this is items to investigate as part of your research plan.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Mar 02 2005 - 15:53:01 PST
Custom Search