AMBER Archive (2002)

Subject: MM-GBSA and counterions

From: Michael Ford (mford_at_ccrc.uga.edu)
Date: Thu Oct 03 2002 - 14:27:27 CDT

A question about using MM-GBSA:

 
I was just wondering about thoughts anyone might have as to whether
counterions neutralizing a ligand charge should be included with
receptor or ligand in MM-PBSA type calculations. I have a negatively
charged ligand, neutralized with a sodium counterion. I'm guessing I
should throw it in with the receptor.

Thanks,

Mike Ford