AMBER Archive (2009)

Subject: [AMBER] scee term

From: Neha Gandhi (n.gandhiau_at_gmail.com)
Date: Fri May 15 2009 - 04:03:48 CDT

Hi List,

I was wondering if anybody has tried using scee=2.0 with mm-pbsa? What
if I use scee=2.0 with latest versions of amber forcefield for
negatively charged ligands?

With negative charged ligands, my experience says we get very negative
energies using mm-pbsa method, because the electrostatic term
dominates and the solvation term is smaller compared to the gas phase.
What parameter would be helpful in such a case?

I appreciate your advice. 

-- 
Regards,
Neha Gandhi,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber