AMBER Archive (2009)
Subject: [AMBER] scee term
From: Neha Gandhi (n.gandhiau_at_gmail.com)
Date: Fri May 15 2009 - 04:03:48 CDT
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.
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845
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