AMBER Archive (2006)

Subject: AMBER: MM-PBSA and first solvation shell

From: Andrea Bortolato (
Date: Mon Jun 05 2006 - 04:42:39 CDT

Dear all,

In the nice article "Free Energy Calculation for
Theophylline Binding to an RNA Aptamer:
Comparison of MM-PBSA and Thermodynamic
Integration Methods" H Gouda, I D Kuntz, D A
Case, P A Kollmann. Biopolymers. 2003 Jan;68
(1):16-34. is discussed the possibility that the
lack of quantitative agreement in the MM-PBSA
free energy estimation can result from a
inadequate treatment of the

I was wondering if exist new approaches to try
to solve this issue.

Thank you very much
Andrea Bortolato

Andrea Bortolato, Ph.D. Student

Molecular Modeling Section
Department of Pharmaceutical Sciences
University of Padova,
Via Marzolo, 5
35131 Padova - ITALY
Phone: +39-049-8275801
Fax: +39-049-8275366 or +39-049-8275704
Webpage URL
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