AMBER Archive (2006)

Subject: AMBER: MM-PBSA and first solvation shell

From: Andrea Bortolato (andrea.bortolato.1_at_unipd.it)
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
first-solvation-shell.

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
e-mail:andrea.bortolato.1_at_unipd.it
Webpage URL http://mms.dsfarm.unipd.it
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