AMBER: Mg2+ radius in my_parse_delphi.siz

From: JunJun Liu <>
Date: Tue, 27 Sep 2005 11:30:14 +0800

Dear Amber Users:

In the example of MM-PBSA that distributed with AMBER8, the
"my_parse_delphi.siz" file says value of Mg is from Biophys J 2001, 80,
1151. And the Mg2+ radius is set as 0.99A. However, when I read the
refered Biophys paper, I'm finding that the author used 1.45A rather than
0.99A for the Mg2+ radius. Is the default Mg value in in
my_parse_delphi.siz wrong?

Below is the original statement that was found in page 3, "Energy
analysis" Section:
"The magnitude and size of the binding free energy was very dependent upon
the size we chose for the radius of the hydrated Mg2+ cation. We used 1.45
Å because this number has been shown to reproduce experimentally
determined hydration free energies"

Best Regards!


JunJun Liu
College of Chemistry
Central China Normal University
WuHan   430079
P.R. China
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Received on Tue Sep 27 2005 - 04:53:00 PDT
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