AMBER Archive (2008)

Subject: AMBER: Non-polar Parameters For MM_PBSA Calculation

From: Neil Bruce (Neil.Bruce_at_postgrad.manchester.ac.uk)
Date: Tue Feb 12 2008 - 05:54:02 CST

Dear Amber Users

I am performing an MM-PBSA analysis of a peptide system and am unsure of the
correct parameters to use for the calculation of the non-polar contributions to
the solvation energy. If I am using Tan and Luo's optimised radii (RADIOPT=1),
a probe radus of 1.6 and separate terms for the dispersion and cavitation
contributions (NPOPT=2), what are the correct values of CAVITY_SURFTEN and
CAVITY_OFFSET to use. If I am reading the information in the manual correctly I
think they are 0.04356 and -1.008 respectively but I am unsure.

Also could someone point me in the direction of any papers from which these
values arise. I've got the following papers:

Tan, Yang, Luo: J. Phys Chem. B, (2006), 110, 18680.
Tan, Tan, Luo: J. Phys. Chem. B, (2007), 111, 12263.

but can't find any mention of the values shown above.

Thanks in advance

Neil
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