AMBER Archive (2008)

Subject: RE: AMBER: Non-polar Parameters For MM_PBSA Calculation

From: rluo_at_uci.edu
Date: Tue Feb 12 2008 - 17:23:40 CST

Neil,

The suggested coefficients in the Amber9 manual were proposed based on our
preliminary study of the nonpolar solvation, which was very closely
related to the PCM treatment. This treatment, termed 6-12 decomposition in
our JPC2007 paper, was further optimized. So if you want to use this
treatment, I recommend you use the newly published coefficients.

However, the two other decomposition schemes in our JPC2007 paper, i.e.
WCA and sigma, were not implemented in Amber9. They are more accurate and
transfer better from training molecules to test molecules.

All the best,
Ray

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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