AMBER Archive (2004)

Subject: AMBER: Parameters for nonpolar contribution to solvation

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Fri Apr 23 2004 - 12:48:42 CDT

Dear Amber users,

I have noticed that the results when running mm_pbsa_statistics.pl
independently on the *.all.out files from a mm_pbsa calculation, the
resulting binding free energies differ in the PBSUR part, the hydrophobic
contribution to the binding free energy.

The cause of that seems to me that if mm_pbsa_statistics.pl is used,
PBSUR is calculated always with the gamma and beta parammeters set to
0.00542 and 0.92, while mm_pbsa.pl uses the gamma and beta parameters as
set in the input file. The default parameters for gamma and beta in
mm_pbsa.in have changed to 0.005 and 0.0 in amber8.

My two questions are:

Is this correct and should mm_pbsa_statistics.pl be changed to accept
different values for gamma and beta?

Should one use the new parameters for calcuations of ligand binding
free energies or the old ones, or what is the motivation of the change?

Kind Regards,

Thomas

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