[Apbs-users] solvation free energies

[Ben C. <bj...@ca...>]

Dear Nathan,

I have calculated the change in the solvation free energy on complexation=
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of a peptide and protein, for various dielectric values and surface=20
definitions. I get results that are much larger than I expected:

=09=09=09=09Dielectric =09=09=09
=09=091=09=092=09=094=09=098
NoSmooth-1.72E+05=09-1.36E+05=09-1.12E+05=09-9.69E+04
Smooth=09-1.72E+05=09-1.36E+05=09-1.12E+05=09-9.69E+04
Cubic=09-1.77E+05=09-1.37E+05=09-1.11E+05=09-9.52E+04

I'm looking for between -80 and -300 kJ/mol (a la "Massova, I.; Kollman, P.=
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A. J. Am. Chem. Soc. 1999, 121, 8133-8143"). I've previously sent you my=20
input files and stdout etc...Is there something glaringly obvious that I'm=
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missing? I have a feeling I've not got the grid sorted properly. (oh and I=
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ran this on an old version, APBS 0.2.1, but doubt that would matter in this=
=20
case)

Cheers,

Ben


Ben Carrington
Department of Pharmacology
University of Cambridge, UK