AMBER Archive (2004)

Subject: AMBER: MMPBSA PB parameters - PARSE implementation in Amber

From: Marc Baaden (baaden_at_smplinux.de)
Date: Wed Oct 13 2004 - 12:42:34 CDT

Dear colleagues,

  as I am currently investigating the MMPBSA approach (as implemented
in Amber), I also had a look at the PARSE parameter set as used in that
implementation. I was a bit surprised to see that the PARSE radii are
used, but in an all-atom fashion, as well as non-PARSE Amber-charges.
Also the delphi input used for the PB calculation is different from the
original conditions as described in the PARSE paper (for example
prbrad should be 1.4 for solution and 0.0 for the reference calculation
in vacuum; indi should be 2; no vacuum reference calculation is carried
out).
The bottom line of my question is:

  The original PARSE parameter set reproduced experimental solvation
free energies for small molecules. Does the radius+charge parameter
set and delphi run parameter file as implemented in Amber reproduce
experimental data ? For which molecules/testsets ?

Thanks in advance,
  Marc Baaden 

-- 
 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden_at_smplinux.de      -      http://www.marc-baaden.de
 FAX: +49 697912 39550  -  Tel: +33 15841 5176 ou +33 609 843217

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