AMBER: PBSA parameter question (Radii and Charges)

From: Marc Baaden <>
Date: Wed, 13 Oct 2004 02:01:19 +0200

Dear colleagues,

  I have a question concerning the parameters used for Poisson-Boltzmann
calculations with the pbsa program. Are those parameters suitable to
reproduce eg protein solvation free energy when used with another "standalone"
PB solver like Delphi or APBS, or are they somehow tied to the pbsa
program ?
In the manual it is also mentioned that the atomic cavity radii for molecular
surface calculation and dielectric assignment used by pbsa are optimized for
model compounds of proteins. Which proteins were used, and which ?experimental?
parameter was reproduced ?

(Should these details be published already, then sorry for having missed the

Thanks in advance,
  Marc Baaden

 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris      -
 FAX: +49 697912 39550  -  Tel: +33 15841 5176 ou +33 609 843217
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Received on Wed Oct 13 2004 - 01:53:00 PDT
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