[gmx-users] Parameters for PB calculation with Delphi from Gromacsdata

Marc Baaden baaden at smplinux.de
Mon Oct 11 23:54:40 CEST 2004

Hi Marco, Ran and others,

thanks a lot for your comments, they are very helpful.

Although I am really not an expert in PB calculations and MMPBSA, I don't
quite agree with Marco's last statement. *If* we want to use PB to 
*reallistically* reproduce/estimate solvation free energies, and there is
one parameter set (PARSE for Delphi) that does this job, then I think that
this fact overrides the "for the sake of consistency let's use the same charges
everywhere" argument.
My justification would be that for every "job" (eg energy type
that you estimate) you should use the best available method.
In this sense, I would tend to regard MM, PB/SA and Entropic parts for
MMPBSA separately. I put PB/SA together because there are two parameters
that link both terms (eg. to calculate a nonpolar energy from the
surface area that is consistent with the solvation part).
Or to put it differently, if one wanted to use forcefield charges and radii,
one would have to justify/prove that this reproduces experimental solvation
free energies and one would have to re-determine a factor to combine this
with the SA term.

Does this make sense, or am I missing something ?


>>> "Marco Ceruso" said:
 >> Hi,
 >> Ran is right. One reason to keep the FF charges instead of the PARSE ones i
 >> to be consistent with what was used to generate your conformation specially
 >> when you use the PB calculation results along with  some-type of MMPBSA
 >> approach in which you have a E_elec term that comes from your FF
 >> electrostatic representation.
 >> In our hands the differences between OPLS-AA and PARSE charges were much
 >> less critical than the differences observed between PARSE radii and the
 >> radii implanted by editconf -mead. 
 >> Hope this helps
 >> Marco
 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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