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

sameer varma varma1 at uiuc.edu
Tue Oct 12 01:25:12 CEST 2004

Hi Marc,

I think it makes complete sense. In my opinion, the choice of all 
parameters in PB based calculations, for example - FFs, dielectric 
constants, boundary conditions, methods to represent ions and even grid 
spacing, depend on how you address the following issues:
1) What is the purpose of your calculation?
2) How accurate a result are you interested in?
3) How, and for what purpose were the FF parameters optimized?

Having said that, in some cases I have found it very useful to investigate 
the effect of some parameters on the results. It helps in identifying the 
roots of ambiguities, if any, that come up in in this comparative study.


At 11:54 PM 10/11/2004 +0200, you wrote:

>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 
>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
>      s
>  >> 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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