Re: [Apbs-users] Reproducing solvation free energies (PARSE) with APBS

[Nathan B. <ba...@bi...>]

The choice of surface definition is a matter of personal taste and the 
charge/radius parameters you choose.  With that said, if you change the 
surface definition during the calculation, you'll need to compensate by 
doing 4 calculations to calculate the solvation energies for both of the 
surface definitions and then calculating the quantity of interest via 
the appropriate free energy cycle.

Good luck,

nathan

Marc Baaden wrote:
> Hi,
> 
> my understanding of the PARSE paper is: use solvated state sdie=80 pdie=2
> and reference (vacuum) state sdie=1 pdie=2. As vacuum is the reference
> state, I can't see why I should use a water (=1.4) radius ? In vacuum
> the "vacuum" medium should directly contact the molecular (VdW) surface,
> as there is no "vacuum molecule" that needs to be rolled over the protein
> surface, hence srad=0.0. In water, as the dielectric is active via
> individual water molecules, one needs to determine their accessibility,
> hence a 1.4 radius. Am I missing something ?
> 
> Yours,
> Marc
> 
> 
>>>>"Nathan Baker" said:
> 
>  >> If the reference calculation is carried out with a homogeneous dielectric
>  >> (SDIE = PDIE), then the results should be insensitive to the SRAD choice fo
>      r
>  >> the reference.  If the dielectric coefficients are not the same, then
>  >> Jessica is right:  you need to be consistent with SRAD.  If you choose SRAD
>  >> = 0.0, then you've basically switched to a VdW surface.

-- 
Nathan A. Baker, Assistant Professor
Washington University in St. Louis School of Medicine
Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology
700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110
Phone:  (314) 362-2040, Fax:  (314) 362-0234
URL:  http://www.biochem.wustl.edu/~baker