Hello –

The answers to questions #1 and #2 are both “no”; however, the answer to question #3 is “yes”.  You can calculate the potential due to polarization of the solvent (reaction field potential) by subtracting the results of a homogeneous electrostatics calculation (both solute and solvent dielectrics set to solute value) from the results of a heterogeneous dielectric calculation.

The net charges in the PQR file include contributions from both the nucleus and the electrons.

The new “atompot” function was just to provide users with an easy way to evaluate the potential at the atomic center.

The atomic radii are determined by parameterization against solvation energy data (as well as other information).

Hope this helps,

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  509-375-3997
http://kdi.pnl.gov/bios/baker.stm

From: M.V.Vulovic@lumc.nl [mailto:M.V.Vulovic@lumc.nl]
Sent: Friday, October 21, 2011 1:05 PM
Cc: apbs-users@lists.sourceforge.net
Subject: [apbs-users] electrostatic potential origin

Dear authors,
I have some basic questions about the theory behind this and the way how electrostatic potential is calculated from P-B equation.
Pardon me for the lack of bio/chem knowledge.
Is it possible to distinguish between:
1. the potential within the atom that originates from the nucleus
2. the potential that originates from shell electrons and
3. the potential that originates from ions in the solvent?
Pqr files contain the net charges of the atoms within a certain radius. So the nuclei are substituted with the net charges? These are usually fractions (< +-1).  Is the final  potential calculated from this contributions (net charges)?
Or you take into account also which atomic number it is (known number of protons in the nucleus) , and compute the potential within the atom itself as well. Is that the idea behind the new 'atompot' function that appeared in the latest release?
Or is the calculation result of "atompot" same as "pot" but just now at the positions of the specific atoms?
How the radius in pqr is calculated?
Thank you a lot! Sorry for so many questions =;)
Best regards

--------------------------------------------------
Dipl.Ing. Milos Vulovic
PhD candidate

Delft University of Technology
Faculty of Applied Sciences / Quantitative Imaging Group
Lorentzweg 1  / 2628CJ  Delft
The Netherlands
E-mail: m.vulovic@tudelft.nl
Tel: (+31)15-278-31-91
Fax: (+31)15-278-6740

Leiden University Medical Center
Department of Molecular Cell Biology / Section Electron Microscopy
Postal Zone S1-P  P.O.Box 9600 / 2300RC Leiden
The Netherlands
E-mail: vulovic@lumc.nl
Tel: (+31)71 526 9449
Fax: (+31)71 526 8270