[Chimera-users] Electrostatic Potential Calculations Using Coulomb's Law

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 24 12:23:25 PDT 2020

Hi Arth,
Coulombic potential is very simple and the equation is shown and explained in the help page for the tool (Click the Help button on the dialog or see copy on our website).


Also depends on what values/parameters you chose in the tool, of course.  

Keep in mind that the coloring is for values at the points on the surface, not values at the atomic centers.  It makes no sense to color by values at atomic centers when you used the charges at the same centers to calculate the electrostatic potential in the first place, because technically (although maybe not actually due to rounding) those points would be singularities with divide-by-zero distance.   The purpose of coloring by electrostatic potential is to show what *other* molecules might "feel" when they bind to the protein.

Furthermore, because the displayed surface is solvent-excluded rather than solvent-accessible, by default the values are actually calculated at positions farther outside of the surface by 1.4 Angstroms (the "Distance from surface" parameter given in the tool).  You could set that to 0.0, but 1.4 is the recommended value and the default.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 24, 2020, at 12:10 PM, Arth Patel <patelarth2604 at gmail.com> wrote:
> Hello Everyone,
> I have a .pqr file generated using the APBS website and I want to calculate the electrostatic potential for each atom of the proteins using this. I did this using the surface analysis --> Coulombic Surface on Chimera. As part of my current research I am supposed to write a code on python for the same but when I compare the results, I am getting different results. Can someone please explain how to calculate the atom electrostatic potentials from a .pqr file theoretically?
> Thanks,
> Arth 

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