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

Arth Patel patelarth2604 at gmail.com
Fri Jul 24 13:08:17 PDT 2020

Hello Elaine,

Thank you for the clarification. I believe I described my question wrong.
So basically my aim is to find the electrostatic energy at all NZ atoms of
a protein. I will describe the exact way I did this is Chimera:

1) After opening the PDB and setting the probe radius as 1.4 Å(default), I
did Actions>Surface>Show.
2) Then in Tools>Surface/Binding Analysis>Coulombic Surface Coloring.This
opened a box where I checked 'Compute Grid' as ON and clicked OK. This led
to another box 'Volume Viewer'.
3) In the volume viewer Box, I did Tools>Values at Atom
Positions>Histogram. After this I saved the file for Attributes of 'Atoms'
and this file contains the values that I am interested in.

My concern is, I have a .PQR file for the same protein and I wanna
calculate these values(at atoms) using my own code and not with the help of
Chimera. I tried to do it based on the formula mentioned on the Chimera's
website page but I was getting different results.Could you explain how to
go about this?


On Fri, Jul 24, 2020 at 3:23 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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).
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html
> >
> 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
> -----
> 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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