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

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 24 13:23:30 PDT 2020

Hi Arth,
It still makes no sense at all to calculate the electrostatic energy at the same atoms whose charges were used to calculate the electrostatic potential.  It would be infinity because the distance of the atom from its own charge is zero, which gives infinity in the Coulombic equation (divide by distance which is zero).  So all your values are infinity.  Not useful.

The steps you described in Chimera with calculating a grid (creating a volume data set) involve a number of intermediate approximations that result in giving you different "values at atom positions" results than if you had calculated it directly.  That is, the Coulombic values are initially calculated only on the grid points, and then the values at the atom positions are determined from trilinear interpolation from the values at the grid points nearest to each atom.  In order to get exactly the same results you would have to know the exact locations of the grid points, calculate the values there, and then interpolate the values from the grid points to the atoms. 

So even if you are doing something sensible like calculating the Coulombic energy at atoms that were not in the pqr file used to calculate the ESP,  I would not expect getting exactly the same answers as the process you described because of those intermediate approximations.
I hope this helps,

> On Jul 24, 2020, at 1:08 PM, Arth Patel <patelarth2604 at gmail.com> wrote:
> 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?
> Thanks,
> Arth
> 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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