[Open Babel] Electrostatic Potential Map Calculations

[J.B. B. <jb...@ku...>]

Thank you for your time today.

I am interested in using OpenBabel to generate Electrostatic Potential Maps
(EPMs) of compounds.
EPMs are readily found in texts such as McMurray's Introduction to Organic
Chemistry (e.g., 6th edition).
A simple example of an EPM is chrolomethane (CH3Cl) with a partially
negative chlorine atom and a partially positive CH3 region (p. 17, 6th
edition).

I understand that the OpenBabel suite has a tool 'obprobe' which outputs a
Gaussian Cube file format for a given input compound.
However, I am unsure how to use this to visualize the electrostatic
potential of a molecular such as CH3Cl.
Guessing by using the phenyl carbon probe (type 37), and with just the
resulting Gaussian Cube file, I was unable to get VMD to produce and display
an EPM, and I suspect that the Gaussian Cube file by itself is not complete
for describe electrostatic potential.

I also have seen the tools PDB2PQR and APBS (which uses .PQR format) to
generate EPMs.
Unfortunately, using OpenBabel to convert a MOL file to PDB, which I then
hand off to PDB2PQR is unsuccesful because PDB2PQR complains: "No Heavy
Atoms found".

To recap, my goal is to do something like this:
GIVEN: MOL file m1.mol
OUTPUT: EPM file m1.epm (or multiple files representing one EPM for each
input MOL file)
PROCEDURE: use tools OpenBabel/PDB2PQR/APBS/(other appropriate tool not
requiring PDB format)

Can anyone assist me with this situation?  I checked openbabel-discuss and
openbabel-scripting, but could not find this question listed in any post in
2009 or 2008.
The closest discussion I found was about Gasteiger calculation in a 2008
post.

I would greatly appreciate any input about this.

With kind thanks,
J.B. Brown
Kyoto University Institute for Chemical Research