obprobe(1) General Commands Manual (urm) obprobe(1)

obprobecreate electrostatic probe grid

obprobe [OPTIONS] type pchg filename

The obprobe tool creates a grid around a molecule, placing a probe atom with a specified atom type and partial charge at each point to calculate the MMFF94 energy. This can be used for docking experiments to test hydrogen-bond affinity, electrostatic potential, etc. Output is sent to standard output using the Gaussian Cube format.

If no filename is given, obprobe will give all options including the example probes.

Set the resolution of the grid (stepsize)
Set the padding -- extra distance on each side of the box formed by the molecule.
MMFF94 atom type
MMFF94 partial charge

Probe the file pyridines.sdf using a carbonyl oxygen -- a hydrogen bond acceptor with partial charge -0.57:

obprobe 7 -0.57 pyridines.sdf

Probe the file pyridines.sdf using a phenyl carbon atom -- a hydrophobic atom with no partial charge:

obprobe 37 0.0 pyridines.sdf


The web pages for Open Babel can be found at: http://openbabel.org/

The obprobe program was contributed by Tim Vandermeersch.

Open Babel is developed by a cast of many, including currrent maintainers Geoff Hutchison, Chris Morley, Michael Banck, and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see http://openbabel.org/wiki/THANKS

Copyright (C) 2006-2008 by Tim Vandermeersch
Some portions Copyright (C) 2004-2008 by Geoffrey R. Hutchison and other contributors.

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation version 2 of the License.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

October 10, 2019 Open Babel 3.1