obprobe (1) - Linux Manuals

obprobe: create electrostatic probe grid


obprobe - create electrostatic probe grid


[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.

-s stepsize
Set the resolution of the grid (stepsize)
-p padding
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 obprobe program was contributed by An Tim Vandermeersch.

An -nosplit Open Babel is developed by a cast of many, including currrent maintainers An Geoff Hutchison , An Chris Morley , An 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.



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