obprobe - Man Page

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.

type

MMFF94 atom type

pchg

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

obabel(1).

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.