obprobe — create electrostatic probe grid
Contents
Copyright
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.
Open Babel 3.1 Oct 10, 2019 obprobe(1)
Description
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.
Examples
Probe the file pyridines.sdf using a carbonyl oxygen -- a hydrogen bond acceptor with partial charge
-0.57:
obprobe7-0.57pyridines.sdf
Probe the file pyridines.sdf using a phenyl carbon atom -- a hydrophobic atom with no partial charge:
obprobe370.0pyridines.sdfName
obprobe — create electrostatic probe grid
Options
If no filename is given, obprobe will give all options including the example probes.
-sstepsize
Set the resolution of the grid (stepsize)
-ppadding
Set the padding -- extra distance on each side of the box formed by the molecule.
type MMFF94 atom type
pchg MMFF94 partial charge
See Also
obabel(1). The web pages for Open Babel can be found at: <http://openbabel.org/>
Synopsis
obprobe [OPTIONS] typepchgfilename
