obprobe(1)
NAME
obprobe -- create electrostatic probe grid
SYNOPSIS
obprobe [OPTIONS] type pchg filename
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.
OPTIONS
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
EXAMPLES
- 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
SEE ALSO
The web pages for Open Babel can be found at: <http://openbabel.org/>
AUTHORS
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
- 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.