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
babel(1).
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.