obprobe(1) | General Commands Manual (urm) | 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
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 VandermeerschThis 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.
July 4, 2008 | Open Babel 2.2 |