Difference between revisions of "Obprobe"
(New page: ==Name== '''obprobe''' -- create electrostatic probe grid ==Synopsis== '''obprobe''' [''OPTIONS''] '''atom type''' '''partial charge''' ''filename'' ==Description== The obprobe tool c...)
Revision as of 09:07, 3 July 2008
obprobe -- create electrostatic probe grid
obprobe [OPTIONS] atom type partial charge filename
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 only a filename is given, obgrep will attempt to guess the file type from the filename extension.
- -s stepsize
- Set the resolution of the grid (stepsize) in Ångstroms
- -p padding
- Set the padding -- extra distance in Ångstroms on each side of the box formed by the molecule.
- atom type
- MMFF94 atom type code
- partial charge
- The partial charge of the probe atom
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
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 the Contributor list
Copyright (C) 2006-2008 by Tim Vandermeersch. Some portions Copyright (C) 2001-2005 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, version 2, as published by the Free Software Foundation.
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.