View source for Obprobe

==Name==

'''obprobe''' -- create electrostatic probe grid

==Synopsis==

'''obprobe''' [''OPTIONS''] '''atom type''' '''partial charge''' ''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 a file created in the same folder as the input file in [[Gaussian Cube]] format.

==Options==

If only a filename is given, obgrep will attempt to guess the file type from the [[List of extensions|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

==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]].

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 the [[THANKS|Contributor list]]

==Copyright==

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 [http://www.fsf.org/licensing/licenses/gpl.html 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.

[[Category:Guides]]