debian man page for obprobe

obprobe(1)						      User's Reference Manual							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 calcu-
     late 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 oth-
     ers 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 MERCHANTABIL-
     ITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Open Babel 2.2							   July 4, 2008 						    Open Babel 2.2