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Man Pages


Manual Reference Pages  -  OBPROBE (1)

NAME

obprobe - create electrostatic probe grid

CONTENTS

Synopsis
Description
Options
Examples
See Also
Authors
Copyright

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
.An Tim Vandermeersch.


.An -nosplit Open Babel is developed by a cast of many, including currrent maintainers
.An Geoff Hutchison ,
.An Chris Morley ,
.An 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.

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