Obprobe

From Open Babel

Contents 1 Name 2 Synopsis 3 Description 4 Options 5 Examples 6 See Also 7 Authors 8 Copyright

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 standard output using the Gaussian Cube format.

Options

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

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 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 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.