obprobe (1) Linux Manual Page
NAME
obprobe – create electrostatic probe grid
SYNOPSIS
[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.