obprobe (1) Linux Manual Page
obprobe – create electrostatic probe grid
Synopsis
[OPTIONS ] type pchg filenameDescription
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 VandermeerschSome portions Copyright (C) 2004-2008 by Geoffrey R. Hutchison and other contributors.