obprobe man page

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 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 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 < http://openbabel.org/wiki/THANKS>

Info

July 4, 2008