obprobe man page

obprobe — create electrostatic probe grid


obprobe [Options] type pchg filename


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.


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.


MMFF94 atom type


MMFF94 partial charge


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


The web pages for Open Babel can be found at: < http://openbabel.org/>


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>


July 4, 2008