logo
Free, unlimited AI code reviews that run on commit
git-lrc git-lrc GitHub Install Now We'd appreciate a star git-lrc - Free, unlimited AI code reviews that run on commit | Product Hunt git-lrc - Free, unlimited AI code reviews that run on commit | Product Hunt

obprobe — create electrostatic probe grid

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>

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.

Examples

       Probe the file pyridines.sdf using a carbonyl oxygen -- a hydrogen  bond  acceptor  with  partial  charge
       -0.57:
             obprobe7-0.57pyridines.sdf

       Probe the file pyridines.sdf using a phenyl carbon atom -- a hydrophobic atom with no partial charge:
             obprobe370.0pyridines.sdf

Name

       obprobe — create electrostatic probe grid

Options

       If no filename is given, obprobe will give all options including the example probes.

       -sstepsize
             Set the resolution of the grid (stepsize)

       -ppadding
             Set the padding -- extra distance on each side of the box formed by the molecule.

       type  MMFF94 atom type

       pchg  MMFF94 partial charge

See Also

obabel(1).

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

Synopsis

obprobe [OPTIONS] typepchgfilename

See Also