1obprobe(1)                  User's Reference Manual                 obprobe(1)
2

NAME

4     obprobe — create electrostatic probe grid
5

SYNOPSIS

7     obprobe [OPTIONS] type pchg filename
8

DESCRIPTION

10     The obprobe tool creates a grid around a molecule, placing a probe atom
11     with a specified atom type and partial charge at each point to calculate
12     the MMFF94 energy. This can be used for docking experiments to test
13     hydrogen-bond affinity, electrostatic potential, etc.  Output is sent to
14     standard output using the Gaussian Cube format.
15

OPTIONS

17     If no filename is given, obprobe will give all options including the
18     example probes.
19
20     -s stepsize
21           Set the resolution of the grid (stepsize)
22
23     -p padding
24           Set the padding -- extra distance on each side of the box formed by
25           the molecule.
26
27     type  MMFF94 atom type
28
29     pchg  MMFF94 partial charge
30

EXAMPLES

32     Probe the file pyridines.sdf using a carbonyl oxygen -- a hydrogen bond
33     acceptor with partial charge -0.57:
34           obprobe 7 -0.57 pyridines.sdf
35
36     Probe the file pyridines.sdf using a phenyl carbon atom -- a hydrophobic
37     atom with no partial charge:
38           obprobe 37 0.0 pyridines.sdf
39

SEE ALSO

41     babel(1).
42
43     The web pages for Open Babel can be found at: <http://openbabel.org/>
44

AUTHORS

46     The obprobe program was contributed by Tim Vandermeersch.
47
48     Open Babel is developed by a cast of many, including currrent maintainers
49     Geoff Hutchison, Chris Morley, Michael Banck, and innumerable others who
50     have contributed fixes and additions.  For more contributors to Open
51     Babel, see <http://openbabel.org/wiki/THANKS>
52

54     Copyright (C) 2006-2008 by Tim Vandermeersch
55     Some portions Copyright (C) 2004-2008 by Geoffrey R. Hutchison and other
56     contributors.
57
58      This program is free software; you can redistribute it and/or modify it
59     under the terms of the GNU General Public License as published by the
60     Free Software Foundation version 2 of the License.
61
62      This program is distributed in the hope that it will be useful, but
63     WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABIL‐
64     ITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
65     License for more details.
66
67Open Babel 2.2                   July 4, 2008                   Open Babel 2.2
Impressum