1obprobe(1) User's Reference Manual obprobe(1)
2
4 obprobe — create electrostatic probe grid
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7 obprobe [OPTIONS] type pchg filename
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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.
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17 If no filename is given, obprobe will give all options including the
18 example probes.
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20 -s stepsize
21 Set the resolution of the grid (stepsize)
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23 -p padding
24 Set the padding -- extra distance on each side of the box formed by
25 the molecule.
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27 type MMFF94 atom type
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29 pchg MMFF94 partial charge
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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
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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
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41 babel(1).
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43 The web pages for Open Babel can be found at: <http://openbabel.org/>
44
46 The obprobe program was contributed by Tim Vandermeersch.
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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