FreeBSD Manual Pages
UNTITLED() LOCAL UNTITLED() NAME 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 calcu- late 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 hydropho- bic atom with no partial charge: obprobe 37 0.0 pyridines.sdf SEE ALSO obabel(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 current maintain- ers Geoff Hutchison, Chris Morley, Michael Banck, and innumerable oth- ers who have contributed fixes and additions. For more contributors to Open Babel, see <http://openbabel.org/wiki/THANKS> COPYRIGHT Copyright (C) 2006-2008 by Tim Vandermeersch Some portions Copyright (C) 2004-2008 by Geoffrey R. Hutchison and other contributors. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MER- CHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. Open Babel 3.1 Oct 10, 2019 obprobe(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | EXAMPLES | SEE ALSO | AUTHORS | COPYRIGHT
Want to link to this manual page? Use this URL:
<https://man.freebsd.org/cgi/man.cgi?query=obprobe&sektion=1&manpath=FreeBSD+Ports+14.3.quarterly>