<!-- manual page source format generated by PolyglotMan v3.2, --> <!-- available at http://polyglotman.sourceforge.net/ --> <html> <head> <title>obprobe</title> </head> <body bgcolor='white'> <a href='#toc'>Table of Contents</a><p> <h2><a name='sect0' href='#toc0'>Name</a></h2> <p> <b>obprobe</b> -- create electrostatic probe grid <p> <h2><a name='sect1' href='#toc1'><b>Synopsis</b></a></h2> <p> <b>obprop</b> <i>[options]</i> <i>type</i> <i>pcharge</i> <i>filename</i> <p> <h2><a name='sect2' href='#toc2'><b>Description</b></a></h2> <p> 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. <p> <h2><a name='options' href='#tocO'><b>Options</b></a></h2> <p> If no filename is given, obprobe will give all options including the example probes. <dl> <dt><b>-s</b> <i>step size</i></dt></dt> <dd> Set the resolution of the grid (stepsize) <p></dd> <dt><b>-p</b> <i>padding</i></dt></dt> <dd> Set the padding -- extra distance on each side of the box formed by the molecule. <p></dd> <dt><i>type</i></dt></dt> <dd> The MMFF94 atom type code of the probe atom. <p></dd> <dt><i>pchg</i></dt></dt> <dd> The partial charge on the probe atom. <p></dd> <p> <h2><a name='sect3' href='#toc3'><b>Examples</b></a></h2> <p> Probe the file pyridines.sdf using a carbonyl oxygen -- a hydrogen bond acceptor with partial charge -0.57: <pre>obprobe 7 -0.57 pyridines.sdf</pre> <p> Probe the file pyridines.sdf using a phenyl carbon atom -- a hydrophobic atom with no partial charge: <pre>obprobe 37 0.0 pyridines.sdf</pre> <p> <h2><a name='sect4' href='#toc4'><b>See</b> <b>Also</b></a></h2> <p> <a href='babel.html'>babel(1)</a>. <p><p> The web pages for Open Babel can be found at: <<b><a href="http://openbabel.org/">http://openbabel.org/</a></b>> <p> <h2><a name='sect5' href='#toc5'><b>Authors</b></a></h2> <p> The obprobe program was contributed by Tim Vandermeersch <p><p> 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 <<b><a href="http://openbabel.org/wiki/THANKS">http://openbabel.org/wiki/THANKS</a></b>> <p> <h2><a name='sect6' href='#toc6'><b>Copyright</b></a></h2> <p> Copyright (C) 2006-2008 by Tim Vandermeersch<br> Some portions Copyright (C) 2004-2008 by Geoffrey R. Hutchison and other contributors. <p><p> 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. <p><p> This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. <p> <hr><p> <a name='toc'><b>Table of Contents</b></a><p> <ul> <li><a name='toc0' href='#sect0'>Name</a></li> <li><a name='toc1' href='#sect1'>Synopsis</a></li> <li><a name='toc2' href='#sect2'>Description</a></li> <li><a name='tocO' href='#options'>Options</a></li> <li><a name='toc3' href='#sect3'>Examples</a></li> <li><a name='toc4' href='#sect4'>See Also</a></li> <li><a name='toc5' href='#sect5'>Authors</a></li> <li><a name='toc6' href='#sect6'>Copyright</a></li> </ul> </body> </html>
