obminimize(1) [debian man page]
obminimize(1) User's Reference Manual obminimize(1) NAME
obminimize -- optimize the geometry, minimize the energy for a molecule SYNOPSIS
obminimize [OPTIONS] filename DESCRIPTION
The obminimize tool can be used to minimize the energy for molecules inside (multi-)molecule files (e.g., MOL2, etc.) OPTIONS
If no filename is given, obminimize will give all options including the available forcefields. -n steps Specify the maximum number of steps (default=2500) -cg Use conjugate gradients algorithm (default) -sd Use steepest descent algorithm -c criteria Set convergence criteria (default=1e-6) -ff forcefield Select the forcefield EXAMPLES
View the possible options, including available forcefields: obminimize Minimize the energy for the molecule(s) in file test.mol2: obminimize test.mol2 Minimize the energy for the molecule(s) in file test.mol2 using the Ghemical forcefield: obminimize -ff Ghemical test.mol2 Minimize the energy for the molecule(s) in file test.mol2 by taking at most 300 geometry optimization steps obminimize -n 300 test.mol2 Minimize the energy for the molecule(s) in file test.mol2 using the steepest descent algorithm and convergence criteria 1e-5: obminimize -sd -c 1e-5 test.mol2 SEE ALSO
babel(1), obenergy(1), obrotamer(1). The web pages for Open Babel can be found at: <http://openbabel.org/> The web pages for Open Babel Molecular Mechanics can be found at: <http://openbabel.org/wiki/Molecular_mechanics> AUTHORS
The minimize 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 oth- ers who have contributed fixes and additions. For more contributors to Open Babel, see <http://openbabel.org/wiki/THANKS> COPYRIGHT
Copyright (C) 2007 by Tim Vandermeersch. 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 MERCHANTABIL- ITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. Open Babel 2.2 July 4, 2008 Open Babel 2.2
Check Out this Related Man Page
obrotate(1) User's Reference Manual obrotate(1) NAME
obrotate -- batch-rotate dihedral angles matching SMARTS patterns SYNOPSIS
obrotate 'SMARTS-pattern' filename atom1 atom2 atom3 atom4 angle DESCRIPTION
The obrotate program rotates the torsional (dihedral) angle of a specified bond in molecules to that defined by the user. In other words, it does the same as a user setting an angle in a molecular modelling package, but much faster and in batch mode (i.e. across multiple molecules in a file). The four atom IDs required are indexes into the SMARTS pattern, which starts at atom 0 (zero). The angle supplied is in degrees. The two atoms used to set the dihedral angle <atom1> and <atom4> do not need to be connected to the atoms of the bond <atom2> and <atom3> in any way. The order of the atoms matters -- the portion of the molecule attached to <atom1> and <atom2> remain fixed, but the portion bonded to <atom3> and & <atom4> moves. EXAMPLES
Let's say that you want to define the conformation of a large number of molecules with a pyridyl scaffold and substituted with an aliphatic chain at the 3-position, for example for docking or 3D-QSAR purposes. To set the value of the first dihedral angle to 90 degrees: obrotate 'c1ccncc1CCC' pyridines.sdf 5 6 7 8 90 Here 6 and 7 define the bond to rotate in the SMARTS patter, i.e., c1-C and atoms 5 and 8 define the particular dihedral angle to rotate. Since the atoms to define the dihedral do not need to be directly connected, the nitrogen in the pyridine can be used: obrotate 'c1ccncc1CCC' pyridines.sdf 4 6 7 8 90 Keep the pyridyl ring fixed and moves the aliphatic chain: obrotate 'c1ccncc1CCC' pyridines.sdf 5 6 7 8 90 Keep the aliphatic chain fixed and move the pyridyl ring: obrotate 'c1ccncc1CCC' pyridines.sdf 8 7 6 5 90 SEE ALSO
babel(1), obchiral(1), obfit(1), obgrep(1), obprop(1), obrotate(1). The web pages for Open Babel can be found at: <http://openbabel.org/> A guide for constructing SMARTS patterns can be found at: <http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html> AUTHORS
The obgrep program was contributed by Fabien Fontaine Open Babel is developed by a cast of many, including currrent maintainers 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) 1998-2001 by OpenEye Scientific Software, Inc. Some portions Copyright (C) 2001-2005 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 MERCHANTABIL- ITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. Open Babel 2.2 July 4, 2008 Open Babel 2.2