obminimize(1) General Commands Manual (urm) 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
obabel(1), obenergy(1), obrotamer(1).
The web pages for Open Babel can be found at:
The web pages for Open Babel Molecular Mechanics can be found at:
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 others who
have contributed fixes and additions. For more contributors to Open
Babel, see
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
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
Public License for more details.
Open Babel 3.1 October 10, 2019 Open Babel 3.1