obminimize
—
optimize the geometry, minimize the energy for a
molecule
obminimize |
[ OPTIONS ]
filename |
The obminimize tool can be used to minimize the energy for molecules inside
(multi-)molecule files (e.g., MOL2, etc.)
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
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
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>
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
<
http://openbabel.org/wiki/THANKS>
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.