obminimize(1) - Linux man page

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 others who have contributed fixes and additions. For more contributors to Open Babel, see <http://openbabel.org/wiki/THANKS>

Copyright

Copyright © 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 2.2 July 4, 2008 Open Babel 2.2

Referenced By