obminimize man page

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>

Referenced By

babel(1), obconformer(1), obenergy(1), obgen(1), obrotamer(1).

July 4, 2008