GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages
obminimize(1) FreeBSD General Commands Manual (urm) obminimize(1)

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.
steps
Specify the maximum number of steps (default=2500)
Use conjugate gradients algorithm (default)
Use steepest descent algorithm
criteria
Set convergence criteria (default=1e-6)
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.
July 4, 2008 Open Babel 2.2

Search for    or go to Top of page |  Section 1 |  Main Index

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with ManDoc.