Difference between revisions of "Obenergy"
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==Synopsis== | ==Synopsis== | ||
| − | '''obenergy''' ['' | + | '''obenergy''' [-h] [-ff ''forcefield''] [-v] [''filename''] |
==Description== | ==Description== | ||
| Line 14: | Line 14: | ||
==Options== | ==Options== | ||
| − | If no filename is given, obenergy will give all options including the available forcefields. | + | If no filename is given, obenergy will give all options including the available forcefields. Note that arguments should be specified in the order shown above. |
| − | ; '''- | + | ; '''-h''' |
| − | : | + | : Add hydrogens |
; '''-ff''' ''forcefield'' | ; '''-ff''' ''forcefield'' | ||
: Select the forcefield | : Select the forcefield | ||
| + | ; '''-v''' | ||
| + | : Verbose: print out all individual energy interactions | ||
==Examples== | ==Examples== | ||
| Line 35: | Line 37: | ||
obenergy -ff Ghemical test.mol2 | obenergy -ff Ghemical test.mol2 | ||
| − | + | Add hydrogens to the molecule(s) in file test.mol2, calculate their energies and print out all individual energy interactions: | |
| − | obenergy -v test.mol2 | + | obenergy -h -ff Ghemical -v test.mol2 |
==See Also== | ==See Also== | ||
Latest revision as of 12:36, 23 February 2009
Name
obenergy -- calculate the energy for a molecule
Synopsis
obenergy [-h] [-ff forcefield] [-v] [filename]
Description
The obenergy tool can be used to calculate the energy for molecules inside (multi-)molecule files (e.g., MOL2, etc.)
Options
If no filename is given, obenergy will give all options including the available forcefields. Note that arguments should be specified in the order shown above.
- -h
- Add hydrogens
- -ff forcefield
- Select the forcefield
- -v
- Verbose: print out all individual energy interactions
Examples
View the possible options, including available forcefields:
obenergy
Calculate the energy for the molecule(s) in file test.mol2:
obenergy test.mol2
Calculate the energy for the molecule(s) in file test.mol2 using the Ghemical forcefield:
obenergy -ff Ghemical test.mol2
Add hydrogens to the molecule(s) in file test.mol2, calculate their energies and print out all individual energy interactions:
obenergy -h -ff Ghemical -v test.mol2
See Also
The web pages for Open Babel Molecular Mechanics can be found at: <http://openbabel.org/wiki/Molecular_mechanics>
Authors
The obenergy 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 the Contributor list
Copyright
Copyright (C) 2007 Tim Vandermeersch.
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 2, as published by the Free Software Foundation.
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.
