Difference between revisions of "Obenergy"

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m (Update according to Chris Swain)
 
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==Synopsis==
 
==Synopsis==
  
'''obenergy''' [''OPTIONS''] ''filename''
+
'''obenergy''' [-h] [-ff ''forcefield''] [-v] [''filename'']
  
 
==Description==
 
==Description==
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==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.
  
; '''-v'''
+
; '''-h'''
: Verbose: print out all individual energy interactions
+
: Add hydrogens
 
; '''-ff''' ''forcefield''
 
; '''-ff''' ''forcefield''
 
: Select the forcefield
 
: Select the forcefield
 +
; '''-v'''
 +
: Verbose: print out all individual energy interactions
  
 
==Examples==
 
==Examples==
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  obenergy -ff Ghemical test.mol2
 
  obenergy -ff Ghemical test.mol2
  
Calculate the energy for the molecule(s) in file test.mol2 and print out all individual energy interactions:
+
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

babel, obminimize.

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.