Skip to content

Open Babel

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It is an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.


  • Puhti: 3.1.1
  • Mahti: 3.1.1


Open Babel is free software available under GNU GPL.


Initialize Open Babel on Puhti like this:

module load openbabel/3.1.1

A simple example, converting a PDB file to a Turbomole coord file:

obabel -ipdb molecule.pdb -otmol -O coord

For a comprehensive list of options and supported file formats, do obabel -H, or obabel -L formats or check the links below.


Please use both of the following references to cite Open Babel:

  • N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison. "Open Babel: An open chemical toolbox." J. Cheminf. (2011), 3, 33. DOI:10.1186/1758-2946-3-33
  • The Open Babel Package, version 3.1.1

More information

Last update: January 4, 2024