High-Performance Computing at the NIH
GitHub YouTube @nih_hpc RSS Feed
Open Babel
Open Babel Logo


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

How to Use

There are multiple versions of Open Babel available. An easy way of selecting the version is to use modules. To see the modules available, type

module avail OpenBabel

To select a module, type

module load OpenBabel/[ver]

where [ver] is the version of choice. This will set your $PATH variable.

The following executables are all available from the commandline:


  • babel - a converter for chemistry and molecular modeling data files
  • obchiral - print molecular chirality information
  • obconformer - generate low-energy conformers
  • obenergy - calculate the energy for a molecule
  • obfit - superimpose two molecules based on a SMARTS pattern
  • obgen - generate 3D coordinates for a molecule
  • obgrep - an advanced molecular grep program using SMARTS
  • obminimize - optimize the geometry, minimize the energy for a molecule
  • obprobe - create electrostatic probe grid
  • obprop - print standard molecular properties
  • obrotamer - generate conformer/rotamer coordinates
  • obrotate - batch-rotate dihedral angles matching SMARTS patterns
  • obspectrophore - calculate a Spectrophore, a one-dimensional descriptor generated from the property field surrounding the molecule

To see all formats available, type:

$ babel -L formats