Skip to content

Open Babel

Open Babel is a chemical toolbox designed to search, convert, analyse or store data from molecular modelling, chemistry, solid-state materials, biochemistry, or related areas.

Open Babel is available as a module on Apocrita.


To run the default installed version of Open Babel, simply load the openbabel module:

$ module load openbabel
$ obabel  -h

obabel [-i<input-type>] <infilename> [-o<output-type>] -O<outfilename> [Options]

For usage documentation, run obabel -H.

Example job

Serial job

Here is an example job running on 1 core and 1GB of memory:

#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load openbabel

obabel -i sdf mymols.sdf \
       -o smi \
       -O outputfile.smi