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.

References:

• Noel M O'Boyle, Michael Banck, Craig A James, Chris Morley, Tim Vandermeersch and Geoffrey R Hutchison Open Babel: An open chemical toolbox Journal of Cheminformatics (2011) 3:33

• Open Babel Wiki Site

• Module Name: openbabel (see the modules page for more information)
• Singlethreaded
• Environment variables set
  • OPENBABEL_HOME
  • OPENBABEL_EXAMPLES
• Example files in $OPENBABEL_EXAMPLES

The executables are version dependent:

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load openbabel
[user@cn3144 ~]$ obabel -ixyz benzene.xyz -O benzene.pdb

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. openbabel.sh). For example:

#!/bin/bash
module load openbabel
obabel -ipdb benzene.pdb -O benzene.xyz

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] openbabel.sh

Create a swarmfile (e.g. openbabel.swarm). For example:

obabel mymols.sdf -f 1 -l 10 -Ooutputfile1.sdf
obabel mymols.sdf -f 11 -l 20 -O outputfile2.sdf
obabel mymols.sdf -f 21 -l 30 -O outputfile3.sdf
obabel mymols.sdf -f 31 -l 40 -O outputfile4.sdf

Submit this job using the swarm command.

swarm -f openbabel.swarm --module openbabel