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

Executables

• 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

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 ~]$ babel -ixyz benzene.xyz -opdb 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
babel -ipdb benzene.pdb -oxyz 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:

babel mymols.sdf -f 1 -l 10 -osdf outputfile1.sdf
babel mymols.sdf -f 11 -l 20 -osdf outputfile2.sdf
babel mymols.sdf -f 21 -l 30 -sdf outputfile3.sdf
babel mymols.sdf -f 31 -l 40 -osdf outputfile4.sdf

Submit this job using the swarm command.

swarm -f OpenBabel.swarm --module OpenBabel