Molecular Docking with AutoDock

AutoDock is the academic, canonical tool to perform molecular docking experiments. We provide a module tools/AutoDock1).

To leverage the task from 1 (or a few) ligands to be screened to several thousand, we provide a wrapper script, which is available as a module:


The code is under version management and hosted internally, here.

The wrapper script will submit a job, it is not intended to be just within a SLURM environment, but rather creates one.

Calling parallel_Autodock -h will display a help message with all the options, the script provides. Likewise the call parallel_Autodock –credits will display credits and a version history.

The AudoDock configuration file is important. Without it or with a minor glitch in it, AutoDock will either refuse to run or might not yield meaningful results. We therefore strongly encourage to run a couple of screenings (different ligands / receptors) per configuration on a login node before launching the wrapper script and producing zillions of error messages whilst wasting time and your productivity.

The invocation

$ parallel_Autodock --wp > <some file>

will write a default parameter file to be edited. If pleased with the (numerical) settings, it can be used as is: All entries reading <field> are substituted per run with the macromolecule file prefixes (see below)

The script, after loading the module, can then be run like:

$ parall_Audodoc [options] -P <path to configuration file> <path to ligand directory> <path to pdbqt receptor file>

The script expects all AudoDock map files to be present in the same directory as the receptor file.

About Arguments:

  • both, the ligand directory and the path to the pdbqt file, are mandatory
  • both can be relative paths
  • the ligand directory should contain one ligand per file
  • -P,–parameterfile is a mandatory flag and supposed to be a (relative) path to the configuration file

The options:

  • parallel_Audodock attempts to deduce your SLURM account. This may fail, in which case -A, –account needs to be supplied.
  • -N,–nodes allows to reserve more than 1 node (the default). This may speed up the screening.
  • -l,–runlimit, this defaults to 300 minutes. If > 300 the partition will automatically be switched to nodelong
  • -p,–partition, the default is nodeshort, no smp-partition should be choosen.
  • -t,–threads, Vina can work in parallel. Please consult the manual. The default is 1.
  • -o,–outdir output directory path (default is the current working directory)

The output will be in the output directory.

As always the version information is omitted. Just loading the module will load the most current version.
  • software/topical/lifescience/autodock.txt
  • Last modified: 2018/08/24 08:32
  • by meesters