start:software:topical:lifesciences:molecular_docking:autodock

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:

bio/parallel_Autodock

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_Audodock [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) - all output is best placed in either the scratch file system (/lustre/scratch/<your project>) or the project file system (/lustre/project/<your project>).

The output will be in the output directory.


1)
As always the version information is omitted. Just loading the module will load the most current version.
  • start/software/topical/lifesciences/molecular_docking/autodock.txt
  • Last modified: 2020/10/31 12:23
  • by meesters