Applications/AutodockVina

Application Details

• Versions: 1.1.2 (old) and 1.2.7 (current)
• Module names: autodock/vina/1.1.2 and autodock/vina/1.2.7

Autodock Vina

AutoDock Vina is an open-source program for doing molecular docking. It was originally designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab (now CCSB) at The Scripps Research Institute https://vina.scripps.edu/

Use on HPC

Job Submission Script

Example Job Submission Script:

#!/bin/bash
#SBATCH --job-name=vina_test
#SBATCH --output=vina_%j.out
#SBATCH --error=vina_%j.err
#SBATCH --time=00:30:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem=4G

module load autodock/vina/1.2.7

vina --config data/receptor_config.txt --ligand data/ligand.pdbqt --out receptor-ligand.pdbqt

Interactive

[username@viperlogin ~]$ interactive
[username@viperlogin ~]$ interactive
salloc: Pending job allocation 268597
salloc: job 268597 queued and waiting for resources
salloc: job 268597 has been allocated resources
salloc: Granted job allocation 268597
salloc: Waiting for resource configuration
salloc: Nodes c109 are ready for job
Job ID 268597 connecting to c109, please wait...
[username@c109 ~]$ module add autodock/vina/1.2.7
[username@c109 ~]$ vina --help
AutoDock Vina v1.2.7

Input:
  --receptor arg             rigid part of the receptor (PDBQT)
  --flex arg                 flexible side chains, if any (PDBQT)
  --ligand arg               ligand (PDBQT)
  --batch arg                batch directory or ligands (PDBQT)
  --scoring arg (=vina)      scoring function (ad4, vina or vinardo)
<etc>

Visualisation

Autodock Vina also contains [MGLTools] for visualisation. To access these, please start a Visualisation node session on Viper OnDemand via [https://viperood.hpc.hull.ac.uk/pun/sys/dashboard/batch_connect/sys/Visu-VNC-gnome] (see Viper Open On Demand for more details). Once in a session:

[username@visu01 ~]$ module add autodock/vina/1.2.7
[username@visu01 ~]$ vglrun pmv

This enables you to run pmv, adt, vision and pythonsh

Further Information

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