Running AutoDock Vina (PyRx) on ASL Slurm Cluster

A guided walkthrough for running AutoDock Vina molecular docking workloads through the ASL Slurm environment.

PyRx is a virtual screening environment built around AutoDock Vina, OpenBabel, and visualization tools. On the cluster, the core components are packaged in Singularity containers for large-scale docking runs.

Required input files

Use this section as a training checklist before submitting a practice or real docking job.

File	Description
receptor.pdbqt	Target protein in .pdbqt format
ligand.pdbqt	Molecule or ligand to dock in .pdbqt format
conf.txt	Configuration file for Vina parameters

Example configuration file

This sample can be used in workshops, classroom demonstrations, or self-study exercises.

receptor = receptor.pdbqt
ligand = ligand.pdbqt

center_x = 10
center_y = 10
center_z = 10

size_x = 20
size_y = 20
size_z = 20

num_modes = 9
exhaustiveness = 8

out = output.pdbqt

Training CPU job script

This example script can be used as a teaching template for a first submission on the ASL Slurm cluster.

#!/bin/bash
#SBATCH --job-name=docking_cpu
#SBATCH --output=output_cpu.log
#SBATCH --ntasks=1
#SBATCH --time=01:00:00
#SBATCH --mem=4G
#SBATCH --partition=ASL-cpu

singularity exec /home/containers/pyrx_components.sif vina --config conf.txt

Training steps: submit, monitor, and check output

sbatch pyrx_cpu_job.slurm
squeue -u $USER
cat output_cpu.log
ls output.pdbqt

Advanced training workflow

An extended vina_split_and_run.slurm example splits ligands with OpenBabel, submits a Slurm array, and writes per-task output and log files — useful as advanced training material.

Reference image