AutoDock Vina is an open-source program for doing molecular docking. The authors suggest that AutoDock Vina significantly improves the average accuracy of the binding mode predictions compared to AutoDock 4.

Documentation

AutoDock Vina home
AutoDock Vina documentation

Slurm script

The data and commands are taken from the AutoDock Vina documentation site. ADFR and meeko were not used for data prep.

#!/bin/bash
#SBATCH --job-name=vina
#SBATCH --time=1:00:00
#SBATCH --partition=norm
#SBATCH --ntasks=8
#SBATCH --mem=4GB
module load autodock_vina
vina --receptor 1iep_receptor.pdbqt --ligand 1iep_ligand.pdbqt --config 1iep_receptor_vina_box.txt \
    --exhaustiveness=32 --out 1iep_ligand_vina_out.pdbqt --cpu ${SLURM_NTASKS}