AutoDock-vina

AutoDock Vina is one of the fastest and most widely used open-source docking engines. It is a turnkey computational docking program that is based on a simple scoring function and rapid gradient-optimization conformational search.

Official Website: https://github.com/ccsb-scripps/AutoDock-Vina

updated : 17 July 2023

Available Version

Version	Module name

Version	Module name
1.2.5	AutoDock-vina/1.2.5

1. Input file

The basic input files for running AutoDock Vina on Lanta are its own inputs (see more on https://autodock-vina.readthedocs.io/en/latest/index.html ) and a job submission script.

2. Job submission script

create a script using vi submit.sh command and specify the following details depending on computational resources you want to use.

#!/bin/bash -l
#SBATCH -p compute                    # select the partition
#SBATCH -N 1                          # Number of nodes
#SBATCH --cpus-per-task=16            # Number of CPU cores per task
#SBATCH -t 2:00:00                    # Wall-time limit
#SBATCH -A ltXXXXXX                   # Account
#SBATCH -J autodock_vina              # Job name

##Module Load##
module purge
module load AutoDock-vina

##Run Vina###
vina --cpu $SLURM_CPUS_PER_TASK --receptor 1iep_receptor.pdbqt --ligand 1iep_ligand.pdbqt \
       --config 1iep_receptor_vina_box.txt \
       --exhaustiveness=32 --out 1iep_ligand_vina_out.pdbqt

The script above using compute partition (-p compute), 1 node (-N 1) with 16 CPU cores per task (--cpus-per-task=16). The account is set to ltXXXXXX (-A ltXXXXXX) that is subjected to change to your own account.

3. Job submission

using sbatch submit.sh command to submit the job to the queuing system.