AutoDock-vina
- Siwakorn Sukharom
Analytics
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 |
|---|---|
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.