Autodock

Using Autodock Vina

Autodock is a docking engine used to simulate the binding of molecules.

Using Autodock Vina with salloc

Vina is a version of Autodock available on the cluster. It requires the use of the Meeko and Autogrid4 dependencies, which should be present when the module is loaded in:

salloc #specify your own parameters if necessary
module load gnu12 python autodock/vina-1.2.3

To simulate basic docking, Autodock Vina requires a receptor file in .pdb format and a ligand in .pdb or .sdf format

Before Vina will simulate docking, both the receptor and the ligand need to be prepared. As part of the tutorial, a receptor file called 1iep_receptorH.pdb and a ligand file called 1iep.sdf are used. Both can be found here. Other .pdb files can be found at RSCB Protein Data Bank.

#receptor preparation
mk_prepare_receptor.py -i 1iep_receptorH.pdb -o 1iep_receptor -p -v -g --box_size 20 20 20 --box_center 15.190 53.903 16.917

#ligand preparation
mk_prepare_ligand.py -i 1iep_ligand.sdf -o 1iep_ligand.pdbqt

Now Docking can occur:

vina --receptor 1iep_receptor.pdbqt --ligand 1iep_ligand.pdbqt --config 1iep_receptor.box.txt --exhaustiveness=32 --out 1iep_ligand_vina_out.pdbqt

Output is in the form of 1iep_ligand_vina_out.pdbqt

Using Autodock Vina with Slurm

The above process can be put into a Slurm file:

#!/bin/bash

#Submit this script with: sbatch thefilename

#SBATCH --job-name=my_job   ##name that will show up in the queue
#SBATCH --output=/scratch/%u/%x-%N-%j.out   ##filename of the output
#SBATCH --error=/scratch/%u/%x-%N-%j.err   ##filename of the error output
#SBATCH --nodes=1  ##number of nodes to use
#SBATCH --ntasks=1  ##number of tasks to run
#SBATCH --time=0-00:01:00  ##time for analysis (day-hour:min:sec)
#SBATCH --cpus-per-task=1  ##the number of threads the code will use
#SBATCH --mem=2GB  ##memory allocation per node
#SBATCH --partition normal  ##the partition to run in


## Commands to Load Modules:
module load gnu12
module load autodock/vina-1.2.3


## Load modules, insert code, and run your programs here.
cd your_working_directory

mk_prepare_receptor.py -i 1iep_receptorH.pdb -o 1iep_receptor -p -v -g --box_size 20 20 20 --box_center 15.190 53.903 16.917

mk_prepare_ligand.py -i 1iep_ligand.sdf -o 1iep_ligand.pdbqt

vina --receptor 1iep_receptor.pdbqt --ligand 1iep_ligand.pdbqt --config 1iep_receptor.box.txt --exhaustiveness=32 --out 1iep_ligand_vina_out.pdbqt

More documentation about the capabilities of Autodock Vina can be found here