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.

AutoDock Vina does not require choosing atom types and pre-calculating grid maps for them. Instead, it calculates the grids internally, for the atom types that are needed, and it does this virtually instantly.

Autodock Vina is apart of the Autodock Suite, along with:

AutodockCrankPrep

Autodock & Autodock-GPU

• Autodock Vina website at Scripps
• Autodock Vina on Github

• Module Name: AutodockVina (see the modules page for more information)
• AutodockCrankPrep is also loaded with Autodock Vina (seeAutodockCrankPrep )
• AutodockVina is multithreaded.
• The mgltools package that is used to create input files for Vina is also installed. When you load the Autodock or AutodockVina modules, you will also get access to the mgltools executables.
• If you wish to run the mgltools Python scripts you may need to use the pythonsh command available when you load the module. This will ensure your environment is properly set up.
• mgltools is a graphics-intensive package, and can easily be installed/run on your desktop system for better performance. It can be downloaded here.
• The entire PDB (updated once a week) database is available in /pdb on all nodes, the Biowulf login node, and Helix.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=8
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load AutodockVina
[+] Loading AutoDockVina  1.2.5
[+] Loading singularity  4.0.1  on cn3144
[+] Loading AutodockCrankprep  1.0  on cn3144
[user@cn3144 ~]$ module list

Currently Loaded Modules:
  1) singularity/4.0.1   2) AutodockCrankprep/1.0   3) AutodockVina/1.2.5

[user@cn3144 ~]$ vina --config conf.txt --cpus $SLURM_CPUS_PER_TASK

#################################################################
# If you used AutoDock Vina in your work, please cite:          #
#                                                               #
# O. Trott, A. J. Olson,                                        #
# AutoDock Vina: improving the speed and accuracy of docking    #
# with a new scoring function, efficient optimization and       #
# multithreading, Journal of Computational Chemistry 31 (2010)  #
# 455-461                                                       #
#                                                               #
# DOI 10.1002/jcc.21334                                         #
#                                                               #
# Please see http://vina.scripps.edu for more information.      #
#################################################################

Output will be ligand_out.pdbqt
Reading input ... done.
Setting up the scoring function ... done.
Analyzing the binding site ... done.
Using random seed: 653328095
Performing search ...
0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
done.
Refining results ... done.

mode |   affinity | dist from best mode
     | (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
   1        -12.3      0.000      0.000
   2        -10.1      5.153      9.937
   3         -9.6      5.800      9.437
   4         -9.5      5.027     10.364
Writing output ... done.

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. autodock.sh). For example:

#!/bin/bash
module load Autodock
autodock4 -p myfile.dpf -l myfile.dlg 

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] autodock.sh

Create a swarmfile (e.g. myfile.swarm). For example:

cd /data/$USER/mydir;  autodock4 -p lig1.macro.def -l lig1.log
cd /data/$USER/mydir;  autodock4 -p lig2.macro.def -l lig2.log
cd /data/$USER/mydir;  autodock4 -p lig3.macro.def -l lig3.log
cd /data/$USER/mydir;  autodock4 -p lig4.macro.def -l lig4.log
[...]

Submit this job using the swarm command.

swarm -f myfile.swarm [-g #] --module Autodock