Overview

AutoDock Vina is a molecular docking program useful for computer aided drug design. In this tutorial, we will learn how to run AutoDock Vina on OSG. We have a separate tutorial for screening a library of several ligands.

Tutorial files

It is easiest to start with the tutorial command. Type:

$ tutorial AutodockVina ### Creates "tutorial-AutodockVina" directory with input, job submission and execution script files

This will create a directory tutorial-AutodockVina. Inside the directory, you will see the following files

receptor_config.txt   # Configuration file (input)
receptor.pdbqt        # Receptor coordinates and atomic charges (input)
ligand.pdbqt          # Ligand coordinates and atomic charges (input)
vina_job.submit       # Job submission file
vina_wrapper.bash     # Execution script

We discuss the details of vina_job.submit and vian_wrapper.bash files. To see how to prepare the input files, receptor_config.txt, receptor.pdbqt and ligand.pdbqt, check the AutoDock website.

Job execution and submission files

The file vina_job.submit is the job submission file and contains the description of the job in HTCondor language.

Universe = vanilla             # The Universe defines an execution environment for Condor 
Executable = vina_wrapper.bash # Executable is either a binary or a shell wrapper script

transfer_input_files = receptor_config.txt, receptor.pdbqt, ligand.pdbqt  # Input files transfred to the worker machine
should_transfer_output_files = Yes    # Transfers all the output files
when_to_transfer_output = ON_EXIT   # File transfers are performed on exit 
output        = job.out.$(Process)             # Standard output from your job goes in this file
error         = job.error.$(Process)           # Standard error from your job goes in this file
log           = job.log.$(Process)             # Status of your job is logged in this file
requirements = (HAS_CVMFS_oasis_opensciencegrid_org =?= TRUE) # Check the availability of OASIS on remote worker machine
Queue 1        # The above job descriptions are send to the queue

Next we see the execution wrapper vina_wrapper.bash. The execution wrapper and its inside content are executed in the remote worker machine.

#!/bin/bash           ### Shell interpreter.
module load autodock  # Sets up the environment (such as path of the binary, libraries ..etc) to run autodock vina.
vina --config receptor_config.txt --ligand ligand.pdbqt --out receptor-ligand_output.pdbqt --log receptor-ligand.log   # Execution of vina with input and output files as arguments.

Running the simulation

We submit the job using condor_submit command as follows

$ condor_submit vina_job.submit # Submit the condor job script "vina_job.submit"

Now you have submitted the AutoDock Vina job on the OSG. The present job should be finished quickly (less than 10 mins). You can check the status of the submitted job by using condor_q command as follows:

$ condor_q username # The status of the job is printed on the screen. Here, username is your login name.

After job completion, you will see the output files receptor-ligand_output.pdbqt and receptor-ligand.log in your work directory.

Getting Help

For assistance or questions, please email the OSG User Support team at user-support@opensciencegrid.org or visit the help desk and community forums.

 

This page was updated on Sep 02, 2015 at 14:45 from tutorials/tutorial-VinaAutodock/README.md.