ospool
path software_examples/drug_discovery/tutorial-AutoDockVina/README.md

Running a Molecule Docking Job with AutoDock Vina

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 the OSPool.

Tutorial Files

It is easiest to start with the git clone command to download the materials for this tutorial. Type:

$ git clone https://github.com/OSGConnect/tutorial-AutoDockVina

This will create a directory tutorial-AutoDockVina. Change into the directory and look at the available files:

$ cd tutorial-AutoDockVina
$ ls
$ ls data/

You should see the following:

data/
    receptor_config.txt  # Configuration file (input)
	receptor.pdbqt       # Receptor coordinates and atomic charges (input)
	ligand.pdbqt         # Ligand coordinates and atomic charges (input)
logs/					 # Empty folder for job log files
vina_job.submit          # Job submission file
vina_run.sh     	     # Execution script

We need to download the AutoDock program separately into the this directory as well. Go to the AutoDock Vina website and click on the Download link at the top of the page. This will then lead you to the GitHub Downloads page. Download the Linux x86_64 version of the program; you can do this directly to the current directory by using the wget command and the download link. If you use the -O option shown below, it will rename the program to match what is used in the rest of the guide.

$ wget https://github.com/ccsb-scripps/AutoDock-Vina/releases/download/v1.2.5/vina_1.2.5_linux_x86_64 -O vina

Once downloaded, we also need to give the program executable permissions. We can test that it worked by running vina with the help flag:

$ chmod +x vina
$ ./vina --help

Files Need to Submit the Job

The file vina_job.submit is the job submission file and contains the description of the job in HTCondor language. Specifically, it includes an "executable" (the script HTCondor will use in the job to run vina), a list of the files needed to run the job (shown in "transfer_input_files"), and indications of where to write logging information and what resources and requirements the job needs.

Change needed: If your downloaded program file has a different name, change the name in the transfer_input_files line below.

executable = vina_run.sh

transfer_input_files    = data/, vina
should_transfer_files   = Yes
when_to_transfer_output = ON_EXIT

output        = logs/job.$(Cluster).$(Process).out
error         = logs/job.$(Cluster).$(Process).error
log           = logs/job.$(Cluster).$(Process).log

request_cpus   = 1
request_memory = 1GB
request_disk   = 512MB

queue 1

Next we see the execution script vina_run.sh. The execution script and its commands are executed on a worker node out in the Open Science Pool.

Change needed: If your vina program file has a different name, change it in the script below:

#!/bin/bash

# Run vina
./vina --config receptor_config.txt \
	 --ligand ligand.pdbqt --out receptor-ligand.pdbqt

Submit the Docking Job

We submit the job using condor_submit command as follows

$ condor_submit vina_job.submit

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

$ condor_q

After job completion, you will see the output file receptor-ligand.pdbqt.

Next Steps

After running this example, you may want to scale up to testing multiple molecules or ligands.

What to Consider

• Decide how many docking runs you want to try per job. If one molecule can be tested in a few seconds, you can probably run a few hundred in a job that runs in about an hour.
• How should you divide up the input data in this case? Do you need individual input files for each molecule, or can you use one to share? Should the molecule files all get copied to every job or just the jobs where they're needed? You can separate groups of files by putting them in separate directories or tar.gz files to help with this.
• Look at this guide to see different ways that you can use HTCondor to submit multiple jobs at once.

If you want to use a different (or additional) docking programs, you can include them in the same job by downloading and including those software files in your job submission.

Example of Multiple Runs

Included in this directory is one approach to analyzing multiple ligands, by submitting multiple jobs. For the given files we are assuming that there are multiple directories with input files we want to run (run01, run02, run03, etc.) and each job will process all of the ligands in one of these "run" folders.

In the script, vina_multi.sh, we had added a for loop in order to process all the ligands that were included with the job. We will also place those results into a single folder to make it easier to organize them back on the access point:

#!/bin/bash

# Make a directory for results
mkdir results

# Run vina on multiple ligands
for LIGAND in *ligand.pdbqt
do 
./vina --config receptor_config.txt \
	 --ligand ${LIGAND} --out results/receptor-${LIGAND}
done

Note that this for loop assumes that all of the ligands have a naming scheme that we can match using a wildcard (the * symbol).

In the submit file, we have added a line called transfer_output_files to transfer back the results folder from each job. We have also replaced the single input directory data with a variable inputdir, representing one of the run directories. The value of that variable is set via the queue statement at the end of the submit file:

executable = vina_multi.sh

transfer_input_files    = $(inputdir)/, vina
transfer_output_files   = results

# ... other job options

queue inputdir matching run*

Getting Help

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