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 OSG.
It is easiest to start with the
tutorial command. Type:
$ tutorial AutoDockVina
This will create a directory
tutorial-AutodockVina. Change into the directory and look at the available files:
$ cd tutorial-AutoDockVina $ ls
You should see the following:
receptor_config.txt # Configuration file (input) data/ 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 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. Download the Linux 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 tar file to match what is used in the rest of the guide.
$ wget http://vina.scripps.edu/download/autodock_vina_1_1_2_linux_x86.tgz -O autodock_vina.tar.gz
Files Need to Submit the Job¶
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 download software tar.gz file has a different name, change the name in the
transfer_input_files line below.
executable = vina_wrapper.bash transfer_input_files = data/, receptor_config.txt, autodock_vina.tar.gz should_transfer_files = Yes when_to_transfer_output = ON_EXIT output = job.$(Cluster).$(Process).out error = job.$(Cluster).$(Process).error log = job.$(Cluster).$(Process).log requirements = (OSGVO_OS_STRING == "RHEL 7") request_cpus = 1 request_memory = 512MB request_disk = 512MB queue 1
Next we see the execution wrapper
vina_wrapper.bash. The execution wrapper and its inside content are executed on a worker node out in the Open Science Pool. The first two commands will unzip the file containing the AutoDock Vina program and make it accessible on the command line; we can then run a typical vina command.
Change needed: If your download tar.gz file has a different name, change it in the
script below, in the
tar command. You will also need to change the name of the
AUTODOCK_FOLDER to match whatever folder appears when you un-tar the downloaded tar.gz file.
1 2 3 4 5 6 7 8 9 10 11 12 13
Running the simulation¶
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 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
After job completion, you will see the output files
receptor-ligand.log in your work directory.
After running this example, you may want to scale up to testing multiple molecules or ligands. Some good starting points for this include:
- 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.