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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 open science grid (OSG).  We have a separate tutorial for screening a library of several ligands.

Autodock Vina tutorial files

It is easy to start with the "tutorial" command. In the command prompt, type

 

This will create a directory “tutorial-VinaAutodock". Inside the directory, you will see the following files

 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 at Scripps Research Institute

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. 

The job description is expressed in key-value(s) pair.  For example, the key is "Universe" and the value is "vanilla". The key "transfer_input_files" can have more than one value. 

 

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

Running the simulation

We submit the job using "condor_submit" command as follows

 

Now you have submitted the autodock vina job on the open science grid. 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

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

References

  1. Autodock Vina  Details about Vina Autodock

  2. OSG  QuickStart.   Getting started with the Open Science Grid (OSG).

  3. Condor Manual.    Manual for the high throughput condor (HTCondor)  software to schedules the jobs on OSG. 

For further assistance or questions, please email connect-support@opensciencegrid.org.

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