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.
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
vian_wrapper.bash files. To see how to prepare the input files,
ligand.pdbqt, check the AutoDock website.
Job execution and submission files
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.log in your work directory.
This page was updated on Sep 02, 2015 at 14:45 from tutorials/tutorial-VinaAutodock/README.md.