Tutorial

Account Creation & Finding the Application

  1. Visit the TACC portal account request page to request an account.
  2. Once approved, login to the UTRC Portal.
  3. Navigate to Applications -> Simulation -> AutoDock Vina v1.2.3.

Submitting a Job

First upload a .pdb or .pdbqt protein receptor file to your TACC storage system work directory from the "Data Files" tab. Then, select the protein file in this box.
Choose a ligand library from the drop down list. Use the "Test-set" library first to make sure your job is working with the inputs as expected before proceeding to the larger libraries. More information on each library can be found in our FAQ.
Specify the X-Y-Z coordinate grid-center for the search area. This must be located inside of the uploaded protein receptor. Units are in Angstroms. Use comma-separated values with no spaces in between.
Specify the search area box's X-Y-Z bounds. Units are in Angstroms. Use comma-separated values with no spaces in between. NOTE: The larger the box size, the longer the job will take to run - be conservative with box size.
Choose how many of the top scoring molecules to be returned (maximum: 1000).
Choose the Lonestar6 compute queue to run your job on. Recommended "development" for the Test-set library and "normal" for all other libraries.
Specify the maximum runtime. Try to choose a time that will allow enough time for the job to finish, with a little extra on top. If your job does not finish by this time, it will exit and no results will be returned. However, a higher maximum runtime may cause your job to wait longer in the queue. Suggested runtimes:
Ligand Library Suggested Max Runtime
Test-set 10 minutes
ZINC-in-trials 4 hours
ZINC-fragments 15 hours
Enamine-PC 8 hours
Enamine-AC 26 hours
Enamine-HTSC 26 hours

Note that these suggested times give a ~2 hour buffer on top of our internal benchmark times for each library and using a 22x22x22 Angstrom box. Given different input parameters (especially box size), these times may need to be significantly adjusted for your job.

Input the exact number of processors and nodes required, depending on the ligand library. You must input based on the table below, or your job will fail. Note that Processors on Each Node is always set to 32.
Ligand Library Processors on Each Node Node Count
ZINC-in-trials 32 1
ZINC-fragments 32 1
Enamine-PC 32 1
Enamine-AC 32 3
Enamine-HTSC 32 10
Default values can be used in the other boxes. Press the "Submit" button when ready.

How do I monitor my job's status?

Navigate to the UTRC Portal -> Log in -> History

How do I retrieve my job's output?

There are two ways:

  1. Navigate to the UTRC Portal -> Log in -> History -> Select the link for your job under the Output Location column.
  2. Navigate to the Output Location on your TACC Storage System that you specified when submitting the job.

How do I view my results interactively?

The user may also choose to visualize their resulting output file utilizing the ChimeraX application on TACC's Lonestar6 supercomputer. To run the application, the user must submit a job using the University of Texas Research Cyberinfrastructure (UTRC) system. A virtual DCV session will be initialized for the user, and a document titled 'ChimeraX_dcvserver.txt' will be created in the user's work folder with connection instructions. Once connected, the University of California San Francisco (UCSF) ChimeraX software will begin running, and a Tapis jobs archive folder will be created on the desktop for the user's convenience. The user may then use the ChimeraX program to open the file containing the top scoring docked ligands.