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AutoDock

AutoDock is a suite of automated docking tooks designed to predict how small molecules, such as drug candidates, bind to a receptor site of a known 3D structure. We have both AutoDock 4 and AutoDockTools (a GUI interface for working with autodock) installed.

  • Version: 4.2.5.1
  • Machines: All clusters
  • Location: /uufs/chpc.utah.edu/sys/pkg/autodock/std

For ADT, we have version MGLtools version 1.5.6 installed.

In addition to Autodock 4, we also have an installation of Autodock Vina, which is a new generation of docking software from the Molecular Graphics Lab. It is reported to achieve significant improvements in the average accuracy of the binding mode predictions, while also being up to two orders of magnitude faster than AutoDock 4. Because the scoring functions used by AutoDock 4 and AutoDock Vina are different and inexact, on any given problem, either program may provide a better result.

  • Version: 1.1.2
  • Machines: All clusters
  • Location: /uufs/chpc.utah.edu/sys/pkg/autodock/autodock_vina_1_1_2_linux_x86/bin

Information on Autodock 4:

To get details of the functionality of AutoDock along with access to the User's Guide and Tutorial go to www.scripps.edu/mb/olson/doc/autodock/index.html. See autodock.scripps.edu/faqs-help/tutorial/using-autodock-4-with-autodocktools for links to tutorials.

To Use:

 

module load autodock

To start the AutoDockTools interface issue the command adt &

Note – you can start AutoDockTools on the frisco nodes using FastX and, if on frisco5 or frisco6, also using vglrun. See the FastX page  FastX documentation page for usage information. 

Information on Autodock Vina:

Detailed infromation on Autodock Vina can be found at http://vina.scripps.edu/

Last Updated: 3/9/17