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AutoDock

AutoDock is a suite of automated docking tools 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 http://autodock.scripps.edu/. 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

vglrun -c proxy adt &

 Note - the node you do this on must have a video card supporting the graphics.  Please use one fo the notchpeak, kingspeak or frisco interactive nodes.

 

Information on Autodock Vina:

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

Last Updated: 6/10/21