AutoDock is a a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. AutoDock has applications in X-ray crystallography, structure-based drug design, lead optimization, etc.
Availability and Restrictions
Versions
AutoDock and AutoDock-GPU are available on the Pitzer and Owens Clusters. The versions currently available at OSC are:
| AutoDock | Owens | Pitzer |
|---|---|---|
| 4.2.6 | X | X |
| AutoDock-GPU | Owens | Pitzer |
|---|---|---|
| 1.5.2 | X | X |
You can use module spider autodock and module spider autodock-gpu to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.
Access for Academic Users
Use of AutoDock is open to all OSC users. Please contact OSC Help for any questions.
Publisher/Vendor/Repository and License Type
Center for Computational Structural Biology, Open source
Usage
Usage on Owens
Set-up on Owens
To load the default version of AutoDock module, use module load autodock/4.2.6. Alternatively to load the accelerated version of AutoDock4 with GPU, use module load autodock-gpu/1.5.2.
Running AutoDock
AutoDock executables can be run as documented in the AutoDock User Manual.
Usage on Pitzer
Set-up on Pitzer
To load the default version of AutoDock module, use module load autodock/4.2.6. Alternatively to load the accelerated version of AutoDock4 with GPU, use module load autodock-gpu/1.5.2.
Running AutoDock
AutoDock executables can be run as documented in the AutoDock User Manual.
Running AutoDock jobs with GPU
A GPU can be utilized for AutoDock. You can acquire a GPU for the job by
#SBATCH --gpus-per-node=1
for Owens, or Pitzer. If running with an OnDemand desktop, select a GPU node to launch the desktop on. For more detail, please read here.
For more information about GPU computing with AutoDock, please read AutoDock-GPU wiki.
Further Reading
