Applications Environment/autodock
AUTODOCK
Description: AutoDock is 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.
Additional Notes: Current distributions of AutoDock consist of two generations of software: AutoDock 4 and AutoDock Vina. The latter is a new generation of docking software from the Molecular Graphics Lab. It achieves significant improvements in the average accuracy of the binding mode predictions, while also being up to two orders of magnitude faster than AutoDock 4.1.
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.
Please note that preparing the input files for AutoDock 4 require use of Autodock tool set. The use of the later is not described in this document.
Availability: PENZIAS and ANDY
Module file: autodock
Limitations: AutoDock is distributed freely under the GNU GPL for all to use. AutoDock Vina is available under the Apache license, allowing commercial and non-commercial use and redistribution.
Citation: Include in published paper the following citation regarding use of:
AutoDock: Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S. and Olson, A. J. (2009)- Autodock4 and AutoDockTools4: automated docking with selective receptor flexiblity. J. Computational Chemistry 2009, 16: 2785-91.
- Morris, G. M., Goodsell, D. S., Halliday, R.S., Huey, R., Hart, W. E., Belew, R. K. and Olson, A. J. (1998), Automated Docking Using a Lamarckian Genetic Algorithm and and Empirical Binding Free Energy Function J. Computational Chemistry, 19: 1639-1662.
- AutoDock Vina: O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010) 455-461
Documentation:
http://autodock.scripps.edu/faqs-help/manual/autodock-4-2-user-guide
Tutorials: http://autodock.scripps.edu/faqs-help/tutorial
Related Packages:
- Pardock
- ICM
- SwissDock
Use: Load module file.
module load autodock
Example: Autodock example requires several files, which are prepared Autodock tool set and placed in /share/apps/autodock/default/example/in directory. Upon running the example the files from this directory must be copied in a user directory by the command:
cp /share/apps/autodock/default/example/in/* .
Below is given an example of job submitting script. Please note that installed version of Autodock is a serial program, so the fields <cpus> and <chunks> must have value of 1. The file aq.dpf below is called docking parameter file and is generated by themkgpf3 and mkdpf3 programs, which are part of Autodock tool set.
PENZIAS or ANDY
#!/bin/bash #SBATCH -- autodock_test #SBATCH -- partition production #SBATCH -- select=<chunks> #SBATCH -- tasks=<cpus> # Explicitly change to the working directory cd $SLURM_SUBMIT_DIR # generate atomic maps autogrid4 -p aq.gpf -l output_mapGeneration.glg # execute autodock autodock4 -p aq.dpf -l output_autodock.dlg #------------------------------ echo "*** Job is done! ***"