Summary
Source: http://autodock.scripps.edu/
License: AutoDock 4 is free and is available under the GNU General Public License. AutoDock Vina is available under the Apache license, allowing commercial and non-commercial use and redistribution
Path: /opt/autodock
Documentation: http://autodock.scripps.edu/faqs-help
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. Current distributions of AutoDock consist of two generations of software: AutoDock 4 and AutoDock Vina. AutoDock 4 actually consists of two main programs: autodock performs the docking of the ligand to a set of grids describing the target protein; autogrid pre-calculates these grids. In addition to using them for docking, the atomic affinity grids can be visualised. This can help, for example, to guide organic synthetic chemists design better binders. AutoDock Vina does not require choosing atom types and pre-calculating grid maps for them. Instead, it calculates the grids internally, for the atom types that are needed, and it does this virtually instantly. Also available is a graphical user interface called AutoDockTools, or ADT for short, which amongst other things helps to set up which bonds will treated as rotatable in the ligand and to analyze dockings.
Using autodock
autodock, vina and related tools can be started via the full path. To initialize the environment use the module command:
[elx]% /opt/autodock/bin/adt # start the autodock gui [elx]% module avail [schluenz@it-aptb4 repos]$ module help md ----------- Module Specific Help for 'md' ------------------------- This module sets the environment for Molecular Dynamics and Modelling - VMD - Autodock4 & Autodock VINA - MGLtools [elx]% module load md # be aware: it add a python 2.5 to your PATH! Make sure to unload the module or start a fresh shell after you're done! [elx]% which vina /opt/autodock/bin/vina