AutoDock
AutoDock: Documentation
AutoDock 3.0.5
The AutoDock 3.0.5 User Guide is available online in HTML format here,
and can also be downloaded in Gnu-zipped PostScript format.
Linux Users:
Pierre Scotney has written a HOWTO
on compiling AutoDock 3.0 under RedHat 6.0 GNU Linux , and is available
at his web site. Remember that Linux sets a limit to the stacksize
of 8MB by default. This is too small for AutoDock (and other programs)
and causes a "segmentation fault" to occur immediately after reading in
a ligand with the "move"
command. The solution is to add this line to your ".cshrc",
".bashrc" or ".tcshrc"
file, whichever is appropriate for your default shell:
limit stacksize unlimited
Then make sure you source your ".{c,ba,tc}shrc"
file before trying to run "autodock3".
AutoDock 2.4
Here is the PDF
version of the user guide. You will need either the Adobe Acrobat Reader,
or the Amber plug-in for Netscape, both available from Adobe's
web-site. You can jump directly to the Acrobat
downloading page.
The HTML
version of the AutoDock 2.4 User Guide can be read here, but it is
based on a conversion by "Quadralay WebWorks HTML Lite 1.5.1" (part of
FrameMaker 5) which does not convert tables, equations, figures, symbols,
superscripts and subscripts. There may be equations and figures missing.
Trajectory Format
You can find more information about trajectories and formats here.
Getting Started
Here is a very brief summary of steps to get started.
-
[Version 3: add solvation parameters to the protein using "addsol".]
-
Create your AutoGrid and AutoDock parameter files. There are scripts to
help you do this.
-
Run AutoTors on the ligand to be docked. Define any torsions here.
-
Run AutoGrid to pre-calculate the grid maps for AutoDock.
-
Run AutoDock.
AutoDock
