AutoGrid README $Id: README,v 1.4 2009/05/29 20:53:16 rhuey Exp $


What is AutoDock?
=================

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.

AutoDock 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.

We have also developed 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.

AutoDock has applications in:

    X-ray crystallography; 
    structure-based drug design; 
    lead optimization; 
    virtual screening (HTS); 
    combinatorial library design; 
    protein-protein docking; 
    chemical mechanism studies.


Installing AutoGrid
===================

Make sure you checkout both "autodock" and "autogrid" at the same 
time and into the same directory.  The compilation of "autogrid4" 
depends on files in the "../autodock" directory, specifically:

    ../autodock/autocomm.h
    ../autodock/paramdat2h.csh
    ../autodock/AD4.1_bound.dat

By default, AutoDock 4.2 uses the AD4.1_bound.dat parameter file,
so AD4.1_compact.dat and AD4.1_extended.dat would not be used,
but if "../autodock/paramdat2h.csh" is changed to use either of
these scoring functions, then either of these other two ".dat"
files would become necessary:

    ../autodock/AD4.1_compact.dat
    ../autodock/AD4.1_extended.dat


Bootstrapping Installation
==========================

The CVS repository does not include the 'configure' file;  this
is used to create a Makefile that is platform-specific.

To generate the `./configure' file, it is necessary to run 'autoreconf -i'.
Once this file has been generated, read the INSTALL file in this directory 
for more information, this will explain how to use './configure' to create 
the necessary Makefile and how to use it to make the executables.


Copying AutoDock
================

Please refer to the file "COPYING" in this directory for
more information on copying AutoDock.
