AutoDock README $Id: README,v 1.8 2013/03/07 22:21:46 mp 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.

Web site and email help for AutoDock Suite
===========================

 http://autodock.scripps.edu
 autodock@scripps.edu

Installing AutoDock
===================

The web site offers pre-compiled executables for several
popular computers and operating systems.  If you wish
to modify AutoDock or build it for other platforms, see
"Building AutoDock from Source Tar File" below.


Bootstrapping Installation from CVS
===================================
Make sure you checkout both "autodock" and "autogrid" at the same 
time and into the same directory.  The compilation of "autogrid" 
depends on certain files in the "../autodock" directory.

The CVS repository does not include the 'configure' file;  'configure'
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, see "From SOURCE Tar File" below,
and read the INSTALL file in this directory for more options.
This will explain how to use '../configure' to create 
the necessary Makefile and how to use it to make the executables.

After the 'cvs co autodock; cvs co autogrid' do:

 % cd autodock; autoreconf -i
 % cd ../autogrid; autoreconf -i

Then continue the installation "Building from Source Tar File".

Building AutoDock from source tar File
======================================

Download the "src" tar file from the web site.
Unzip the downloaded tar file into a directory of your choice;
this will create directories src/autodock and src/autogrid.

For ARCHOSV below, substitute your
computer type and operating system version, such as "i86Linux2".
You can use any name you like; nothing in the build process depends
on the name. We suggest:
  i86Linux2 : 32-bit Intel Linux
  x86_64Linux2 : 64-bit Intel Linux
  universalDarwin9 : Mac OS X 10.5 and 10.6 Intel or PPC
  universalDarwin11 : Mac OS X 10.7 and 10.8 Intel
  i86Windows : Microsoft Windows Intel
  sun4SunOS5 : SPARC Solaris

First, build autodock.

 % cd src/autodock
 % mkdir ARCHOSV
 % cd ARCHOSV
 % ../configure    (* see below)
 % make 

 # (on Microsoft Windows when building for MINGW within Cygwin, 
 #  you need to type here:   rm -rf .deps; ../configure
 #  to run "configure" a second time for reasons we do not understand)

 % make check   ( optional, recommended, requires "python")
 % make install
 
 This will create and install autodock4 executable.

Second, in the src/autogrid directory, do the same steps 
to configure, build, and install autogrid4.
 
 * On Mac OS X, use instead "../configure-universalDarwin"
   if you wish to compile a "universal binary" for PPC/Intel 32/64 bit
   as appropriate for your OS X version.

Configuration notes
==================

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 4.1 scoring functions, then either of these other two ".dat"
files would become necessary:

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


Copying AutoDock and AutoGrid
=============================

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