AutoDock README $Id: README,v 1.14 2014/07/17 18:07:42 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 parent directory.  The compilation of "autogrid" 
depends on certain files in the "../autodock" directory.

You must install "autoconf" and "automake" if they are not already
installed on your computer.  Both are from the Free Software Foundation's
Autotools system, available at
http://www.gnu.org/software/autoconf
and
http://www.gnu.org/software/automake
On many Linux systems you can do this by running
  sudo apt-get (or yum) install autoconf automake

To generate a `configure' file, you need to run 'autoreconf -i'
in first the autodock, and then the autogrid directory;
You will need autoconf version 2.62 or later.
Proceed to the next section, "Building AutoDock from source tar
File", omitting the download and unzipping step.


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.

We suggest creating subdirectories within each of "autodock" and "autogrid"
to do the compilations in.  We suggest naming them after the computer
architecture and operating system, which we abbreviate as 'ARCHOSV'.

For ARCHOSV, 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 following these patterns:
  i86Linux2 : 32-bit Intel Linux
  x86_64Linux2 : 64-bit Intel Linux
  MacOSX : Mac OS X PPC or Intel
  i86Windows : Microsoft Windows Intel
  sun4SunOS5 : SPARC Solaris

The general process is:

  First, build autodock:

 "cd" to autodock source directory
 "autoreconf -i"  [ optional, see below: "Modifying AutoDock and AutoGrid" ]
 "mkdir" and "cd" to your architecture's build directory (such as x86_64Linux3)
 ../configure    (* see below)
 make
    On Microsoft Windows when building for MINGW within Cygwin, 
    you need to type here:   rm .deps/*; ../configure
    to run "configure" a second time for reasons we do not understand.
 make check  (optional but recommended, requires "python")
 make install (optional, this will install autodock4 executable)

 Second, in the src/autogrid directory, do the same steps 
 to configure, build, and install autogrid4.

 "cd" to autogrid source directory
 "autoreconf -i"  [ optional, see below: "Modifying AutoDock and AutoGrid" ]
 "mkdir" and "cd" your architecture's build directory (such as x86_64Linux3)
 ../configure  (* see below)
 make
 make check 
 make install (optional)

 * On Mac OS X, you can instead use "../configure-universalDarwin"
   if you wish to compile a "universal binary" for PPC/Intel 32/64 bit
   as appropriate for your OS X version.

Troubleshooting Compilations
=============================

 If "autoreconf -i" hangs or runs very slowly with messages:
    autom4te: cannot lock autom4te.cache/requests with mode 2: Input/output error
  this is caused by building on a remote-mounted NFS file system
  that does not support certain kinds of file locking.  You can
  either wait for the autoreconf to finish (if it does) or do the
  autoreconf on the NFS host computer, where the files are local.

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

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


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

If you want to build in a custom parameter file to be used
as the default, such as for a new atom type "K", add your
parameters to the end of AD4.1_bound.dat and save as (for example)
/home/myusername/AD4.1_bound_plusK.dat

In the autodock source directory, edit Makefile.am the same way (about line 646)
from
csh $(srcdir)/paramdat2h.csh $(srcdir)/AD4_parameters.dat $(srcdir)/AD4.1_bound.dat > $@
to
csh $(srcdir)/paramdat2h.csh $(srcdir)/AD4_parameters.dat /home/myusername/AD4.1_bound_plusK.dat > $@

run "autoreconf -i; cd $ARCHOSV; ../configure;  make"
where $ARCHOSV is your computer type, such as "i86Linux2"


In the autogrid source directory, edit Makefile.am and change the line (about line 159)
csh $(srcdir)/../autodock/paramdat2h.csh $(srcdir)/../autodock/AD4_parameters.dat  $(srcdir)/../autodock/AD4.1_bound.dat > $@
to
csh $(srcdir)/../autodock/paramdat2h.csh  $(srcdir)/../autodock/AD4_parameters.dat /home/myusername/AD4.1_bound_plusK.dat > $@
and again run "autoreconf; cd $ARCHOSV; ../configure;  make"


Modifying AutoDock and AutoGrid
=============================

Please feel free to change the programs to suit your needs.
If you have suggestions for improvements, please email us.


If you add source files you will need to modify Makefile.am to include any
new source files.  If you add source files or change the dependencies
of one source file upon another, you will need to generate a new 'configure'
file (for AutoDock or for AutoGrid), using 'autoreconf' as above.

