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       autodock - docking of chemical ligands to protein receptors


       autodock4 [options]


       AutoDock  perfoms  the  automated  docking  of  chemical  compounds  to
       proteins, i.e. it predicts how small molecules, such as  substrates  or
       drug candidates, bind to a receptor of known 3D structure.

       The  AutoDockSuite  consists  of  two  main  programs of which AutoDock
       performs the docking of the ligand to a set  of  grids  describing  the
       target protein and AutoGrid pre-calculates these grids.


       -p     parameter_filename

       -l     log_filename

       -o     Use old PDBQ format, charge q in columns 55-61

       -k     Keep original residue numbers

       -i     Ignore header-checking

       -t     Parse the PDBQ file to check torsions, then stop.

       -c <   command_file Command mode, by file

       -c |   control_program Command mode, by control_program


       On  Debian,  the  directory  /usr/share/doc/autodock offers examples to
       run. Change to that directory and unpack  (as  root)  the  gzipped  map
       files, then execute AutoDock as shown below:
       gunzip *.map.gz
       autodock4 -p 1pgp.dpf -l /tmp/1pgp.dlg

       The  interpretation  of  results  is  aided by the AutoDockTools suite.
       Please also inspect the tutorials offered online.


       autogrid(1), runAdt(1).


       This  software  is  made  available  under  the terms of the GNU Public
       License version 2 or later. This implies  that  this  software  may  be
       redistributed  if  the  source is made available. It would however help
       the future development of the AutoDockSuite if you register yourself at


       The  most  prominent  author  of the version 4 of autodock is G. Morris
       <>. See the AUTHORS file in  /usr/share/doc/autodock
       for details.

       This  manual  page was written by Steffen Moeller <>,
       for the Debian project (but may be used  by  others  and  is  hopefully
       adopted by the upstream developers).

                                 Juli 23, 2007                     AUTODOCK(1)