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       autogrid - preparing protein and ligand for AutoDock analysis


       autogrid4 [options] -p gridparameterfile


       AutoGrid   prepares  a  3D  grid  representation  of  the  non-covalent
       interaction energies that various user-specified ligand atom types will
       experience  around a user-specified target macromolecule.  In addition,
       the electrostatic potential and desolvation free energy grid  maps  may
       also  be calculated.  The grid maps are stored in plain text files with
       the extension  ’.map’  and  are  required  by  AutoDock  4  to  perform
       dockings.   AutoGrid  also  outputs  a  ’.xyz’ file which describes the
       spatial extents of the grid box, and an AVS  field  ’.fld’  file  which
       describes  the  consistent  set  of atomic affinity grid maps that were
       calculated together for a  given  target  macromolecule.  Note:  it  is
       necessary  to compute grid maps for all the atom types in the ligand or
       set of ligands that  will  be  docked,  as  well  as  an  electrostatic
       potential grid map and a desolvation free energy map. For example, if a
       ligand has an aliphatic carbon  and  a  hydrogen-bond-accepting  oxygen
       atom,  it would be necessary to compute both a ’C’ map and an ’OA’ map.
       autodock-4-force-field-parameters for more information about AutoDock 4
       atom types.

       The  input  to  AutoGrid  is  best  prepared  with  the  program  suite
       AutoDockTools.  There is no way to run autodock4 without a grid.


       -o Use old PDBq format (q in columns 55-61)

       -u     Usage information, also -h on Debian.

       -d     Increased verbosity of messages to help debugging.

       -l     logfile

       -p     filename Specifies Grid Parameter File


       A range of tests is made available with the AutoGrid sources that can
       be used as follows:
       $ D=/usr/share/doc/autogrid/Tests
       $ cd /tmp
       $ ln -s $D/AD4_parameters.dat .
       $ gunzip -c $D/hsg1_sm.pdbqt.gz > hsg1_sm.pdbqt
       $ autogrid4 -p $D/hsg1_no_receptor_types.gpf -l

       This  command  prepares  grid  map  files for each of the AutoDock atom
       types  specified  in  the  grid   parameter   file   (in   this   case:,,,,,,,, the AVS
       field  file  (hsg1_sm.maps.fld)  and  To perform the
       cocking calculation, AutoDock should be executed, though it  demands  a
       separate  docking  parameter  file  (with  extension  .dpf).  The ’DPF’
       refers to the grid map files that are  necessary  to  the  docking  and
       allows  the  setting  of other important parameters, such as the search
       method and how many dockings to perform.


       autodock(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/autogrid
       for details.

       This  manual  page  was written by Steffen Moeller <>
       and much revised by upstream author Garrett Morris.   It  was  prepared
       for  the  Debian  project  but  may  be used by others and is hopefully
       adopted by the upstream developers.

                                 Juli 23, 2007                     AUTOGRID(1)