NAME

       autogrid - preparing protein and ligand for AutoDock analysis

SYNOPSIS

       autogrid4 [options] -p gridparameterfile

DESCRIPTION

       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.
       See   http://autodock.scripps.edu/faqs-help/faq/where-do-i-set-the-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.

OPTIONS

       -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

EXAMPLE

       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 hsg1_no_receptor_types.glg

       This  command prepares grid map files for each of the AutoDock atom types specified in the grid parameter
       file  (in  this  case:  hsg1_sm.A.map,  hsg1_sm.C.map,  hsg1_sm.d.map,   hsg1_sm.e.map,   hsg1_sm.HD.map,
       hsg1_sm.NA.map,   hsg1_sm.N.map,   hsg1_sm.OA.map),   the   AVS   field   file   (hsg1_sm.maps.fld)   and
       hsg1_sm.maps.xyz. 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.

SEE ALSO

       autodock(1), runAdt(1).
       http://autodock.scripps.edu

LICENSE

       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
       http://autodock.scripps.edu/downloads.

AUTHOR

       The most prominent author of the version 4 of  AutoDock  is  G.  Morris  <garrett@scripps.edu>.  See  the
       AUTHORS file in /usr/share/doc/autogrid for details.

       This  manual page was written by Steffen Moeller <moeller@debian.org> 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)