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)