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)