NAME

       AutoLigand: - identification of a receptor's ligand binding site

SYNOPSIS

       It  is  suggested  to  start  AutoLigand through the GUI that the autodocktools provide.
       autoligand r FileBaseName -p #_of_pts  The above is  a  simplification  provided  for  the
       Debian   package.   The   regular   command   line   invocation   is   through      python
       /usr/share/pyshared/AutoDockTools/AutoLigand.py -r FileBaseName -p #_of_pts

DESCRIPTION

       autoligand is a symbolic link to the Python  script  AutoLigand.py.  That  performs  a  an
       automated  investigation  of  the  likelihood of a particular part of a protein to bind to
       ligands.

              Description of command...

       -r FileBaseName = just the name part from receptor map files (i.e., FileBaseName.C.map)

       -p #_of_pts = number of fill points to use (int)

              Note: can be omitted if -a option used.

              Optional parameters:

              [-a #] = number of heavy atom for ligand (#_of_pts will be set to 6x atoms)  [-x  #
              -y # -z #] = optional x,y,z co-ords for starting fill (float)

              when starting point is input, only one fill will be run

              [-i # -j # -k #] = optional x,y,z co-ords for second point (float)

              when  second point is input, the fill will connect both points NOTE: the connection
              path has not been optimized - use with discretion

              [-f #] = number of fills to generate - default is 10  [-e] =  use  the  extra  atom
              types NA, N, SA, and A

              NOTE: these results can be problematic - use with discretion

              [-m] = make a movie of output fill progress

SEE ALSO

       A             tutorial             is            available            online            on
       http://autodock.scripps.edu/resources/autoligand/AutoLigand_tutorial.pdf

AUTHORS

       Rodney M. Harris and colleagues at The Scripps Institute, San Diego, California