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

AutoLigand                                          July 2011                                      AUTOLIGAND(1)