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

AUTHORS

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