SYNOPSISIt 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
DESCRIPTIONautoligand 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
AUTHORSRodney M. Harris and colleagues at The Scripps Institute, San Diego, California