debian man page for vina

AUTODOCK(1)						      General Commands Manual						       AUTODOCK(1)

NAME
       vina - docking small molecules against proteins

DESCRIPTION
   Input:
       --receptor arg
	      rigid part of the receptor (PDBQT)

       --flex arg
	      flexible side chains, if any (PDBQT)

       --ligand arg
	      ligand (PDBQT)

   Search space (required):
       --center_x arg
	      X coordinate of the center

       --center_y arg
	      Y coordinate of the center

       --center_z arg
	      Z coordinate of the center

       --size_x arg
	      size in the X dimension (Angstroms)

       --size_y arg
	      size in the Y dimension (Angstroms)

       --size_z arg
	      size in the Z dimension (Angstroms)

   Output (optional):
       --out arg
	      output models (PDBQT), the default is chosen based on the ligand file name

       --log arg
	      optionally, write log file

   Misc (optional):
       --cpu arg
	      the number of CPUs to use (the default is to try to detect the number of CPUs or, failing that, use 1)

       --seed arg
	      explicit random seed

       --exhaustiveness arg (=8) exhaustiveness of the global search (roughly
	      proportional to time): 1+

       --num_modes arg (=9)
	      maximum number of binding modes to generate

       --energy_range arg (=3)
	      maximum energy difference between the best binding mode and the worst one displayed (kcal/mol)

   Configuration file (optional):
       --config arg
	      the above options can be put here

   Information (optional):
       --help display usage summary

       --help_advanced
	      display usage summary with advanced options

       --version
	      display program version

SEE ALSO
       AutoDock Vina home page on http://vina.scripps.edu.

AutoDock Vina 1.1.1 (Apr 20, 2010)				   November 2010						       AUTODOCK(1)