vina - docking small molecules against proteins

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

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

       --ligand arg
              ligand (PDBQT)

   Searchspace(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)

   Configurationfile(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

       vina - docking small molecules against proteins

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

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