vina(1) docking small molecules against proteins



--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):

display usage summary
display usage summary with advanced options
display program version