DOKK / manpages / debian 12 / autodock-vina / vina.1.en

General Commands Manual

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.

November 2010

AutoDock Vina 1.1.1 (Apr 20, 2010)