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AUTODOCK(1) General Commands Manual AUTODOCK(1)


vina - docking small molecules against proteins



rigid part of the receptor (PDBQT)
flexible side chains, if any (PDBQT)
ligand (PDBQT)

Search space (required):

X coordinate of the center
Y coordinate of the center
Z coordinate of the center
size in the X dimension (Angstroms)
size in the Y dimension (Angstroms)
size in the Z dimension (Angstroms)

Output (optional):

output models (PDBQT), the default is chosen based on the ligand file name
optionally, write log file

Misc (optional):

the number of CPUs to use (the default is to try to detect the number of CPUs or, failing that, use 1)
explicit random seed
proportional to time): 1+
maximum number of binding modes to generate
maximum energy difference between the best binding mode and the worst one displayed (kcal/mol)

Configuration file (optional):

the above options can be put here

Information (optional):

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


AutoDock Vina home page on

November 2010 AutoDock Vina 1.1.1 (Apr 20, 2010)