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| AUTODOCK(1) |
General Commands Manual |
AUTODOCK(1) |
NAME¶
vina - docking small molecules against proteins
DESCRIPTION¶
- --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
- --help
- display usage summary
- --help_advanced
- display usage summary with advanced options
- --version
- display program version
