Autodock Vina 1.2.5

1
2
3
4

$ which vina
/local/cluster/bin/vina
$ vina --version
AutoDock Vina 616d6c8-mod

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54

$ vina --help
AutoDock Vina 616d6c8-mod

Input:
  --receptor arg             rigid part of the receptor (PDBQT)
  --flex arg                 flexible side chains, if any (PDBQT)
  --ligand arg               ligand (PDBQT)
  --batch arg                batch ligand (PDBQT)
  --scoring arg (=vina)      scoring function (ad4, vina or vinardo)

Search space (required):
  --maps arg                 affinity maps for the autodock4.2 (ad4) or vina
                             scoring function
  --center_x arg             X coordinate of the center (Angstrom)
  --center_y arg             Y coordinate of the center (Angstrom)
  --center_z arg             Z coordinate of the center (Angstrom)
  --size_x arg               size in the X dimension (Angstrom)
  --size_y arg               size in the Y dimension (Angstrom)
  --size_z arg               size in the Z dimension (Angstrom)
  --autobox                  set maps dimensions based on input ligand(s) (for
                             --score_only and --local_only)

Output (optional):
  --out arg                  output models (PDBQT), the default is chosen based
                             on the ligand file name
  --dir arg                  output directory for batch mode
  --write_maps arg           output filename (directory + prefix name) for
                             maps. Option --force_even_voxels may be needed to
                             comply with .map format

Misc (optional):
  --cpu arg (=0)             the number of CPUs to use (the default is to try
                             to detect the number of CPUs or, failing that, use
                             1)
  --seed arg (=0)            explicit random seed
  --exhaustiveness arg (=8)  exhaustiveness of the global search (roughly
                             proportional to time): 1+
  --max_evals arg (=0)       number of evaluations in each MC run (if zero,
                             which is the default, the number of MC steps is
                             based on heuristics)
  --num_modes arg (=9)       maximum number of binding modes to generate
  --min_rmsd arg (=1)        minimum RMSD between output poses
  --energy_range arg (=3)    maximum energy difference between the best binding
                             mode and the worst one displayed (kcal/mol)
  --spacing arg (=0.375)     grid spacing (Angstrom)
  --verbosity arg (=1)       verbosity (0=no output, 1=normal, 2=verbose)

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