Repository revision
9:90ea16534012

Repository 'autodock_vina'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina

VINA Docking tool metadata
Miscellaneous
VINA Docking
tool to perform protein-ligand docking with Autodock Vina
docking
toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/1.2.3+galaxy0
1.2.3+galaxy0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/1.2.3+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/1.1.2+galaxy0
toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/0.3.0
toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/0.2.1
toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/0.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/0.1.0
docking
Requirements (dependencies defined in the <requirements> tag set)
name version type
vina 1.2.3 package
python 3.9 package
openbabel 3.1.1 package
parallel 20211022 package
Functional tests
name inputs outputs required files
Test-1 receptor: protein.pdbqt
ligands: input_ligands.sdf
config_params|box: box.txt
protein.pdbqt
input_ligands.sdf
box.txt
Test-2 receptor: protein.pdbqt
ligands: input_ligand.pdbqt
config_params|box: box.txt
protein.pdbqt
input_ligand.pdbqt
box.txt
Test-3 receptor: protein.pdbqt
ligands: input_ligand.pdbqt
config_params|box: box.txt
settings|scoring: vinardo
settings|num_modes: 20
settings|min_rmsd: 0.5
settings|energy_range: 5
protein.pdbqt
input_ligand.pdbqt
box.txt
Test-4 receptor: protein.pdbqt
ligands: input_ligand.pdbqt
config_params|center_x: 36.454
config_params|center_y: -43.608000000000004
config_params|center_z: 75.176
config_params|size_x: 18.768
config_params|size_y: 10.205999999999996
config_params|size_z: 15.521999999999991
config_params|exh: 10
config_params|seed|seed_value: 8
config_params|seed|seed: True
config_params|config_params: vals
protein.pdbqt
input_ligand.pdbqt
Test-5 receptor: protein_rigid.pdbqt
ligands: input_ligands.sdf
flex: protein_flex.pdbqt
config_params|center_x: 15.2
config_params|center_y: 53.9
config_params|center_z: 16.9
config_params|size_x: 20
config_params|size_y: 20
config_params|size_z: 20
config_params|exh: 10
config_params|seed|seed_value: 8
config_params|seed|seed: True
config_params|config_params: vals
output: pdbqt
protein_rigid.pdbqt
input_ligands.sdf
protein_flex.pdbqt