- Docking Simulation 139
centerz=−2.5
sizex=10
sizey=10
sizez=10
energyrange = 4
exhaustiveness = 16
Modify the fields when needed.
VIII. Run Autodock Vina by (assume the configuration file is saved to
myConfig.conf)
vina --config myConfig.conf
Docking will be finished soon ifexhaustivenessis not set too high.
IX. The result will be stored inoutput.pdbqtor where you specify in
‘out’field of the configuration file. Please open it with your text
editor.
X. After browsing the whole file, you may note thatvinawill give some
(usually more than one) poses, and sorted by binding energy from low
to high. (Since higher binding energy means that the binding mode is
not stable, thus may not be preferred).
From the result file, you can see a line like the following:
REMARK VINA RESULT: −6.6 0.000 0.000
The number marked with underline (−6.6 here) is binding energy. In
most cases, you can just use the first model (pose) in the result pdbqt
file without caring about others, since it will be the one with lowest
binding energy.
The lower the binding energy is, the better the pose is.XI. If you want to view the result in your molecular editor, please load the
structure and the result file into the same view.
In PyMol, use the following commands to view the binding:
load protein.pdbqt, target
load result.pdbqt, ligands- Running docking simulation with SwissDock (Fig. 6)
SwissDock is a docking web service provided by Swiss Institute of
Bioinformatics. It can automatically setup input protein and ligand for
the user.