Autodock Vina Tutorial | Molecular Docking

Command:
./vina --receptor receptor.pdbqt --ligand ligand.pdbqt --config config.txt --exhaustiveness=32 --out rec_lig.pdbqt --num_modes=20 --spacing 1.000 --verbose 2 --scoring vina

[@user-dv6uw5nl5g]

I can say that you have helped me a lot to understand both Autodock4 and Autodock vina properly. Thank you. now that I am able to run sucessfully in both programs. I would be happy if you can say a bit on the effect of spacing and the size for x, y, z values in the grid box settings

[@BioinfoCopilot]

Effect of spacing is an utmost important factor in determining the best binding poses. Typical grid point spacing varies from 0.2 to 1.0A, and the default is 0.375A (roughly a quarter of the length of a carbon-carbon single bond). Each point within the grid map stores the potential energy of a 'probe' atom or functional group that is due to all the atoms in the macromolecule. x y z points are simply a human readable or I should say visual help to set up a box. These are just points to correctly place the box. The important factor is search space which is defined in Angstrom.

[@michael_kzn]

If I understood Vina manual right, you make mistake with grid box size. In Vina the size_x, size_y, size_z should be given in Angstrom. Your size_x value is 126, so even if you choose spacing 0.583, the grid box will be 126x126x126 A^3 that is much higher than protein size. So when you select grid box in AutoDockTools program for Vina, you need to set spacing to 1.0. In this case, the cube that you see in the program window will correspond to the actual search space in Vina.

[@alfredakinlalu8230]

This has been a problem I've been facing, thanks for this comment!

[@user-kh2fs5cn3u]

Hi, great video! I noticed that the affinity scores in each run were different (you had around -5.5, then -7.1 and finally -6.4) why is that? Thank you

[@BioinfoCopilot]

Thank you 🙏🏼! It depends on the scoring parameters e.g scoring=vina or the default one and conformational search space! Read the documentation of vina. The scorings that you get are absolute values. So do not depend on those values rather see the trend and conformations. Then validate with MD simulation. So, my suggestion would be not to rely on absolute values. It is based on manual inspection that which conformation is the best.

[@vclibgar5]

Thank you very much for the video!! Do you know if in catalina version is facing some problems with Vina instalation?

[@BioinfoCopilot]

Thank you! Yes, I have shown in my video how to install vina on Catalina OS. Its a security concern but can be resolved by giving permission. Check 8:55 time point onwards.

[@phuochuynh1777]

Thank you, How can i create the .log file to save energy?

[@BioinfoCopilot]

From the terminal itself or you can specify log file output during execution of vina

[@BioinfoCopilot]

vina --receptor receptor.pdbqt --ligand out1.pdbqt --config conf.txt > my.log

[@phuochuynh1777]

@@BioinfoCopilot thank you so much sir

[@aasthagarg5396]

please show the docking for batch ligands

[@BioinfoCopilot]

Will make a video soon!