Did you try to google "youtube autodock virtual screening"?

Problem is that most these videos on YouTube does not cover virtual screening for multiple compounds (like he is wiling to screen a whole library). Most of them only try to demonstrate how Vina works by taking example of a single molecule. In your case, first you need to know how you can download compounds from ZINC because become it's a bit tricky now and then you will need some script to automate the process for you will be dealing with n number of compounds. People in RG have already shared PERL/bash scripts for automating Vina. You can search through RG. If you still face any problem please let us know in the comment section.

Regards

That's why you have to include "Virtual Screening" amongst the search terms

One of the first hits says "100 Ligands virtual screening" on the title slide

https://www.youtube.com/watch?v=tFFxNTvvoJI

Annemarie Honegger Abu Turab Naqvi thank you so much for your help.

Could you please share the link to this script?

you can do it using linux as a bash script, but the easier way is to use a tool like pyrx on windows. Check this link:

https://www.youtube.com/watch?v=2t12UlI6vuw&t=740s

Thank you Amira Alakhdar . I tried it but when I tried to make some amino acids as flexible residues it stopped working.

Is there a solution to this?

I don't have a solution unfortunately, but Pyrx stopped working for no reason several times when I was working with it. I would just restart the program and start over.

Which script?

This is a bash script to loop through multiple ligands with vina:

https://github.com/Bioinformatics-Review/Virtual-Screening-files/blob/master/vina_vs.sh

Annemarie Honegger Ma'am there is a problem with this script. There should be ./vina --config conf_vs.txt --ligand $f --out ${b}/out.pdbqt --log ${b}/log.txt in the vina command.

Exactly, in my answer to https://www.researchgate.net/post/vina_command_not_found_error_in_virtual_screening_using_autodock_vina, I mentioned that you would have to either add the path to vina to the PATH variable, or to use the explicit path.

You can try using Raccoon to convert all the ligands to pdbqt format. Then used vina_vs.sh, that somebody else hace recommended to you. I don't understand pretty well your doubts about this script.