Multiple ligand docking | dock 400 ligands using Autodock Vina

This tutorial presents step by step process for multiple ligand docking using autodock vina. Enjoy and learn.
#How to prepare 400 ligand files (smiles strings) into *.pdbqt format for multiple ligand docking
• How to prepare 400 lig...
#Link to essential files
bit.ly/3zi4F7z
#Extract top scores from 400 log output files
• Extract Top Scores fro...

[@amalzulkipli2248]

I learned a lot by following your channel, keep on sharing!

[@educont22]

Thank you for your encouraging words.

[@hrithikjain2789]

Awesome Video.... Thanks for help

[@themusicdoctor9796]

Thanks for informative tutorial.

[@FiifiAB]

Thanks @Bioinforphile for this excellent video. However, when I tried the step, I get to a point with an error saying "Error: could not open "conf_vs.txt" for reading. Can you help?

[@FiifiAB]

I've solved it. Working now. Thanks

[@educont22]

There may be an error in the file path. Please check.

[@RajashreeRJK]

how did u solve it can u help​@@FiifiAB

[@JungYoontae-dx5sm]

The conf_vs.txt does not contain the Spacing (anstrom). How can I add it and what is it basically set to? Thanks.

[@educont22]

In AutoDock Vina, the "Spacing" parameter in the configuration file (conf.txt) specifies the spacing (grid spacing) between grid points in the grid box used for docking. This parameter determines the resolution of the grid, which affects the accuracy and speed of the docking calculations. The default value used by AutoDock Vina is 1 Ångstrom. f the conf_vs.txt file generated by AutoDock Vina does not contain the Spacing parameter, you can add it manually to the configuration file (conf.txt). Typically, the Spacing parameter is set to a value between 0.375 Ångstrom and 1 Ångstrom. spacing = 1.0

[@70pradeepyadav5]

Output will be 10_out.pdbqt Detected 4 CPUs Reading input ... Error: could not open "receptor.pdbqt" for reading. i am getting this error kindly help me. what to do

[@balogunchristianah6734]

I keep getting the error ,command line parse error: unrecognized option. ‘-log’

[@70pradeepyadav5]

Getting error space volume > 2700 Angstrom 3 Could not open receptor. Pdbqt

[@educont22]

This part of the error message indicates that the software is encountering an issue related to the size of the search space volume specified for docking. AutoDock Vina has a limit on the size of the search space volume, and it seems that the specified volume exceeds this limit (which is set to 2700 Angstrom^3). You may need to adjust the size of your search space to be within this limit.