Hi Caroline,

AutoDock Vina can generate only the ligand conformations in a search area of a protein. So you need to open a protein structure in PyMOL prior to open your Vina's results.

Caroline Jilbert

Hi

Autodock Vina only provide the ligand confirmation during dock with macromolecule. After completing docking, you open path folder and open .pdbqt file of macromolecule in PyMOL and then same workspace open ligand.out file. One more thing is very important if you wanna see the interaction between macromolecule and ligand so you have to go tool bar right side select on action of all go to preset and select cartoon so you can see interaction between them first pose will be the lowest binding energy which showed through docking.

Thank you so much Waseem Ahmad Ansari, I have tried using the preset and now I can see the binding between my macromolecules and ligand with the lowest binding energy.

Dear, First upload protein molecule on Pymol then upload vina complex then you can see interaction at bond length.

https://www.youtube.com/watch?v=6zuNyy5umJc

Dear Caroline Jilbert,

Autodock Vina output consists of all possible ligand orientations of ligand only. So you have to open Autodock Vina output and docked protein structure in the same PyMOL window to have the complex.