Mohammad al-Attar if you already know which residues belongs to the binding site, you can extract the coordinates for those residues by using PyMOL:

1- open your receptor.pdb

2-select the residues that belong to the binding site

3-type in the command input area:

centerofmass sel

this will give you the center of mass of your selection and you can use it for defining the center of your box when using autodock-vina

4-save the selection:

File--Save Molecule (select the row that contains the word "sele")--OK

hope this helps!

There are several ways to obtain this information, a couple of quick ones:

In Windows, you may use PyRx or autodock tools (ADT) to obtain the binding site location.

In Linux, you could use ADT or a script from OpenGrowth ("CenterOfMolecule.exe").

Or you could use Chimera (for both Windows/Linux) to define a centroid for ligand atoms (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html) and get said coordinates in the ReplyLog.

Hope this helps

You can use AUTODOCK Software to fix active sites and get x,y,z coordinates of the same based on your grid box size

Mario E. Valdés-Tresanco Would you by any chance know how to get the XYZ size as well as the coordinates for a ligand binding site using PyMOL?

Thank you in anticipation of your help :)

@Ellie Edwards you can check AMDock, a program to assist docking with Vina and Autodock4... This is probably exactly what you are looking for

https://github.com/Valdes-Tresanco-MS/AMDock-win/wiki/4.2.3-Centered-on-residue(s)-using-AutoDock-Vina

Mario E. Valdés-Tresanco I am so grateful for you getting back to me! This is exactly what I needed, thank you so much! :) I really appreciate your help