After adding hydrogen atoms,

add kollman charge to the protein receptor

and then check totals on Residues.

finally, spread that evenly on protein.

Now your receptor has charge information and is ready and can be saved as

pdbqt format.

You have to treat the ligand seperately if you are planning to use protein-ligand complex as receptor. As in case of Ligand Gastieger huckel charges are used.

Also I wanted to know if the protonotation state of molecules should be checked before docking in a docking study? Yes.

Fore an accurate docking score you have to generate the protonation state of molecules by providing the pH at which your receptor is crystalized.

@ Kiran Lokhande

Could you please explain what would be the next steps after generation of protonotation state of molecules? Where and what necessary changes should be made (if any needed) during the docking process?

Before docking, ligands must be prepared to create 3-dimensional geometries, assign proper bond orders, and generate accessible tautomer and ionization states prior to virtual screening. The interactions between a ligand and a target protein can be significantly affected as a result of tautomerism and ionization, potentially having a direct impact when identifying new hits for a given receptor. Hence, the enumeration of the tautomeric and protonation (ionization) states are an important step in in-silico drug discovery tasks such as virtual screening.

Your next step is, resulting output (ligand library) need to docked with your interested receptor.

Please read this article: Article Novel B, C-ring truncated deguelin derivatives reveals as po...

Tanuj Sharma

It would be very helpful for me if you explain briefly on how to " TREAT THE LIGAND SEPARATELY" when using protein-ligand complex as the target for docking in autodock.

I could successfully dock a ligand to a receptor protein but failed when i tried using protein-ligand complex as the receptor.