I want to dock a protein with a chemical ligand that is already docked from another program (MAESTRO), I made a PDB file with the protein and the ligand (as HETATM) and want to dock it to a receptor but HADDOCK doesn’t recognize the chemical ligand in the first molecule. Is there a way to do this?
I want to dock a protein with a chemical ligand that is already docked from another program (MAESTRO), I made a PDB file with the protein and the ligand (as HETATM) and want to dock it to a receptor but HADDOCK doesn’t recognize the chemical ligand in the first molecule. Is there a way to do this?
Are you using the web server?
Define “HADDOCK doesn’t recognise the chemical ligand”?
What is exactly the problem?
Yes, I’m using the web server
This is what happens when I upload the PDB file with the ligand and protein, and then in the docking the ligand is not in the structure
The ligand is the X 
Did you actually tried a full docking and checked if the ligand is present at the end?
Thank you very much for your time, indeed the ligand is there. I just didn’t see it in the preview but is present in the final docking