Protein docking with two ligands, then confusion regarding the output of pdb file results

HADDOCK
1

Hello,

I attempted to perform a simultaneous docking of a protein with ligand A and ligand B using HADDOCK 2.4. I successfully generated the results from HADDOCK. However, when I examined the 3D structure, I found that the two ligand molecules shown in the pdb file were both ligand A. I’m certain that I added two different ligands. Could you please tell me how I should modify my input to obtain the 3D structure diagram of the protein-ligand docking with the two different molecules?

Warm regards

Boson

2

In HADDOCK, one molecule only has one chain. So if the ligand was part of the protein it will have inherited its chainID.