Hello!

I am studying the receptor-ligand interactions of the docking results I’ve generated using AutoDock Vina. I attempted to open 2 file types of my receptor-ligand complex and noticed that the 2D diagrams vary between the 2 file types. In my first attempt, I opened the PDBQT file of my protein, and then I opened the PDBQT file of my ligand in the same tab before I finally viewed their interactions and generated the 2D diagram of it. In my second attempt, I opened the PDB file of the receptor-ligand complex that I’ve generated through PyMOL, and then did the same succeeding procedures. When I compared the 2D diagrams of the two, they were not the same. Could you help me?

1. Is it okay to open PDBQT files in Discovery Studio? Can the program read this type of file without any errors?
2. Did I perhaps make a mistake in the definition of the receptor and the ligand for the receptor-ligand complex PDB file? If so, could you help me out on this?