Unable to reproduce hydrated docking results. dry.py not removing water molecules.

ccsb-scripps / AutoDock-Vina

AutoDock Vina

http://vina.scripps.edu

Apache License 2.0

561 stars 199 forks source link

Unable to reproduce hydrated docking results. dry.py not removing water molecules. #258

Open enjamamulhoq opened 7 months ago

enjamamulhoq commented 7 months ago

I have followed the instructions from this tutorial: https://autodock-vina.readthedocs.io/en/latest/docking_hydrated.html. After implementing step 5, I get similar results for vina command but dry,py is not removing 5 water molecules. Its not working even if I use the files 1uw6_receptor.pdbqt, 1uw6_receptor.w.map, 1uw6_ligand_ad4_out.pdbqt from their solution files. Has anyone else faced this issue before?

rwxayheee commented 7 months ago

Hi, I never noticed this issue before. Changing if pdb_atom_type(entry) == "W": to if pdb_atom_type(entry) == "WAT": (2 instances in current dry.py) works for me, but I'm not entirely sure if that might have changed the original intent of this.

Edit: I made the changes based on the hydrated docking example in the meeko repository. In this hydrated ligand PDBQT, waters used to have W in columns 12-15