AutoDock scripts prepare_ligand4.py and prepare_receptor4.py are used to prepare the corresponding .pdqt files that will be used as input for AutoDock Vina scorer.
If we use these scripts with deafult repair/cleanup options, problems appear with the actualization of coordinates in "_update_pdbqt_coordinates" method, because the order/number of is not necessarily the same after the repairs/cleanups. So:
No repairs nor cleanups will be performed on ligand/receptor molecules, so the user has to take into account that provided .mol2 or .pdb files have correct atom types and correct structure (including Hydrogen atoms that will be taken into account in the docking evaluation). Otherwise, AutoDock errors/warnings could appear (e.g. ValueError: Could not find atomic number for Lp Lp)
Gasteiger charges will be added during the preparation of the .pdbqt files.
All torsions of the ligand will be marked as inactive for AutoDock, because torsion changes are part of GaudiMM genes.
New test mol2 files and a fixed testcase file are provided.
prepare_ligand4.py
andprepare_receptor4.py
are used to prepare the corresponding .pdqt files that will be used as input for AutoDock Vina scorer.ValueError: Could not find atomic number for Lp Lp
)inactive
for AutoDock, because torsion changes are part of GaudiMM genes.