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ccsb-scripps / AutoDock-Vina

AutoDock Vina
http://vina.scripps.edu
Apache License 2.0
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Multiple-ligand docking pose PDBQT cannot be (re)scored #327

Open rwxayheee opened 1 week ago

rwxayheee commented 1 week ago

Not working with binary and Python API. Might be due to the multiple appearances of ROOT keyword in a PDBQT pose containing multiple fragments

File ~/micromamba/envs/meeko_eco/lib/python3.10/site-packages/vina/vina.py:182, in Vina.set_ligand_from_file(self, pdbqt_filename)
    179         raise TypeError('Error: Vina requires a PDBQT file for the ligand.')
    181 if len(pdbqt_filename) == 1:
--> 182     self._vina.set_ligand_from_file(pdbqt_filename[0])
    183 else:
    184     self._vina.set_ligand_from_file(pdbqt_filename)

File ~/micromamba/envs/meeko_eco/lib/python3.10/site-packages/vina/vina_wrapper.py:710, in Vina.set_ligand_from_file(self, *args)
    709 def set_ligand_from_file(self, *args):
--> 710     return _vina_wrapper.Vina_set_ligand_from_file(self, *args)

TypeError: 

PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
 > ROOT
rwxayheee commented 1 week ago

A walkaround to this at the moment is to read individual PDBQT files.