In your pdb files there are lines where the atom name is "Ap". Please correct this error and upload your protein again.
pharmaco19 wrote:
I was trying to upload my protein and gave me this error message
Traceback (most recent call last):
File "tools/prepare_receptor4.py", line 168, in ?
delete_single_nonstd_residues=delete_single_nonstd_residues)
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 520, in __init__
version=version, delete_single_nonstd_residues=delete_single_nonstd_residues)
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 120, in __init__
self.repairMol(mol, self.repair_type_list)
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 161, in repairMol
self.newHs = self.addHydrogens(mol)
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 174, in addHydrogens
HB.addHydrogens(mol)
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/MolKit/hydrogenBuilder.py", line 61, in addHydrogens
babel.assignHybridization(mol.allAtoms)
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/PyBabel/atomTypes.py", line 127, in assignHybridization
a.babel_atomic_number = self.get_atomic_number(a.babel_type)
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/PyBabel/atomTypes.py", line 102, in get_atomic_number
raise ValueError( "Could not find atomic number for %s %s"%
ValueError: Could not find atomic number for Ap Ap
my proteine name 1GL3_M0_P0_site