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Error Message trying to convert PDB to PDBQT
http://mgl.scripps.edu/forum/viewtopic.php?f=31&t=2965
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Author:  soccerguy282 [ Thu Jun 04, 2015 1:58 pm ]
Post subject:  Error Message trying to convert PDB to PDBQT

Could someone tell me what this error message indicates? i.e. how can i fix the pdb files so that raccoonn will convert them successfully to pdbqt? Thanks


Error: 1
<type 'exceptions.ValueError'> Exception in Tk callback
Function: <function openReceptorDir at 0x0466F9B0> (type: <type 'function'>)
Args: ()
Traceback (innermost last):
File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\Pmw\Pmw_1_3\lib\PmwBase.py", line 1747, in __call__
return apply(self.func, args)
File "raccoon.py", line 2284, in openReceptorDir
genPDBQTrec(file, output_file)
File "raccoon.py", line 2435, in genPDBQTrec
delete_single_nonstd_residues=delete_single_nonstd_residues)
File "C:\Program Files (x86)\MGLTools-1.5.6\AutoDockTools\MoleculePreparation.py", line 560, in __init__
version=version, delete_single_nonstd_residues=delete_single_nonstd_residues)
File "C:\Program Files (x86)\MGLTools-1.5.6\AutoDockTools\MoleculePreparation.py", line 143, in __init__
self.addCharges(mol, charges_to_add)
File "C:\Program Files (x86)\MGLTools-1.5.6\AutoDockTools\MoleculePreparation.py", line 229, in addCharges
chargeCalculator.addCharges(mol.allAtoms)
File "C:\Program Files (x86)\MGLTools-1.5.6\MolKit\chargeCalculator.py", line 80, in addCharges
babel.assignHybridization(atoms)
File "C:\Program Files (x86)\MGLTools-1.5.6\Lib\site-packages\Updates\nightly_2013_08_30\PyBabel\atomTypes.py", line 136, in assignHybridization
self.valence_three()
File "C:\Program Files (x86)\MGLTools-1.5.6\Lib\site-packages\Updates\nightly_2013_08_30\PyBabel\atomTypes.py", line 230, in valence_three
angle2 = bond_angle(k.coords, a.coords, m.coords)
File "C:\Program Files (x86)\MGLTools-1.5.6\Lib\site-packages\Updates\nightly_2013_08_30\PyBabel\util.py", line 53, in bond_angle
else: angle = (math.acos(cos_theta)) * RAD_TO_DEG
<type 'exceptions.ValueError'>: math domain error

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