After selecting the residues of the protein for flexible docking, when I click on "Choose Torsions In Currently Selected Residues", under the " Flexible Residues" tab, I get this error:
prot:A:MET1:HN1 and prot:A:MET1:HN1 have the same coordinates
ERROR *********************************************
Traceback (most recent call last):
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\ViewerFramework\VF.py", line 941, in tryto
result = command( *args, **kw )
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\autoflexCommands.py", line 369, in doit
map(self.setAutoFlexFields, flex_residues)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\autoflexCommands.py", line 414, in setAutoFlexFields
rotatables = rbs.select(bondlist)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\MolKit\bondSelector.py", line 534, in select
rotatable = BondOrderBondSelector().select(bnds,1)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\MolKit\bondSelector.py", line 507, in select
atype.assignHybridization(allAts)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\PyBabel\atomTypes.py", line 137, in assignHybridization
self.valence_two()
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\PyBabel\atomTypes.py", line 266, in valence_two
angle1 = bond_angle(k.coords, a.coords, l.coords)
File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\PyBabel\util.py", line 47, in bond_angle
raise ZeroDivisionError("Input used:", a, b, c)
ZeroDivisionError: ('Input used:', [2.015, -1.769, 0.66], [2.015, -1.769, 0.66], [2.015, -1.769, 0.66])
Is there a way to solve this problem?
Have you looked at your pdb file in a text editor and in a molecular viewer? Potential sources of this error are - alternative conformation, multiple chains with the same chain label, duplication in your residue selection. Have a close look at the N-terminal residue of chain A to get to the source of the problem.
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