Hi, i have added the parameter of Mercury (Hg2+) " atom_par Hg 2.71 0.385 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding Mercury" in the AD4_parameters.dat file in Autodock 4.2 but still coud not prepare the ligand as I did successfully with gold (Au+). For Au prep, i clicked:

Read molecule > Gold.pdb > Open

Ligand > Input > Choose > Gold.pdb > OK

Ligand > Output > Save as PDBQT > Save

For mercury, it when error when i clicked ligand> input> Choose>Mercury.pdb and it popped up

Mercury: :UNL1:HG and Mercury: :UNL1:HG have the same coordinates

ERROR *********************************************

Traceback (most recent call last):

File "/home/zakwan/MGLTools-1.5.6/MGLToolsPckgs/ViewerFramework/VF.py", line 898, in tryto

result = command( *args, **kw )

File "/home/zakwan/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/autotorsCommands.py", line 867, in doit

initLPO4(mol, cleanup=cleanup)

File "/home/zakwan/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/autotorsCommands.py", line 292, in initLPO4

root=root, outputfilename=outputfilename, cleanup=cleanup)

File "/home/zakwan/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 1019, in __init__

detect_bonds_between_cycles=detect_bonds_between_cycles)

File "/home/zakwan/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 779, in __init__

detectAll=self.detect_bonds_between_cycles)

File "/home/zakwan/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 1798, in __init__

self.__classifyBonds(molecule.allAtoms, allow_guanidinium_torsions)

File "/home/zakwan/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 1836, in __classifyBonds

dict =self.dict = ADBC.classify(mol.allAtoms.bonds[0])

File "/home/zakwan/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/AutoDockBondClassifier.py", line 58, in classify

rotatables = self.d['rotatable'].select(bonds)

File "/home/zakwan/MGLTools-1.5.6/MGLToolsPckgs/MolKit/bondSelector.py", line 535, in select

rotatable = BondOrderBondSelector().select(bnds,1)

File "/home/zakwan/MGLTools-1.5.6/MGLToolsPckgs/MolKit/bondSelector.py", line 508, in select

atype.assignHybridization(allAts)

File "/home/zakwan/MGLTools-1.5.6/MGLToolsPckgs/PyBabel/atomTypes.py", line 137, in assignHybridization

self.valence_two()

File "/home/zakwan/MGLTools-1.5.6/MGLToolsPckgs/PyBabel/atomTypes.py", line 266, in valence_two

angle1 = bond_angle(k.coords, a.coords, l.coords)

File "/home/zakwan/MGLTools-1.5.6/MGLToolsPckgs/PyBabel/util.py", line 47, in bond_angle

raise ZeroDivisionError("Input used:", a, b, c)

ZeroDivisionError: ('Input used:', [-1.7549999999999999, 8.5790000000000006, 14.122], [-1.7549999999999999, 8.5790000000000006, 14.122], [-1.7549999999999999, 8.5790000000000006, 14.122])

Can somebody help me? Attached is the file of Mercury 3D conformer from pdb and i converted it into pdb file from sdf by using babel.