The Molecular Graphics Laboratory Forum

I have a file of 48k smiles which I wish to screen. I used babel to convert to mol2 with 3D coords. It looks OK, displays properly. When I try to add the molecules to raccoon (or when I use prepare_ligand4.py, which is what I presume raccoon also does) I get the following error:

rwharper@rwharper-desktop:~/D3/docking$ prepare_ligand -l cdd_48k_30jun11b.mol2
setting PYTHONHOME environment
Traceback (most recent call last):
File "/home/rwharper/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py", line 195, in <module>
attach_nonbonded_fragments=attach_nonbonded_fragments)
File "/home/rwharper/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 942, in __init__
detect_bonds_between_cycles=detect_bonds_between_cycles)
File "/home/rwharper/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 692, in __init__
delete_single_nonstd_residues=False)
File "/home/rwharper/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 140, in __init__
self.addCharges(mol, charges_to_add)
File "/home/rwharper/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 226, in addCharges
chargeCalculator.addCharges(mol.allAtoms)
File "/home/rwharper/MGLTools-1.5.4/MGLToolsPckgs/MolKit/chargeCalculator.py", line 80, in addCharges
babel.assignHybridization(atoms)
File "/home/rwharper/MGLTools-1.5.4/MGLToolsPckgs/PyBabel/atomTypes.py", line 136, in assignHybridization
self.valence_three()
File "/home/rwharper/MGLTools-1.5.4/MGLToolsPckgs/PyBabel/atomTypes.py", line 229, in valence_three
angle1 = bond_angle(k.coords, a.coords, l.coords)
File "/home/rwharper/MGLTools-1.5.4/MGLToolsPckgs/PyBabel/util.py", line 48, in bond_angle
(a[2] - b[2]) * (c[2] - b[2]) ) / dist
ZeroDivisionError: float division
rwharper@rwharper-desktop:~/D3/docking$ ls

If this has already been addressed, I apologize.

Hi,

the error is from AutoDockTools that encountered a problem when trying to generate the corresponding PDBQT file.
Try to inspect the original file, or better, the the exact splitted mol2 and see if there are structure anomalies (i.e. wrong angles, too many hydrogens, etc..).
When you mention Babel, do you mean you generated the 3D coordinates with it starting from a 2D file? Sometimes resulting structures are not very reliable.
From the error message, it seems there are either condensed rings or multiple rings connected with each others for which it is impossible to calculate an angle.

If you identify the problematic ligand and you can send it, we can try to find how to convert it.

Stefano

I think you are right Stefano. Can you suggest another way to convert a smiles file to 3d mol2 (or whatever is best) with hydrogens.

Thanks for the help,
Dick

ChemAxon tools are very good for all kind of chemical structure management.
The MolConverter performs the operations you were trying to do with Babel. It is very accurate and fast and provide options for generate multiple protonation states and tautomers. Other tools allow to calculate properties, filter and so on...
They have a free Academic License, so if you happen to be in Academia, this would be the best choice (at least for me).

Happy dockings,

Stefano