ADL: PDB to PDBQT and hydrogens

Raja S rs0504 at hotmail.com
Tue Mar 4 10:31:43 PST 2008


Hi all,
 
I drew a few molecules on chemdraw, but did not specify the full geometry of the molecule. (all the angles, dihedreal angles, lengths, etc). I converted the chemdraw file (a cdx into a pdb)using openbabel. I opened the file in Autodock tools. It opened. I tried to save it as a PDBQT. When i go to open the PDBQT to try and do a docking I get this error message: 
 
Traceback (most recent call last):  File "C:\cygwin\home\mgl\releases\MGLToolsPckgs\ViewerFramework\VF.py", line 724, in tryto  File "C:\cygwin\home\mgl\releases\MGLToolsPckgs\AutoDockTools\autotorsCommands.py", line 755, in doit  File "C:\cygwin\home\mgl\releases\MGLToolsPckgs\AutoDockTools\autotorsCommands.py", line 287, in initLPO4  File "C:\cygwin\home\mgl\releases\MGLToolsPckgs\AutoDockTools\MoleculePreparation.py", line 925, in __init__  File "C:\cygwin\home\mgl\releases\MGLToolsPckgs\AutoDockTools\MoleculePreparation.py", line 691, in __init__  File "C:\cygwin\home\mgl\releases\MGLToolsPckgs\AutoDockTools\MoleculePreparation.py", line 1359, in __init__  File "C:\cygwin\home\mgl\releases\MGLToolsPckgs\AutoDockTools\MoleculePreparation.py", line 1397, in __classifyBonds  File "C:\cygwin\home\mgl\releases\MGLToolsPckgs\AutoDockTools\AutoDockBondClassifier.py", line 57, in classify  File "C:\cygwin\home\mgl\releases\MGLToolsPckgs\MolKit\bondSelector.py", line 515, in select  File "C:\cygwin\home\mgl\releases\MGLToolsPckgs\MolKit\bondSelector.py", line 491, in select  File "C:\cygwin\home\mgl\releases\MGLToolsPckgs\PyBabel\atomTypes.py", line 136, in assignHybridization  File "C:\cygwin\home\mgl\releases\MGLToolsPckgs\PyBabel\atomTypes.py", line 262, in valence_two  File "C:\cygwin\home\mgl\releases\MGLToolsPckgs\PyBabel\util.py", line 48, in bond_angleZeroDivisionError: float division
 
i tried to edit the PDB file by adding hydrogens but I get this error message:
 
Traceback (most recent call last):  File "C:\cygwin\home\mgl\releases\MGLToolsPckgs\ViewerFramework\VF.py", line 724, in tryto  File "C:\cygwin\home\mgl\releases\MGLToolsPckgs\Pmv\editCommands.py", line 953, in doit  File "C:\cygwin\home\mgl\releases\MGLToolsPckgs\PyBabel\addh.py", line 92, in addHydrogens  File "C:\cygwin\home\mgl\releases\MGLToolsPckgs\PyBabel\addh.py", line 115, in place_hydrogens1  File "C:\cygwin\home\mgl\releases\MGLToolsPckgs\PyBabel\addh.py", line 345, in add_tertiary_hydrogenTypeError: 'NoneType' object is unsubscriptable
 
 
I need to get a docking done ASAP and am not able to load the ligand to do such a docking. I hope somebody can help me.
 
I am wondering how most people prepare their ligand for docking. Is chemdraw used? Is there a different program?
 
Please help me i am stuck as of now
 
Regards,
 
Raja 
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