protein model is not cleaning up properly

arcady · **Joined:** Tue Mar 16, 2010 10:07 pm **Posts:** 2

here is what I get (the pdb file is sendaimt.pdb in ARCFOLDER)

Traceback (most recent call last):
File "tools/prepare_receptor4.py", line 168, in ?
delete_single_nonstd_residues=delete_single_nonstd_residues)
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 520, in __init__
version=version, delete_single_nonstd_residues=delete_single_nonstd_residues)
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 120, in __init__
self.repairMol(mol, self.repair_type_list)
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 161, in repairMol
self.newHs = self.addHydrogens(mol)
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 174, in addHydrogens
HB.addHydrogens(mol)
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/MolKit/hydrogenBuilder.py", line 81, in addHydrogens
hat = AddHydrogens().addHydrogens(mol.allAtoms, method=self.method)
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/PyBabel/addh.py", line 92, in addHydrogens
Hatoms = self.place_hydrogens1(atoms, num_H_to_add)
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/PyBabel/addh.py", line 156, in place_hydrogens1
Hat = Hat + self.add_vinyl_hydrogens(a ,SP2_C_H_DIST)
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/PyBabel/addh.py", line 444, in add_vinyl_hydrogens
c3 = c2.bonds[1].atom1
File "/usr/lib/python2.4/UserList.py", line 28, in __getitem__
def __getitem__(self, i): return self.data[i]
IndexError: list index out of range

-- any suggestions?

Thank you!

Arcady

hazaie · **Joined:** Wed Oct 29, 2008 2:24 pm **Posts:** 40

Probably there was a probleim with your protein. Could you please upload your protein and leave it there, so I can further check the problem?

Thanks
Eszter

arcady · **Joined:** Tue Mar 16, 2010 10:07 pm **Posts:** 2

Eszter,

I think I did yesterday, and I uploaded it (I think) again, with the same error message. Is there a way to send you a pdb file if you do not see it?

Thank you!

Arcady

hazaie · **Joined:** Wed Oct 29, 2008 2:24 pm **Posts:** 40

Dear Arcrady,

Please send your pdb file to the following emailaddress: info@dockingserver.com, so I can analyze the problem.

Thanks
Eszter

hazaie · **Joined:** Wed Oct 29, 2008 2:24 pm **Posts:** 40

Dear Arcady,

we have upgraded the DockingServer to handle your protein, it should work now.

Kind Regards,
Eszter