Molecular Docking Server

unknown error message
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Author:  gtombline [ Tue Mar 16, 2010 4:03 am ]
Post subject:  unknown error message

Can someone please explain why i get this error message when i try to dock:
(note, my pdb file is legit, and my ligand was drawn and saved and all apepared to cleanup well-
ie there were no apparent issues until i tried to dock them)

Traceback (most recent call last):
File "tools/", line 197, in ?
File "tools/", line 55, in set_ligand
self.ligand = Read(ligand_filename)[0]
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/MolKit/", line 51, in Read
molecules = parser.parse()
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/MolKit/", line 681, in parse
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/MolKit/", line 1496, in parse_PDB_ROOT
self.mol.ROOT = self.mol.chains.residues.atoms.get(lambda x: x._uniqIndex==0)[0]
File "/usr/lib/python2.4/", line 28, in __getitem__
def __getitem__(self, i): return[i]
IndexError: list index out of range


Author:  hazaie [ Tue Mar 16, 2010 10:36 am ]
Post subject:  Re: unknown error message

I have checked your docking calculation, and your ligand was not cleaned up properly. After restarting the ligand parameters button, everything was fine. Your docking calculation is now fine (After restarting it).
It is useful to check the ligand after cleanup- if no 3D structure is shown that means that something went wrong during the cleanup process, even of no error is indicated.


Author:  gtombline [ Tue Mar 16, 2010 3:01 pm ]
Post subject:  Re: unknown error message


thanks so much....that was really helpful

i will probably subscribe now....very exciting

best regards,

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