Molecular Docking Server

Error in docking
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Author:  ismaelb [ Thu May 15, 2014 10:35 pm ]
Post subject:  Error in docking

Hi. While I trying to do a docking (after ligand and protein preparation), I get this error message:

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

What's wrong?


Author:  bikadi [ Tue May 20, 2014 1:47 pm ]
Post subject:  Re: Error in dockingg

Hi Ismael,

most probably an unknown atom type. Can you please send me the link and I can investigate it in more detail.


Author:  ismaelb [ Tue May 20, 2014 2:17 pm ]
Post subject:  Re: Error in docking


Is the only docking in my account. I cannot link it without the login data.

Thank you.

Author:  bikadi [ Thu May 22, 2014 4:46 pm ]
Post subject:  Re: Error in docking


the problem is with your ligand, it is too small to dock.

Best Regards,

Author:  JavenLoh [ Mon Aug 25, 2014 4:11 pm ]
Post subject:  Re: Error in docking


My docking results show error as well. Kindly guide me.

Author:  bikadi [ Thu Aug 28, 2014 2:52 pm ]
Post subject:  Re: Error in docking

I have checked your account and there are 40 correctly finished calculations there. Please let me know if you need further assistance.

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