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 Post subject: Error in docking
PostPosted: Thu May 15, 2014 10:35 pm 

Joined: Tue Jul 28, 2009 7:01 pm
Posts: 6
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/prepare_dpf4.py", line 197, in ?
dm.set_ligand(ligand_filename)
File "tools/prepare_dpf4.py", line 55, in set_ligand
self.ligand = Read(ligand_filename)[0]
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/MolKit/__init__.py", line 51, in Read
molecules = parser.parse()
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/MolKit/pdbParser.py", line 681, in parse
self.pdbRecordParser[record](records)
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/MolKit/pdbParser.py", 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/UserList.py", line 28, in __getitem__
def __getitem__(self, i): return self.data[i]
IndexError: list index out of range


What's wrong?

Regards
Ismael


Last edited by ismaelb on Tue May 20, 2014 2:15 pm, edited 1 time in total.

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 Post subject: Re: Error in dockingg
PostPosted: Tue May 20, 2014 1:47 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 197
Hi Ismael,

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

Thanks


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 Post subject: Re: Error in docking
PostPosted: Tue May 20, 2014 2:17 pm 

Joined: Tue Jul 28, 2009 7:01 pm
Posts: 6
Hi

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

Thank you.


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 Post subject: Re: Error in docking
PostPosted: Thu May 22, 2014 4:46 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 197
Hi,

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

Best Regards,
Zsolt


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 Post subject: Re: Error in docking
PostPosted: Mon Aug 25, 2014 4:11 pm 

Joined: Sun Jul 20, 2014 3:14 pm
Posts: 6
Hi,

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


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 Post subject: Re: Error in docking
PostPosted: Thu Aug 28, 2014 2:52 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 197
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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