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prepare_ligand4.py error when using -C option

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Douglas Houston

Post subject: prepare_ligand4.py error when using -C option

Posted: Thu Aug 16, 2012 11:12 am

Micromolar User

Joined: Tue Jan 26, 2010 7:41 am
Posts: 45

I'm trying to use the ADT script prepare_ligand4.py to convert a mol2 file while preserving the charges. I get the errors below. The script converts the file successfully if I leave out the -C option. I have attached the file in question.

Is this a bug?

Code:

Traceback (most recent call last):
  File "/usr/people/douglas/programs/mgltools_i86Linux2_1.5.4/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py", line 195, in <module>
    attach_nonbonded_fragments=attach_nonbonded_fragments)
  File "/usr/people/douglas/programs/mgltools_i86Linux2_1.5.4/MGLToolsPckgs/Updates/tested/AutoDockTools/MoleculePreparation.py", line 952, in __init__
    detect_bonds_between_cycles=detect_bonds_between_cycles)
  File "/usr/people/douglas/programs/mgltools_i86Linux2_1.5.4/MGLToolsPckgs/Updates/tested/AutoDockTools/MoleculePreparation.py", line 702, in __init__
    delete_single_nonstd_residues=False)
  File "/usr/people/douglas/programs/mgltools_i86Linux2_1.5.4/MGLToolsPckgs/Updates/tested/AutoDockTools/MoleculePreparation.py", line 140, in __init__
    self.addCharges(mol, charges_to_add)
  File "/usr/people/douglas/programs/mgltools_i86Linux2_1.5.4/MGLToolsPckgs/Updates/tested/AutoDockTools/MoleculePreparation.py", line 212, in addCharges
    mol.chains.residues.atoms))
  File "/usr/people/douglas/programs/mgltools_i86Linux2_1.5.4/MGLToolsPckgs/Updates/tested/AutoDockTools/MoleculePreparation.py", line 211, in <lambda>
    len_zero_charges = len(filter(lambda x: x.charge==0, 
  File "/usr/people/douglas/programs/mgltools_i86Linux2_1.5.4/MGLToolsPckgs/Updates/tested/MolKit/molecule.py", line 387, in __getattr__
    return self._charges[self.chargeSet]
KeyError: None

Attachments:

2D3U_ligand_MOPAC1.mol2 [4.19 KiB]
Downloaded 54 times

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Ruth Huey

Post subject: Re: prepare_ligand4.py error when using -C option

Posted: Thu Aug 16, 2012 5:46 pm

Nanomolar user

Joined: Sun Jun 21, 2009 11:37 pm
Posts: 97

This appears to be a problem with the mol2Parser in the version of MGLToolsPckgs you are using (?1.5.4?).
Apparently, the 'run-on' string "N.pl31001" in the atom record for N17 is not correctly parsed:
17 N17 7.3010 33.2370 77.1370 N.pl31001 CCT1001 -0.8758

In consequence, the atom created from this line does not have any charge at all, hence the error.

You might consider updating to a newer version of MGLToolsPckgs...

Best wishes,
Ruth

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Douglas Houston

Post subject: Re: prepare_ligand4.py error when using -C option

Posted: Fri Aug 17, 2012 9:15 am

Micromolar User

Joined: Tue Jan 26, 2010 7:41 am
Posts: 45

Thanks Ruth that was very helpful.

I am indeed using 1.5.4, I was going to wait until 1.5.6 RC3 became an official release ... is there 1.5.5 available? I notice on the MGLTools download page 1.5.4 is still the current release ...

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Douglas Houston

Post subject: Re: prepare_ligand4.py error when using -C option

Posted: Tue Aug 21, 2012 5:38 pm

Micromolar User

Joined: Tue Jan 26, 2010 7:41 am
Posts: 45

I assume it's pretty safe to use the release candidate, i.e. no bugs have been reported for it?

Is there a date set for the final release?

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