[MMTK] global name 'conf' is not defined - problem reading in pdb with MMTK.Proteins.Protein

Juergen Haas Juergen.Haas at unibas.ch
Tue Feb 24 08:36:49 UTC 2009

On Monday 23 February 2009 17:20:21 Juergen Haas wrote:
> Dear All,
> I have recently started using MMTK and while starting to implement an
> interface it to suit our needs I stumbled upon this error, which I get when
> reading in the attached pdb file:
> dng> from MMTK import *
> dng> from MMTK.Proteins import Protein
> dng> from MMTK.ForceFields import Amber99ForceField
> dng> universe =
> InfiniteUniverse(Amber99ForceField(mod_files=['frcmod.ff99SB']))
> dng> universe.protein = Protein('t.pdb')
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/usr/lib/python2.5/site-packages/MMTK/Proteins.py", line 671, in
> __init__
>     items = conf.createPeptideChains(model)
> NameError: global name 'conf' is not defined
> I am guessing it could lie in the nature of the pdb file, however, I agree
> with the error in the way that I alos do not see where conf was
> defined/instantiated.
> thanks in advance
> Juergen

I found the reason, embarrasingly, but true...:(

since the error occured as well when I tested with 'insulin' I compared the 
source and found the two lines missing where conf and model are defined.

sorry to bother you with that.

Dr. Juergen Haas
 Swiss Institute of Bioinformatics
 Klingelbergstr. 50-70
 CH 4056 Basel, Switzerland

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