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

Juergen Haas Juergen.Haas at unibas.ch
Mon Feb 23 16:20:21 UTC 2009

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 = 
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 
    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 

thanks in advance


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