[MMTK] Examples/construction.py

Sanzo Miyazawa miyazawa at smlab.sci.gunma-u.ac.jp
Fri Jun 26 14:41:50 UTC 2009

I installed ScientificPython-2.9.0 and MMTK-2.6.0 with python 2.5.3.
I tried to run Examples/construction.py but it ended with
the following error; it says that  Groups/lysine_neutral_noh is missing.

% mmtk construction.py
Traceback (most recent call last):
  File "construction.py", line 47, in <module>
    chains = configuration.createPeptideChains(model = 'no_hydrogens')
  File "/usr/local/lib/python2.5/site-packages/MMTK/PDB.py", line 314, in createPeptideChains
    for chain in self.peptide_chains]
  File "/usr/local/lib/python2.5/site-packages/MMTK/PDB.py", line 76, in createPeptideChain
    chain = apply(Proteins.PeptideChain, (self,), properties)
  File "/usr/local/lib/python2.5/site-packages/MMTK/Proteins.py", line 304, in __init__
    r = Residue(residue, model)
  File "/usr/local/lib/python2.5/site-packages/MMTK/Proteins.py", line 52, in __init__
    blueprint = _residueBlueprint(name, model)
  File "/usr/local/lib/python2.5/site-packages/MMTK/Proteins.py", line 205, in _residueBlueprint
    blueprint = Database.BlueprintGroup(name)
  File "/usr/local/lib/python2.5/site-packages/MMTK/Database.py", line 412, in __init__
    BlueprintObject.__init__(self, type, group_types, memo)
  File "/usr/local/lib/python2.5/site-packages/MMTK/Database.py", line 382, in __init__
    original = database.findType(original)
  File "/usr/local/lib/python2.5/site-packages/MMTK/Database.py", line 81, in findType
    filename = databasePath(name, self.directory, 0)
  File "/usr/local/lib/python2.5/site-packages/MMTK/Database.py", line 56, in databasePath
    raise IOError("Database entry %s/%s not found" % (directory, filename))
IOError: Database entry Groups/lysine_neutral_noh not found

More information about the mmtk mailing list