[MMTK] dcd_to_nc : IOError: Database entry Atoms/ not found

hkeer at uci.edu hkeer at uci.edu
Wed Jul 30 22:17:59 UTC 2008

Dear All,

 I have been facing a problem in converting a xplor formatted dcd file of
a molecular system, consisting of DMPC lipids and water, into the nc
file. I am puzzled about how to resolve the issue, do I need to create
database entry for DMPC ?

I would highly appreciate any help in this regard. Please find below the
output from dcd_to_nc program.


Following is the output of running the dcd_to_nc program :

dcd_to_nc tmp.pdb test.dcd test.nc
Traceback (most recent call last):
  File "/usr/bin/dcd_to_nc", line 110, in <module>
  File "/usr/lib/python2.5/site-packages/MMTK/PDB.py", line 373, in createAll
    molecules = self.createMolecules(molecule_names, permit_undefined)
  File "/usr/lib/python2.5/site-packages/MMTK/PDB.py", line 329, in
    a = ChemicalObjects.Atom(element, name = aname)
  File "/usr/lib/python2.5/site-packages/MMTK/ChemicalObjects.py", line
485, in __init__
    ChemicalObject.__init__(self, blueprint, _memo)
  File "/usr/lib/python2.5/site-packages/MMTK/ChemicalObjects.py", line
32, in __init__
    blueprint = self.blueprintclass(blueprint)
  File "/usr/lib/python2.5/site-packages/MMTK/Database.py", line 395, in
    BlueprintObject.__init__(self, type, atom_types, memo)
  File "/usr/lib/python2.5/site-packages/MMTK/Database.py", line 370, in
    original = database.findType(original)
  File "/usr/lib/python2.5/site-packages/MMTK/Database.py", line 76, in
    filename = databasePath(name, self.directory, 0)
  File "/usr/lib/python2.5/site-packages/MMTK/Database.py", line 51, in
    raise IOError("Database entry %s/%s not found" % (directory, filename))
IOError: Database entry Atoms/  not found

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