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

Harindar Keer hkeer at uci.edu
Fri Aug 1 01:57:11 UTC 2008


 I am trying to convert a dcd, file  consisting of lipids and water, to 
the corresponding nc file but getting error as listed below. I have 
added entry for the lipid in Database/Molecules as suggested in MMTK 
tutorial up to best of my understanding still I am getting the exactly 
same error. I have been trying to resolve the issue for quite some time 
but had no success. It would be great if you can provide some assistance 
or some pointers to resolve the issue. Many thanks!


hkeer at uci.edu wrote:
> 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.
> Thanks,
> Harindar
> 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>
>     universe.addObject(conf.createAll())
>   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
> createMolecules
>     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
> __init__
>     BlueprintObject.__init__(self, type, atom_types, memo)
>   File "/usr/lib/python2.5/site-packages/MMTK/Database.py", line 370, in
> __init__
>     original = database.findType(original)
>   File "/usr/lib/python2.5/site-packages/MMTK/Database.py", line 76, in
> findType
>     filename = databasePath(name, self.directory, 0)
>   File "/usr/lib/python2.5/site-packages/MMTK/Database.py", line 51, in
> databasePath
>     raise IOError("Database entry %s/%s not found" % (directory, filename))
> IOError: Database entry Atoms/  not found

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