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

Harindar Keer hkeer at uci.edu
Wed Aug 6 06:33:03 UTC 2008

Hi Konrad,

I was able to use already available dcd_to_nc converter after processing 
the dcd files with catdcd3.0, earlier version of catdcd. As you 
suggested the cause may be the formatting of new vs old dcd files. But I 
am not getting time information , in the GUI upon loading the trajectory 
as well as when computed the MSD, all the entries in the first column of 
MSD.plot file are 0.0. Do I need to supply this information by some 
means also I am recorded frames in the trajectory at every 5 ps.

Thanks so much for sending the new dcd to nc converter. I tried it but 
running into following errors on using the new converter.
./dcd_to_nc2.0 tmp.pdb test.dcd test2.0.nc
Traceback (most recent call last):
  File "./dcd_to_nc2.0", line 303, in <module>
    if len(universe.cellParameters()) == 9:
TypeError: object of type 'NoneType' has no len()
I appreciate all your help. Thanks!

Best regards,
>> Now in some cases, I have been running into DCD read error. For the 
>> same system it works for some dcd files but not on others, I am still 
>> not able to narrow down to specific cause of the problem.
>> Traceback (most recent call last):
>>  File "/usr/bin/dcd_to_nc", line 121, in <module>
>>    dcd_reader()
>>  File "/usr/lib/python2.5/site-packages/MMTK/DCD.py", line 64, in 
>> __call__
>>    self.getActions(), self.getOption('dcd_file'))
>> IOError: DCD read error
> If this occurs very early in the conversion (before you have any 
> simulation steps in the netCDF file), this probably indicates a format 
> problem. MMTK uses a rather old DCD reader which cannot read some more 
> recent variants such as DCD files containing variable box shape data 
> at each time step. I will send you a test version of a newer 
> DCD->netCDF converter that knows about those newer formats, but hasn't 
> been tested much yet.
> If the error occurs when some steps have already been converted, your 
> DCD has probably been corrupted. You could check if you can read it 
> completely with other tools, e.g. VMD.
> Konrad.
> -- 
> ---------------------------------------------------------------------
> Konrad Hinsen
> Centre de Biophysique Moléculaire, CNRS Orléans
> Synchrotron Soleil - Division Expériences
> Saint Aubin - BP 48
> 91192 Gif sur Yvette Cedex, France
> Tel. +33-1 69 35 97 15
> E-Mail: hinsen at cnrs-orleans.fr
> Web: http://dirac.cnrs-orleans.fr/~hinsen/
> ---------------------------------------------------------------------

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