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

Harindar Keer hkeer at uci.edu
Sun Aug 3 03:34:45 UTC 2008

Hi Jaroslaw,

 Many thanks for providing the detailed explanation, it got me into 
thinking in terms of tracking the source of the problems. The format of 
pdb file was incorrect and also there are more than 100, 000 atoms 
numbered as ***** after 99999, that was also creating the trouble. After 
changing every such "*****" entry to 99999 it works and no further 
errors are reported  but I am skeptical if there would be problem in 
further analysis of the system.

 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>
  File "/usr/lib/python2.5/site-packages/MMTK/DCD.py", line 64, in __call__
    self.getActions(), self.getOption('dcd_file'))
IOError: DCD read error

Many thanks,

Jaroslaw Kalinowski wrote:
>  Hi,
> Seems that your problem is not dcd-related.
> You have:
>>>   File "/usr/bin/dcd_to_nc", line 110, in <module>
>>>     universe.addObject(conf.createAll())
> And the important fragments fom dcd_to_nc script are:
>    16 usage = """Usage: dcd_to_nc [options] pdb_file dcd_file nc_file
>    17
>    18 pdb_file and dcd_file must describe the same system.
>   109 conf = PDBConfiguration(pdb_file)
>   110 universe.addObject(conf.createAll())
> It means that the problem occurs while reading pdb file.
> You also have:
>>>     raise IOError("Database entry %s/%s not found" % (directory,
>>> filename))
>>> IOError: Database entry Atoms/  not found
> Which means that for some reason it is looking for an atom that has space
> (' ') as a symbol, which obviously it can not find.
> Check your pdb file. Make sure it has well formatted atom names in correct
> columns. Please note that atom field is 4 characters long and must have
> spaces in right place. For example you should have ' C  ' or  and not '  
> C' or '  C ' or 'C   '. See Notes on atom naming in
> http://bmerc-www.bu.edu/needle-doc/latest/atom-format.html
> Best wishes,

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