VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 29 2004 - 10:46:44 CDT

Karunesh,
  I'm afraid that if you got corrupt files on one of NCSA's machines,
the best course of action is probably to request a refund of SUs for
the simulation time for which you got garbage output. People in our
lab have seen similar problems on occasion, though their DCD files
haven't had corrupt headers, instead they've sometimes gotten blocks
of atom data where the coordinates are all zero's. There's not much
you can do with such files, they are essentially trash if you really
needed the timesteps that contain the garbled data.

Your problem is more severe than most because the error you got
indicates that not only was the file corrupt, but some of the
critical timestep header information in the file was destroyed, and so
there's nothing VMD was able to do to save it. You might try
loading the trajectory skipping frames in the hope that it's only
the header information for a particular group of timesteps, but
it's basically a trial-and-error process to try and skip around
damaged timesteps. I'd suggest starting by skipping the frames
near the point where VMD returns the error.

If you get the error immediately on loading the trajectory file,
before any timesteps are actually read, then it's a lost cause, as
the main header data must be corrupt, hopefully this is not the case however.

Good luck,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jul 29, 2004 at 11:09:40AM -0400, Karunesh Arora wrote:
> Hi,
>
> I am having trouble reading some of the binary dcd files generated using
> NAMD on NCSA Platinum IA32 Linux cluster. On loading the trajectory in VMD
> following error message is obtained.
>
> read_dcdstep returned -6
>
> Though most of the dcd files generated after these corrupted files in
> between are fine. Is there way to retrive data from these corrupted
> dcd files?
>
> Thanks
> Karunesh 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
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