Re: corrupt DCD file

From: Axel Kohlmeyer (
Date: Wed Aug 27 2008 - 18:56:20 CDT

On Wed, 27 Aug 2008, Forbes, Jeff (NIH/NIAMS) [E] wrote:

JF> I have a DCD trajectory file which should have 39496 frames in it according to the log file.
JF> However, catdcd gives this error:
JF> dcdplugin) read_dcdstep: corruption or unrecognized file structure
JF> Read 20600 frames from file
JF> Is there anyway to recover the rest of the trajectory data in this file?


in principle, yes.

it requires some knowledge of the binary structure of the dcd file,
though. if you are somewhat familiar with hex-viewers and the 'dd'
command, you can make a backup copy of the dcd header part, then
skip over the frames that you can read ok, use the hex-viewer to
find the location where the file is good again and then write this
segment out as well and combine the header and this segment to a
new .dcd file. if this all sounds like greek to you (i've learned
using hexviewers/editors at times when you would use it to change
already running programs), then you're probably better off re-running
that segment.


JF> Jeff Forbes

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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