Re: AW: Corrupt dcd files

From: Marc Baaden (baaden_at_smplinux.de)
Date: Sun May 15 2011 - 06:28:38 CDT

Hi,

as a follow-up, I may have found a (surprising) solution. The MD
analysis tool wordom [1] was able to read the "corrupt" dcd file and
re-write it to a new dcd file. The latter could be analyzed eg with
catdcd without yielding any errors.
Initial and final dcd files differ, but are of the same size. The
command line I used was:

  wordom -F all -itrj bcl1.prod.4.dcd -imol nachr_ph46.pdb -otrj test.dcd

Running catdcd on test.dcd yields

CatDCD 4.0
Reading indices from file 'loop.ndx'
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
Opening file 'tmp.trr' for writing.
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
Opened file 'test.dcd' for reading.
Read 3999 frames from file test.dcd, wrote 3999.
Total frames: 3999
Frames written: 3999
CatDCD exited normally.

Whereas running on the original dcd file yields

CatDCD 4.0
Reading indices from file 'loop.ndx'
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
dcdplugin) Warning: DCD header claims 4000 frames, file size indicates there are actually 3999 frames
Opening file 'tmp.trr' for writing.
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
dcdplugin) Warning: DCD header claims 4000 frames, file size indicates there are actually 3999 frames
Opened file 'bcl1.prod.4.dcd' for reading.
dcdplugin) read_dcdstep: corruption or unrecognized file structure
Read 1585 frames from file bcl1.prod.4.dcd, wrote 1585.
Total frames: 1585
Frames written: 1585
CatDCD exited normally.

Hope this may help others,
Best,
Marc Baaden

[1] http://wordom.sourceforge.net/

-- 
 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden_at_smplinux.de      -      http://www.baaden.ibpc.fr
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217

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