Incomplete coord file after crash

From: Michael Cooney <>
Date: Thu 25 Jan 2001 14:09:47 -0500 (EST)

Dear Amber users,

Recently I was running a long dynamics job when the workstation I was
using crashed (for an unrelated reason). I successfully restarted the job
using ntx=7 (this was a PME run), but the CRD file from the job that
crashed is incomplete. As a result I cannot carry out certain CARNAL
procedures, namely stripping waters from the files after merging the
incomplete file with the new file from the restarted job. The output gives
the following message:

bmd_merged.crd: too many numbers on box line for mdcrd format -
     bad coord file or carnal bug

Is there any way to recover the CRD file from the crash or to extract a
restart file from before the time of the crash, i.e. is the CRD file
corrupted so that I have to start the MD all over from the beginning?

Thanks very much for any suggestions.


Michael G. Cooney
Dept. of Biochemistry and Molecular Biology
The University of Georgia
Athens, GA 30602, USA
Received on Thu Jan 25 2001 - 11:09:47 PST
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