Could it be that those mdcrd files that give the error message have the
last snapshot incomplete? I am just guessing - but if you 'killed' the
MD run, it may happen that Amber has not finished writing the output
into the mdcrd file and thus some of the coordinates are missing at the
end.
Hope it helps :-)
Martina
nie beining wrote:
> Dear Amber users,
>
> Our system contains one protein molecule and ions in a
> rectangular box containing 4000 water molecules. We ran Sander for a
> few nanoseconds and found that the coodinates of our system were
> migrating. Therefore, we wrote a small Fortran code to transform
> coordinates back into a box. However, some mdcrd files gave me the
> following error message and others worked well.
>
> "fmt: read unexpected character
> apparent state: unit 1 named mdcrd.transtest2
> last format: (10F8.3)
> lately reading sequential formatted external IO
> Abort (core dumped)"
>
> What does it mean? I checked the mdcrd files for some "unexpected
> character" and didn't find any. Are there any Amber users who have
> encountered this strange problem?
> Would you please give me some suggestions? Thanks a lot!
>
> regards,
> Beining
>
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--
......................................................................
Dr. Martina Roeselova Tel: +1-949-824-9921
Department of Chemistry Fax: +1-949-824-9920
University of California
Irvine, CA 92697-2025 USA office: 3218, Natural Sciences I
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Received on Tue Feb 03 2004 - 20:53:00 PST
