AMBER Archive (2003)

Subject: Re: AMBER: pmemd

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon Aug 18 2003 - 10:45:47 CDT

James -
Have you tried to read it in either sander 6 or 7 (depending on which mode
you are running pmemd in)? It could just be a corrupted file. If you wish,
feel free to make a gzipped tarball of the various files needed to repro the
problem, and I'll take a look. I would bet on a truncated or otherwise
corrupted restrt, though (what happens if you redo the run that creates the
restart - do you get exactly the same thing; is there any platform mixing
with binary files?)
Regards - Bob Duke
----- Original Message -----
From: "james tomomi macdonald" <j.macdonald_at_mail.cryst.bbk.ac.uk>
To: <amber_at_scripps.edu>
Sent: Monday, August 18, 2003 11:18 AM
Subject: AMBER: pmemd

>
> Hi,
>
> I am having a peculiar problem with pmemd. I have been able to run pmemd
> with no problem for a few weeks, but i have recently got a problem i can't
> understand. For some reason it has become unable to read my restart
> coordinate file reporting the error:
>
> FATAL: Could not read coords from production_105.xyz
>
> I have looked at the file production_105.xyz manually (and it looked OK)
> and tried regenerating it to see if there was some kind of one-off error
> when it was written.
>
> I would be very grateful if anyone could help me, and i could forward on
> the file should that be necessary.
>
> Thanks very much in advance.
>
> James.
>
>
>
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