AMBER Archive (2009)

Subject: RE: [AMBER] Exclamation marks in trajectory

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Jul 13 2009 - 14:20:37 CDT

Hi Hugh,

This is bad!!! (exclamation marks intended).

If cp on your machine is not giving you perfect copies I would suggest
chucking the hard disk away and starting a fresh. You might also want to run
a full memory check on the hardware. This is likely a very serious hardware
issue that is going to lead to more and more file corruption if left
unchecked.

Sorry to be the bearer of bad news.

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Hugh Heldenbrand
> Sent: Monday, July 13, 2009 11:53 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Exclamation marks in trajectory
>
> Hello Ross and Everyone,
>
> I was able to add 4 random exclamation points to another trajectory
> simply by making a copy (using the cp program in linux) of it on my
> machine. Making another copy yielded a different number of exclamation
> points in different places. So it looks like it is particular to my
> system/situation and not of interest to the wider community. Since
> AMBER is not doing it I will just delete them and carry on.
>
> Thanks,
> Hugh
>
>
> Ross Walker wrote:
> > Hi Hugh,
> >
> >
> >> I recently had a trajectory generated by PMEMD 10 that would only
> >> partially load in VMD. A few hundred frames along it would stop and
> >> print the error, "Problem loading CRD file." Upon closer
> examination
> >> of
> >> the trajectory I found several exclamation points in the file,
> always
> >> appearing just in front of a number. After I removed them the
> >> trajectory loaded normally into VMD. Does anyone have any idea why
> >> these exclamation points would appear or what they might mean?
> >>
> >
> > I honestly have no idea how you could get such characters in your
> trajectory
> > file. There is certainly nothing in the code that would print this.
> It is
> > possible to get *'s in the trajectory file if the coordinates become
> too
> > large but in your case this is not what is happening. The fact that
> removing
> > them makes it work is amazing. I would have suggested that what you
> had was
> > file corruption, this can happen sometimes due to disk / network
> errors etc
> > but normally this results in a whole block just being garbage.
> >
> > Thus in conclusion I have no idea how the !'s would have got there
> except if
> > someone somehow edited the file and added them for some strange
> reason.
> >
> > Sorry I can't be of any more help. If you can find a way to reliably
> > reproduce the problem please post it and then we can look into how it
> > happens.
> >
> > All the best
> > Ross
> >
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | Assistant Research Professor |
> > | San Diego Supercomputer Center |
> > | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> > | http://www.rosswalker.co.uk | PGP Key available on request |
> >
> > Note: Electronic Mail is not secure, has no guarantee of delivery,
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> > be read every day, and should not be used for urgent or sensitive
> issues.
> >
> >
> >
> >
> >
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