AMBER Archive (2009)

Subject: Re: [AMBER] Exclamation marks in trajectory

From: Hugh Heldenbrand (helde010_at_umn.edu)
Date: Mon Jul 13 2009 - 13:52:37 CDT

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 |
>
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