Re: [AMBER] Exclamation marks in trajectory

From: Hugh Heldenbrand <>
Date: Mon, 13 Jul 2009 19:52:37 +0100

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.


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:- |
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Received on Mon Jul 13 2009 - 18:08:03 PDT
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