AMBER Archive (2004)

Subject: Re: AMBER: trajectory file question?

From: Melinda Layten (mlayten_at_gmail.com)
Date: Thu Oct 28 2004 - 14:35:17 CDT

If you look at the file with a text viewer, there is probably obvious
corruption at that frame (wrong characters, out of alignment, etc)

I've even seen whole files inserted into trajectory files.

If you aren't running replica exchange type data, the easiest solution
is to manually delete the corrupted frame and then you should be able
to analyze the rest of your data normally.

You can write a small perl script to do this automatically. Adding
this ability to ptraj is on the "wish-list"

Melinda Layten

On Thu, 28 Oct 2004 13:15:12 -0500, opitz_at_che.udel.edu
<opitz_at_che.udel.edu> wrote:
> Dear Amber Community,
>
> I ran an MD of a polymer in explicit solvent. I ran the simulation in
> several parts for a total of 3 nanoseconds. The version of Amber I am
> using is Amber7.
> When putting these trajectories through ptraj to get a complete
> trajectory from 20 ps to 3ns, one of the trajectories turned out to be
> corrupted. It simply stopped reading in this trajectory, stated that it
> was corrupted and went to the next trajectory. That basically looked like this:
>
> Set 300 . . . . . . . . . . . . . . . . . . . . . . . . .
> Set 350 . . . . . . . . . . . . . . . . . . . . . . . . .
> Set 400
> Processing AMBER trajectory file g224_solv_bio_md5.mdcrd
>
> Set 1 .................................................
> Set 50 .................................................
> Set 100 .................................................
> Set 150 .................................................
> Set 200 .................................................
> Set 250 .................................................
> Set 300 .................................................
> Set 350 .................................................
> Set 400 .................................................
> Set 450 .................................................
> Set 500 ...........................
> ERROR in readAmberTrajectory(): Set #528 is corrupted ( 40)...
>
> Processing AMBER trajectory file g224_solv_bio_md6.mdcrd
>
> Set 1 .................................................
>
> When looking at the trajectory in question in moil-view the trajectory is
> fine to frame 527. Frame 528 the bonds get all jumbled up, similar to
> when the wrong topology file is used with the wrong coordinates.
> The next trajectory file is fine again, and can be viewed through moil-view.
> Can this be fixed somehow? Or do I need to run everything starting from
> that frame 528 onwards again?
> Any suggestions or explantions?
>
> Best Regards,
>
> Armin
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