Re: [AMBER] AMBER Autoimage Warning

From: Daniel Roe <>
Date: Mon, 24 Aug 2015 11:42:42 -0600


On Mon, Aug 24, 2015 at 10:42 AM, Brittany Boykin
<> wrote:
> 14 frames 58360-58373 of 60000 frames showed this Warning:
> Frame 58360 imaging failed, box lengths are zero

This usually occurs when there are problems with the underlying file
system (disk full, IO timeout, etc). Unfortunately unless this
trajectory was generated from another existing trajectory that might
have intact unit cell information for those frames, that information
is lost. However, if you ran the simulation under NVT (ntb=1) you can
manually set the box dimensions with the 'box' command.

> Since I now know this happened for whatever reason, the unit cell dimensions were set to 0. I did this system no differently than my other systems using cpptraj. Also, when I ran the Trajin analysis, it processed 60000 frames successfully with no Warnings, do you know why this is?

This warning will only happen if the action in question needs the unit
cell dimensions for imaging. If you're doing something that doesn't
require imaging (like e.g. radius of gyration) you won't see this
warning. Note it may be worthwhile to run some additional checks on
those frames with the 'check' command to make sure you don't have
partial corruption of the coordinates as well.


> Also, now the bigger question is how this happened and how I can go about fixing the Warning?
> Thank you in advance.
> Brittany Boykin
> Graduate Student
> Auburn University
> Department of Chemistry and Biochemistry
> e:
> c: (404)545.1036
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Aug 24 2015 - 11:00:08 PDT
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