Re: [AMBER] question about commutation of sub-trajectories and frame aligning

From: Daniel Roe <>
Date: Wed, 10 May 2017 11:46:12 -0400


On Wed, May 10, 2017 at 8:56 AM, Gordon Richard Chalmers
<> wrote:
> e.g., Warning: Frame 54683 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 54684 coords 1 & 2 overlap at origin; may be corrupt.
> ...

This output is the result of a simple check cpptraj does to warn of
possible problems with an input trajectory. It simply checks if the
first 6 values of a coordinate frame (i.e. XYZ of the first two atoms)
are all zero. This is a relatively inexpensive way to warn that there
may be an issue with the input coordinates, which can cause all sorts
of problems (like issues with best-fit alignment).

> I don't think it matters what frame it is happening it, except I know it has no
> overlapping coordinates in the unaligned 0-200ns segment of the 1000ns
> trajectory.

The only way to get this message is to have zeros in all of the first
6 values of your input coordinates. The only way to do that is if
there are corrupt trajectory frames or if there is some sort of disk
I/O error. One way to check is to grab one of your problems frames and
check it, e.g.

trajin rST6Gal1.hLoop.reduce.nowat.nobox_0-200ns.mdcrd 54684 54684
trajout frame.54684.crd

I also recommend checking that frame of the original trajectory as
well in this manner to ensure nothing went wrong with the write.

Now a few cpptraj notes on cpptraj usage. Amber atom masks can handle
dashes to indicate a range in addition to commas, so you can shorten
your masks quite a bit, e.g.

rmsd first :6-296.CA

Also, you don't necessarily need to create unaligned trajectory chunks
- you can align and write out each segment in one shot, e.g.

parm rST6Gal1.hLoop.reduce.nowat.nobox.prmtop
trajin rST6Gal1.hLoop.reduce.nowat.nobox.mdcrd 1 100000
rms first :6-296.CA

Finally, unless you have some specific reason for using the Amber
ASCII trajectory format, I *strongly* recommend you use the NetCDF
format. It is more compact (compared to an uncompressed ASCII
trajectory), faster to process, and far more robust.

Hope this helps,


Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Wed May 10 2017 - 09:00:03 PDT
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