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

From: Gordon Richard Chalmers <>
Date: Wed, 10 May 2017 17:36:08 +0000

Hi Daniel,

Thank you for response.

First, I do know how to shorten my cpptraj input and also how

to use the hyphen in the masking. Sometimes I want to be

explicit to check certain things, such as frame aligning without

some of the residues. About netCDF, that is a good

idea, and I will make it a priority to start reading in the netCDF

format in my programs.

It must have had a disk I/O problem or whatever. For the past 2 days?
I checked this 5 times before asking. Today, no problem.

1) No problem with the unaligned 0-200ns segment of the

unaligned 1000ns trajectory. I checked the frames after 54683

- there are no zeros for the coordinates.

2) No problem with the unaligned 0-1000ns total trajectory.

3) No problem with the aligned 1000ns trajectory.

4) No problem with the 0-200ns segment, using cpptraj, of the

aligned 1000ns trajectory.

-- 5) Now no problem with the aligning the 0-200ns segment of the

unaligned 0-1000ns trajectory. This was a problem.

Thank you for the time. I do check these things, and there was no

problem with the 400-600ns and 800-1000ns segments earlier, just

the 0-200ns segment.

Gordon Chalmers
Department of Computer Science
Complex Carbohydrate Research Center
University of Georgia
From: Daniel Roe <>
Sent: Wednesday, May 10, 2017 11:46:12 AM
To: AMBER Mailing List
Subject: Re: [AMBER] question about commutation of sub-trajectories and frame aligning


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 - 11:00:03 PDT
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