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 <daniel.r.roe.gmail.com>
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
Hi,
On Wed, May 10, 2017 at 8:56 AM, Gordon Richard Chalmers
<gordoncs.uga.edu> 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
trajout trajectory_no_tumbling_align_0_200.nc
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,
-Dan
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
The Laboratory of Computational Biology<https://www.lobos.nih.gov/lcb>
www.lobos.nih.gov
The Laboratory of Computational Biology is an interdisciplinary group of scientists who study biological processes via computer simulation. It is part of the ...
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Received on Wed May 10 2017 - 11:00:03 PDT
