Thank you for your response.
I have used the verbose version and the test systems to diagnose the problem, and I've made some progress. With the test system, it still gives me a 0 on the first CRYST1 record, which it never used to do. The real issue I've found is the autoimage command; when used with one of my trajectories, it causes the output pdb to have nan in the pdb. Even worse, the command hangs indefinitely when used with the test system. Again, this autoimage command seemed to work fine when I used it up to two days ago.
I'm not sure what the code of the autoimage command is, where to find it and what might have gone wrong. Maybe it relies on another python library that was updated recently.
Pietro
________________________________
From: Hai Nguyen <nhai.qn.gmail.com>
Sent: Thursday, November 19, 2020 8:26 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] pytraj
Dear Pietro,
> Has there been an update to pytraj in the past 24-48 hours?
No, I don't think so. There has been NO update for pytraj for at least the
last 6 months from the release.
How did you install pytraj (via ambertools?)
Can you turn on the pytraj's verbose to see the message from cpptraj (which
is used by pytraj under the hood):
pytraj._verbose()
pytraj.write_traj(...)
What's your exact commands?
Can you reproduce the issue If you replace your systems with the tests
system (tz2.ortho.nc, tz2.ortho.parm7) in here:
https://github.com/Amber-MD/pytraj/tree/master/tests/data
Hai
On Wed, Nov 18, 2020 at 12:04 PM Pietro ARONICA <pietroa.bii.a-star.edu.sg>
wrote:
> Hello all,
> Has there been an update to pytraj in the past 24-48 hours? My code, which
> relies on the python implementation of cpptraj, no longer works. It reads
> trajectory and restart files fine, as far as I can tell; they seem to have
> all the correct box parameters. However, using pytraj.write_traj to write
> them into pdb gives a file where the CRYST1 record either has all zeroes
> for the box, or the first one is a zero and the others are correct.
> Furthermore, it also outputs the coordinates of all waters as nan. This
> code worked perfectly fine up to a few days ago, so I'm wondering what
> happened. Trying different pytraj commands like load, save and write_traj
> with different options do not seem to solve the issue; in each case, the
> CRYST1 records are incorrect and in some cases the waters have nan
> coordinates.
> The problem seems to be only with pytraj. Loading, reading and writing the
> same files with the interactive, normal version of cpptraj has no issue,
> but my workflow requires the python implementation.
> Does anyone have any clues?
> Pietro
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Received on Wed Nov 18 2020 - 20:30:02 PST
