Hello,
It is definitely the autoimage command that is misbehaving. It works fine if I use it with cpptraj, but not with pytraj.
I generated a capped alanine residue with leap and solvated it. Then I autoimaged it using the two programs.
With cpptraj, I did:
cpptraj Solvated_capALA.pdb -y Solvated_capALA.pdb
autoimage
trajout Imaged_cpptraj.pdb
With python, I did:
import pytraj as pt
pdb = pt.load('Solvated_capALA.pdb')
ima = pdb.autoimage()
pt.write_traj('Imaged_python.pdb', ima)
As you can see, the version imaged by python gives nan for all the waters (as well as a 0 in the box X dimension), while the cpptraj version is perfectly fine.
I don't know which specific binary the two are using and whether there is a difference between the two. My pytraj is located here:
/usr/local/amber18/lib/python2.7/site-packages/pytraj-2.0.5-py2.7-linux-x86_64.egg/pytraj/__init__.pyc
If I can't figure out how to fix this, how can I at least point to the correct autoimage code used by cpptraj?
Thank you for any help
Pietro
________________________________
From: Hai Nguyen <nhai.qn.gmail.com>
Sent: Thursday, November 19, 2020 10:43 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] pytraj
Do you mean the 'autoimage' command in pytraj? If "yes", it should be fine
since it's from cpptraj itself.
Hai
On Wed, Nov 18, 2020 at 11:22 PM Pietro ARONICA <pietroa.bii.a-star.edu.sg>
wrote:
> 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 Mon Nov 23 2020 - 02:30:02 PST
