hi Pietro,
I don't know "why" but here is what I tried with your commands (in my
macbook) and I did not get NAN.
conda create -n at20 python=3.8 -y
conda activate at20
conda install ambertools -c conda-forge
This will create a new python environment with ambertools 20.
Please give it a try.
Hai
On Mon, Nov 23, 2020 at 5:16 AM Pietro ARONICA <pietroa.bii.a-star.edu.sg>
wrote:
> 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 - 10:30:02 PST
