thanks. Can you please provide us a small .nc file with prmtop file so we
can reproduce your issue with ParmEd.
(We might fix in next AmberTools17 but just want to make sure). thanks
By the way, it's ok to use
parm = pmd.load_file('state00.parm7', 'frame.nc')
(vs parm = pmd.load_file('state00.parm7', 'frame.rst7')
If you want to update coordinates for given frame number, try
parm.coordinates = parm.get_coordinates(frame_number)
thx
Hai
On Thu, Feb 23, 2017 at 11:18 AM, Elisa Pieri <elisa.pieri90.gmail.com>
wrote:
> Sorry, I didn't mean "useless" in general, but just to my case :)
> Actually, it is not just VMD that cannot read it: it is unreadable to the
> script too. This is what you get using the rst7 file as provided by cpptraj
> without removing this energies:
>
> Traceback (most recent call last):
> File "qmmm_sander.py", line 10, in <module>
> parm = pmd.load_file('state00.parm7', 'frame.rst7')
> File
> "/home/elisa/amber16/lib/python2.7/site-packages/
> ParmEd-2.7.2-py2.7-linux-x86_64.egg/parmed/formats/registry.py",
> line 197, in load_file
> return cls.parse(filename, *args, **kwargs)
> File
> "/home/elisa/amber16/lib/python2.7/site-packages/
> ParmEd-2.7.2-py2.7-linux-x86_64.egg/parmed/amber/amberformat.py",
> line 353, in parse
> return LoadParm(filename, *args, **kwargs)
> File
> "/home/elisa/amber16/lib/python2.7/site-packages/
> ParmEd-2.7.2-py2.7-linux-x86_64.egg/parmed/amber/readparm.py",
> line 73, in LoadParm
> f = load_file(xyz)
> File
> "/home/elisa/amber16/lib/python2.7/site-packages/
> ParmEd-2.7.2-py2.7-linux-x86_64.egg/parmed/formats/registry.py",
> line 182, in load_file
> raise FormatNotFound('Could not identify file format')
> parmed.exceptions.FormatNotFound: Could not identify file format
>
> So maybe the way cpptraj is creating a rst7 file is just incompatible with
> the parmed.load_file.
> Sorry again!
>
> On Thu, Feb 23, 2017 at 5:10 PM, Nhai <nhai.qn.gmail.com> wrote:
>
> >
> >
> > > On Feb 23, 2017, at 10:54 AM, Elisa Pieri <elisa.pieri90.gmail.com>
> > wrote:
> > >
> > > So..I solved two problems:
> > >
> >
> >
> > > -for some reason, cpptraj is adding two useless numbers to the rst7,
> > which
> > > makes it unreadable. Nothing that sed cannot handle, I guess.
> >
> > ? Why do you think it's useless? If vmd can not read it, it's vmd
> problem,
> > not ours.
> >
> > > -"coordinates" has to be used instead of "coords" as attribute. The
> > manual
> > > would need an extensive debug.
> >
> > Thx. I will update the manual.
> >
> > Hai
> > >
> > > Now it is working on my computer, we can try it tomorrow on yours!
> > >
> > > Elisa
> > >
> > > On Thu, Feb 23, 2017 at 4:43 PM, Elisa Pieri <elisa.pieri90.gmail.com>
> > > wrote:
> > >
> > >> Uh, thanks! Easier than expected! I took the main structure from the
> > >> manual examples, I don't know if the same correction should be applied
> > to
> > >> the manual..
> > >> BTW, I discovered that the RST7 was unreadable for VMD just because on
> > >> line 2 cpptraj adds two numbers (energy and force?) after the number
> of
> > >> atoms; another possible bug to be fixed?
> > >>
> > >> Thank you!
> > >> Elisa
> > >>
> > >>> On Thu, Feb 23, 2017 at 4:36 PM, Nhai <nhai.qn.gmail.com> wrote:
> > >>>
> > >>> Hi
> > >>>
> > >>> Change coords to coordinates.
> > >>>
> > >>> Hai Nguyen
> > >>>
> > >>>> On Feb 23, 2017, at 10:05 AM, Elisa Pieri <elisa.pieri90.gmail.com>
> > >>> wrote:
> > >>>>
> > >>>> coords
> > >>>
> > >>> _______________________________________________
> > >>> AMBER mailing list
> > >>> AMBER.ambermd.org
> > >>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>
> > >>
> > >>
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> >
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> >
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Received on Thu Feb 23 2017 - 10:00:02 PST
