thank you.
Hai
On Fri, Feb 24, 2017 at 9:23 AM, Elisa Pieri <elisa.pieri90.gmail.com>
wrote:
> Yes, of course! I hope they are small enough.
>
> Anyway, if I use the NC, I get this:
>
> Traceback (most recent call last):
> File "qmmm_sander.py", line 22, in <module>
> with sander.setup(parm, parm.coordinates, parm.box, inp, qm_inp):
> File "/home/elisa/amber16/lib/python2.7/site-packages/
> sander/__init__.py",
> line 268, in __init__
> box = _np.array([float(x) for x in box])
> TypeError: only length-1 arrays can be converted to Python scalars
>
> On Thu, Feb 23, 2017 at 6:55 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > 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
> > > > >>>
> > > > >>> _______________________________________________
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Received on Fri Feb 24 2017 - 07:00:02 PST
