Re: [AMBER] Sander python API problem (?)

From: Elisa Pieri <elisa.pieri90.gmail.com>
Date: Fri, 24 Feb 2017 15:23:19 +0100

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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> > > >>
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Received on Fri Feb 24 2017 - 06:30:03 PST
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