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

From: Elisa Pieri <elisa.pieri90.gmail.com>
Date: Fri, 24 Feb 2017 11:24:33 +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 Fri, Feb 24, 2017 at 11:22 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
>
> Elisa
>
> 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 - 02:30:03 PST
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