ah, can you also provide exact cpptraj command to convert that .nc file to
rst7?
Hai
On Fri, Feb 24, 2017 at 9:35 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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
>> > > > >>>
>> > > > >>> _______________________________________________
>> > > > >>> AMBER mailing list
>> > > > >>> AMBER.ambermd.org
>> > > > >>> http://lists.ambermd.org/mailman/listinfo/amber
>> > > > >>>
>> > > > >>
>> > > > >>
>> > > > > _______________________________________________
>> > > > > AMBER mailing list
>> > > > > AMBER.ambermd.org
>> > > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > >
>> > > > _______________________________________________
>> > > > AMBER mailing list
>> > > > AMBER.ambermd.org
>> > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > >
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 24 2017 - 07:00:03 PST
