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
>
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Received on Thu Feb 23 2017 - 08:30:03 PST
