You didn't attach any files I could see.
On Fri, Nov 5, 2021 at 9:49 AM Sangeetha B <jvbsangeetha.gmail.com> wrote:
> Thank you for the reply.
> These files are the ones I used to run the simulations with Gromacs.
> I haven't modified anything in these files generated by Gromacs and I do
> not find this number in those files.
>
> I could atleast use "outparm" or something like that if parmed loads.
> Simply typing "parmed" in terminal prints the following error instead of
> the artful PARMED fist...
>
> Traceback (most recent call last):
> File "/mnt/c/amber20/bin/parmed", line 33, in <module>
> sys.exit(load_entry_point('ParmEd==0+unknown', 'console_scripts',
> 'parmed')())
> File "/mnt/c/amber20/bin/parmed", line 25, in importlib_load_entry_point
> return next(matches).load()
> StopIteration
>
>
>
> On Fri, Nov 5, 2021 at 6:46 PM Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > On Wed, Nov 3, 2021 at 7:40 AM Sangeetha B <jvbsangeetha.gmail.com>
> wrote:
> >
> > > Traceback (most recent call last):
> > > File "parmediting.parmed", line 3, in <module>
> > > gmx_top = pmd.load_file('topol.top', xyz='RRM_RNA_sol_ions.gro')
> > > File
> > >
> "/mnt/c/amber20/lib/python3.8/site-packages/parmed/formats/registry.py",
> > > line 214, in load_file
> > > return cls(filename, *args, **kwargs)
> > > File
> > >
> >
> "/mnt/c/amber20/lib/python3.8/site-packages/parmed/gromacs/gromacstop.py",
> > > line 251, in __init__
> > > self.read(fname, defines, parametrize)
> > > File
> > >
> >
> "/mnt/c/amber20/lib/python3.8/site-packages/parmed/gromacs/gromacstop.py",
> > > line 396, in read
> > > a, b, c, t, ut = self._parse_angletypes(line)
> > > File
> > >
> >
> "/mnt/c/amber20/lib/python3.8/site-packages/parmed/gromacs/gromacstop.py",
> > > line 780, in _parse_angletypes
> > > k = (float(words[5]) / 2) * (u.kilojoules_per_mole / u.radians**2)
> > > ValueError: could not convert string to float: '538.874?'
> > >
> >
> > Look for this string in one of your input files or include topology
> files.
> > There's a character (question mark maybe) that is preventing ParmEd from
> > being able to parse the files. This looks like a broken file in some
> way -
> > where did you get these input files?
> >
> > HTH,
> > Jason
> >
> >
> > --
> > Jason M. Swails
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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--
Jason M. Swails
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Received on Fri Nov 05 2021 - 14:30:02 PDT
