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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>
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Received on Fri Nov 05 2021 - 07:00:03 PDT
