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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Received on Fri Nov 05 2021 - 06:30:02 PDT
