Dear Jason,
That was my silly mistake.
I found this string in the modified ff, which I ignored to check because I
never got any warnings before.
Correcting it solved my problem and I am able to convert the topology.
Thanks a lot for pointing that out.
But still the problem of "parmed doesn't load" still exists.
When I try to load parmed by typing "parmed" in the terminal, I get the
following error.
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
Any help regarding this?
On Sat, Nov 6, 2021 at 2:41 AM Jason Swails <jason.swails.gmail.com> wrote:
> 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
> > > _______________________________________________
> > > 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
> >
>
>
> --
> Jason M. Swails
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>
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Received on Sat Nov 06 2021 - 04:00:03 PDT
