This is still unsolved.
Any help or guidance would be appreciated
Thanks
Sangeetha
On Wed, Nov 3, 2021 at 5:09 PM Sangeetha B <jvbsangeetha.gmail.com> wrote:
> Dear Amber Users,
>
> I want to convert a few gromacs topology files to amber format using
> ParmEd.
> I have installed Gromacs and Amber in my machine and all the paths set
> fine.
> When I try to load parmed, 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
>
>
> I have also tried to use amber.python to do the file format conversion
> using the script,
>
> import parmed as pmd
> gmx_top = pmd.load_file('topol.top', xyz='system.gro')
> gmx_top.save('complex.top', format='amber')
> gmx_top.save('complex.crd', format='rst7')
>
>
> when I run this using amber.python, I always end up with the following
> error:
>
> 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?'
>
>
>
> My system is a protein-rna complex so the gromacs topology includes two
> .itp files corresponding to the two different chains.
> Also, I am using a modified force field which is present in the Gromacs
> path and in the working folder.
>
> I am sure the script seems to recognize the files but I am unable to
> translate the error.
>
> I have also tried by installing parmed separately using pip in amber.python
>
> All the installations seem to be fine but it just doesn't work.
>
> Any guidance on how to make parmed work or "gromacs to amber conversion"
> would be helpful...
>
>
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Received on Fri Nov 05 2021 - 07:00:03 PDT
