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 Wed Nov 03 2021 - 05:00:03 PDT
