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However, I encountered the following error message:
Traceback (most recent call last):
File "../MARTINI/.martini_env/lib/python3.12/site-packages/vermouth/parser_utils.py", line 239, in parse_section
return method(self, line, lineno, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "../MARTINI/.martini_env/lib/python3.12/site-packages/vermouth/map_parser.py", line 718, in _blocks
block = getattr(self.force_fields[self.ff[direction]], map_type+'s')[attrs['resname']]
~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^
KeyError: 'universal'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "../MARTINI/.martini_env/lib/python3.12/site-packages/vermouth/map_input.py", line 435, in read_mapping_directory
new_mappings = read_mapping_file(infile, force_fields)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "../MARTINI/.martini_env/lib/python3.12/site-packages/vermouth/map_input.py", line 178, in read_mapping_file
for mapping in mappings:
^^^^^^^^
File "../MARTINI/.martini_env/lib/python3.12/site-packages/vermouth/parser_utils.py", line 110, in parse
result = self.dispatch(line)(line, lineno)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "../MARTINI/.martini_env/lib/python3.12/site-packages/vermouth/parser_utils.py", line 241, in parse_section
raise IOError("Problems parsing line {}. I think it should be a "
OSError: Problems parsing line 8. I think it should be a '['modification', 'from blocks']' line, but I can't parse it as such.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "../MARTINI/.martini_env/bin/martinize2", line 1114, in <module>
entry()
File "../MARTINI/.martini_env/bin/martinize2", line 755, in entry
partial_mapping = read_mapping_directory(directory, known_force_fields)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "../MARTINI/.martini_env/lib/python3.12/site-packages/vermouth/map_input.py", line 437, in read_mapping_directory
raise IOError('An error occured while reading "{}".'.format(path))
OSError: An error occured while reading "../MARTINI/tia1/martini_v300_pps/mappings/modifications.mapping".
I suspect there may be an issue with how I’ve set up the mappings or force field directories, but I’m not sure how to resolve it. Has anyone encountered this issue or have advice on troubleshooting? Any guidance would be appreciated.
Thank you.
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I am trying to construct a protein model with a new force field downloaded from the following repository:
https://github.com/KULL-Centre/_2023_Thomasen_Martini/tree/main/force_field
I attempted to generate a topology file using the following command:
martinize2 -f t4l_clean.pdb -o t4l.top -x t4l_cg.pdb -ff-dir martini_v3.0.0_proteins/force_fields/ -map-dir martini_v3.0.0_proteins/mappings/
However, I encountered the following error message:
I suspect there may be an issue with how I’ve set up the mappings or force field directories, but I’m not sure how to resolve it. Has anyone encountered this issue or have advice on troubleshooting? Any guidance would be appreciated.
Thank you.
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