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marrink-lab / vermouth-martinize

Describe and apply transformation on molecular structures and topologies
Apache License 2.0
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No module named 'core' #508

Closed Clare-xiong closed 1 year ago

Clare-xiong commented 1 year ago

I'm trying to follow the procedure from the following website: http://cgmartini.nl/index.php/martini-3-tutorials/small-molecule-binding#1A. , with the command line being:

./martinize -f 181L.pdb -ff martini303v.partition -x CG.pdb -o topol.top -dssp dssp -elastic

And the output I got this:

Traceback (most recent call last): File "D:\program\lib\runpy.py", line 193, in _run_module_as_main "main", mod_spec) File "D:\program\lib\runpy.py", line 85, in _run_code exec(code, run_globals) File ".\martinize__main.py", line 3, in File ".\martinize\martinize\init__.py", line 37, in ModuleNotFoundError: No module named 'core'

I was wondering if anyone could give me some pointers with this?

pckroon commented 1 year ago

You're not running martinize2, so this is the wrong place for this error.

Clare-xiong commented 1 year ago

You're not running martinize2, so this is the wrong place for this error.

When I run the martinize2, it says ValueError: Unknown force field "martini303v.partition". The command is martinize2 -f 5oqv.pdb -ff martini303v.partition -x CG.pdb -o topol.top -dssp dssp -elastic