normal Martinize 2 with MARTINI 3

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3 years 1 month ago #8933 by shtkddud123
Martinize 2 with MARTINI 3 was created by shtkddud123
Hello all,

I'm currently running into some issues with trying to martinize glycophorin A ( www.rcsb.org/3d-view/1AFO ). I'm trying to follow the procedure from the following website: cgmartini.nl/index.php/martini-3-tutoria...all-molecule-binding , with the command line being:

./martinize -f 1afo.pdb -ff martini303v.partition -x CG.pdb -o topol.top -dssp dssp -elastic

However, I seem to be getting the error:

raceback (most recent call last):
File "/usr/lib/python2.7/runpy.py", line 174, in _run_module_as_main
"__main__", fname, loader, pkg_name)
File "/usr/lib/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "./martinize/__main__.py", line 10, in <module>
File "./martinize/martinize/cli.py", line 204, in main
File "./martinize/martinize/core.py", line 556, in main
File "./martinize/martinize/core.py", line 441, in do_topology
File "./martinize/martinize/core.py", line 85, in average_secstruc
NameError: global name 'options' is not defined


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

Thanks

Sang

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3 years 1 month ago #8936 by riccardo
Replied by riccardo on topic Martinize 2 with MARTINI 3
I don't know if this is really causing that error but for sure you should be using python3 (instead of python2 that you are currently using).

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3 years 1 month ago #8938 by peterkroon
Replied by peterkroon on topic Martinize 2 with MARTINI 3
Plus, it looks like you're actually running martinize1, not 2.

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1 year 4 months ago #9561 by omkar73
Replied by omkar73 on topic Martinize 2 with MARTINI 3
I am trying to follow the small molecule binding tutorial, and when I proceed with this command:
./martinize -f 181L.pdb -ff martini303v.partition -x CG.pdb -o topol.top -dssp dssp -elastic

I get the error:
Traceback (most recent call last):
File "/usr/lib/python3.8/runpy.py", line 194, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/usr/lib/python3.8/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "./martinize/__main__.py", line 3, in <module>
File "<frozen zipimport>", line 259, in load_module
File "./martinize/martinize/__init__.py", line 37, in <module>
ModuleNotFoundError: No module named 'core'

how to address this?

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1 year 4 months ago #9562 by riccardo
Replied by riccardo on topic Martinize 2 with MARTINI 3
That looks like you're using martinize 1. Please make sure to be following the latest tutorial:

cgmartini.nl/index.php/2021-martini-onli...all-molecule-binding

(and martinize2). Hope this helps

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