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cgkmw-durham / cg_param_m3

Coarse-grained mapping and parametrisation for the Martini 3 forcefield
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SyntaxWarning #6

Open 550cw opened 2 months ago

550cw commented 2 months ago

I have a issue with python cg_param_m3.py "CC[C@@H]1C@HC(=O)OC)C9=[N]6C(=C4)C@HC)C)C(=O)C)C" BCL_CG.gro BCL_CG.itp BCL y. This is my error:

/home/zhangyq/cg_param/cg_param_m3.py:637: SyntaxWarning: invalid escape sequence ']' lc = re.compile('[cn([nH])os]+') Traceback (most recent call last): File "/home/zhangyq/cg_param/cg_param_m3.py", line 1317, in tuning = bool(int(sys.argv[4])) ^^^^^^^^^^^^^^^^ ValueError: invalid literal for int() with base 10: 'BCL' (cg_param) [zhangyq@arg cg_param]$ python cg_param_m3.py "CC[C@@H]1C@HC(=O)OC)C9=[N]6C(=C4)C@HC)C)C(=O)C)C" BCL_CG.gro BCL_CG.itp BCL n /home/zhangyq/cg_param/cg_param_m3.py:637: SyntaxWarning: invalid escape sequence ']' lc = re.compile('[cn([nH])os]+') Traceback (most recent call last): File "/home/zhangyq/cg_param/cg_param_m3.py", line 1317, in tuning = bool(int(sys.argv[4])) ^^^^^^^^^^^^^^^^ ValueError: invalid literal for int() with base 10: 'BCL'

Do you know how can I solve it? Thank you so much.

550cw commented 2 months ago

(cg_param) [zhangyq@arg cg_param]$ python cg_param_m3.py "CC[C@@H]1C@HC(=O)OC)C9=[N]6C(=C4)C@HC)C)C(=O)C)C" BCL_CG.gro BCL_CG.itp 0 /home/zhangyq/cg_param/cg_param_m3.py:637: SyntaxWarning: invalid escape sequence ']' lc = re.compile('[cn([nH])os]+') False [N-]->Mg+2(<-N)<-N not on list [N-]->Mg+2(<-N)<-N Data from Wildmann-Crippen [20:38:47] UFFTYPER: Unrecognized charge state for atom: 11 new issu

EKearn commented 2 months ago

Hi there,

I don't recognise your SMILES, could you simplify it or tell me what molecule it is? Is it pentane? I cannot currently reproduce your UFFTYPER error.

The error above is due to a redundant line, 637, that you can comment out. It wasn't causing problems until a recent python update, but I will remove it in the main branch shortly.

Thanks for messaging, Eoin