The "molname" parameter was passed incorrectly.

[123chayu]

python "D:\分子模拟\GoMartini\vermouth-martinize-master\bin\martinize2" -f "D:\测试\3SN6_clean.pdb" -x D:\测试\Protein_Active_cg.pdb -o D:\测试\system.top

An error occurred while using the above command.How to deal with?

Traceback (most recent call last):
File "D:\分子模拟\GoMartini\vermouth-martinize-master\bin\martinize2", line 1167, in
entry()
File "D:\分子模拟\GoMartini\vermouth-martinize-master\bin\martinize2", line 1025, in entry
vermouth.NameMolType(deduplicate=not args.keep_duplicate_itp, molname=args.molname).run_system(system)
TypeError: init() got an unexpected keyword argument 'molname'

[csbrasnett]

hi, which version of martinize2 are you using for this please? Does the behaviour change if you give -name as an argument?

[123chayu]

hi, which version of martinize2 are you using for this please? Does the behaviour change if you give -name as an argument?

python "D:\分子模拟\GoMartini\vermouth-martinize-master\bin\martinize2" -f "D:\分子模拟\GoMartini\vermouth-martinize-master\bin\3SN6_clean.pdb" -x "D:\分子模拟\GoMartini\vermouth-martinize-master\bin\Protein_Active_cg.pdb" -o "D:\分子模拟\GoMartini\vermouth-martinize-master\bin\system.top" -name Protein_Active_cg

INFO - general - Applying modification mapping ('C-ter',)
INFO - general - Applying modification mapping ('N-ter',)
INFO - general - Applying modification mapping ('C-ter',)
INFO - step - Averaging the coordinates.
INFO - step - Applying the links.
INFO - step - Placing the charge dummies.
Traceback (most recent call last):
File "D:\分子模拟\GoMartini\vermouth-martinize-master\bin\martinize2", line 1167, in
entry()
File "D:\分子模拟\GoMartini\vermouth-martinize-master\bin\martinize2", line 1025, in entry
vermouth.NameMolType(deduplicate=not args.keep_duplicate_itp, molname=args.molname).run_system(system)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: NameMolType.init() got an unexpected keyword argument 'molname'

the same error !And the version of martinize2 that I'm using comes from the martinize2 file in the bin folder of the vermouth package on GitHub.

[csbrasnett]

the -name argument for martinize2 was only introduced recently. The error raised suggests to me that you're using a new version of the martinize2 script but somehow haven't updated the rest of the vermouth package. I'd suggest installing vermouth in a fresh virtual environment and running from there, that should fix the issue you have

[csbrasnett]

hi @123chayu did you have success?

[123chayu]

Sorry, I'm very busy today. I'll try again tomorrow.👻

…

---- Replied Message ---- | From | Chris ***@***.***> | | Date | 01/03/2025 17:21 | | To | ***@***.***> | | Cc | ***@***.***>***@***.***> | | Subject | Re: [marrink-lab/vermouth-martinize] The "molname" parameter was passed incorrectly. (Issue #646) | hi @123chayu did you have success? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>

[123chayu]

您好，您成功了吗？

(vermouth) C:\Windows\system32>python "D:\Anaconda\envs\vermouth\Scripts\martinize2" -f "D:\测试\3SN6_clean.pdb" -o "D:\测试\system.top" -x "D:\测试\Protein_Active_cg"
INFO - step - Averaging the coordinates.
INFO - step - Applying the links.
INFO - step - Placing the charge dummies.
INFO - step - Sorting atomids
INFO - step - Writing output.
INFO - model - Disulfide bridge found between residues A-CYS77 and A-CYS162
INFO - model - Disulfide bridge found between residues A-CYS155 and A-CYS161
INFO - general - Please cite: Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Gr眉newald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Doma艅ski, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3
INFO - general - A martini should always be stirred, not shaken, so that the molecules lie sensuously on top of one another. -- Somerset Maugham

Yes! I did success! very thanks!
The problem indeed lies in the environment on which Vermouth depends. It is necessary to create a new virtual environment and configure the Python interpreter to version 3.9

[csbrasnett]

Great, glad it worked! Happy simulating!