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tbereau / auto_martini

Automatic MARTINI parametrization of small organic molecules
GNU General Public License v2.0
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Error run auto_martini #21

Closed georopon closed 4 years ago

georopon commented 4 years ago

Hi have installed auto_martini and using following command: auto_martini --smi "N1=C(N)NN=C1N" --mol GUA get following file sanitize.log with followin erros: [16:32:27] Can't kekulize mol. Unkekulized atoms: 1 2 3 4 5

WARNING:main:Bad smiles format Nc1ncnn1 found [16:32:27] Can't kekulize mol. Unkekulized atoms: 1 2 3 4 5

WARNING:main:Fixed smiles format to Nc1nnc[nH]1 WARNING:main:Error with BeautifulSoup constructor

AND NOT GET .gro or itp FILES.

Please help me.

tbereau commented 4 years ago

The kekulize issues sound like you're using an old version of RDKIT. Maybe try to updating that.

For issues with "BeautifulSoup constructor," it's also likely that you're using an inappropriate version. Maybe try installing it with pip for instance.

If these don't help, you can always try using either the dev branch (requires Python 3) or the refactor branch.

tbereau commented 4 years ago

Given your other comment I understand you've been able to run the code, so I'll close this issue.