Can't kekulize mol about auto_martini HOT 4 OPEN

!pip install selfies

import selfies as sf
sm = "NC(CC1=CC(NN=C1C=1OC=CC1)=O)CC)"

new_sm = sf.decoder(sf.encoder(sm))

Chem.MolFromSmiles(new_sm)

from auto_martini.

Dear Mei Woo,

Yes, that unfortunately happens once in a while. I don't have a systematic fix. That often happens on some aromatic nitro groups. I would suggest trying to parametrize a molecule that's similar but doesn't have the problematic group. I'm not sure which one it is here, but you could play around with the chemistry and see what works. Also, it doesn't seem like the SMILES you provide is valid. Did you check that?

Best,
Tristan

from auto_martini.

Hi Tristan,

Thanks for your reply.
I have tried another SMILES translator and tired this SMILES ( CCC(N)Cc1cc(=O)[nH]nc1c2ccco2 ) as well but I still got the same error. Do you get the same error as well? Are there any ways those we can work around this problem. I have a set of molecules to parametrize with this starting structure.

Regards,
Mei Woo

from auto_martini.

I do get the same error.

I would replace the aromatic nitrogens by carbon and try to parametrize that. For instance, the slightly different compound CCC(N)Cc1cc(=O)ncc1c2ccco2 does go through in the Master branch. You'll then need to manually adjust the bead type to correct for the change in water/oil partitioning.

Not extremely systematic unfortunately, but that might do it.

Best,
Tristan

from auto_martini.