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tbereau / auto_martini

Automatic MARTINI parametrization of small organic molecules
GNU General Public License v2.0
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ALOGPS can't predict fragment #38

Open luisakaermer opened 1 year ago

luisakaermer commented 1 year ago

Hi,

When running python -m auto_martini --smi "c1ccccc1" --mol benz --top benz.itp --verbose

i get the error message:

ALOGPS can't predict fragment: c1ccccc1

What might be the issue here?

Kind regards, Luisa

tbereau commented 1 year ago

Hi Luisa,

Apparently the ALOGPS webserver is down (http://vcclab.org/web/alogps). Without it, auto-martini cannot make the original predictions of water/octanol partitioning. You could try using the flag that enables atomic (i.e., probably not as accurate) predictions --fpred.

Tristan

luisakaermer commented 1 year ago

Hi Tristan,

Thanks for the info and alternative!