Re: [Rdkit-discuss] [ext] online sdf to mol2 converter

The joy of aromaticity models. Via Noel if you're running the (dev/master) version of OpenBabel you can specify *-aa* to take the aromaticity from the input. For example >obabel -:o11 -omol2 -aa > @MOLECULE > * > 5 5 0 0 0 > SMALL > GASTEIGER > @ATOM > 1 O 0.

Re: [Rdkit-discuss] [ext] online sdf to mol2 converter

Maybe try NAOMI from Matthias Rarey's group (https://www.zbh.uni-hamburg.de/forschung/amd/software/naomi.html) Best, Andrea Prof. Dr. Andrea Volkamer In-silico Toxicology Group, Institute of Physiology,

[Rdkit-discuss] online sdf to mol2 converter

Greetings, Is anybody aware of a good sdf to mol2 file converter that is not based on OpenBabel? I want to avoid problems like the following, which I currently solve with Maestro. Basically, the problem is with O40 which -according to antechamber from AmberTools- should be sp3 within a