principev

Not too sure what exactly you mean by this. In the API-reference for _Feature and Sample Selection_ it states that: "scikit-matter contains multiple data sub-selection modules, primarily corresponding to methods...

Ah that'll be it! I used ANI on a charged Arginine residue so that's probably where it went wrong. I'll try again without using ANI on that residue and see...

Thanks for the suggestions. I've just finished running simulations using ANI on only uncharged binding site residues but the protein still unfolded throughout the simulation. As @peastman said, I guess...