Coarse Graining Generation

Cannot get coarse graining using GRiTS to work in the [coarse-grain.ipynb](https://github.com/cmelab/pl-validation/blob/clean-attempt/coarse-grain.ipynb). Produced mol2 and xml using the SMILES string shown in the attached image but it "cannot be found in the molecule."

A single frame GSD of this molecule can be produced using the single molecule sim in poly_min_working_example.ipynb as set up [here](http://localhost:8888/lab/tree/repos/pl-validation/poly_min_working_example.ipynb)