Analysis does not work properly for proteins with multiple chains

[hannahbaumann]

In the Tnks2 system from the protein ligand benchmark set, the ligand RMSD, ligand COM drift and protein RMSD are likely not calculated properly. The protein consists of two chains which may have led to PBC not being removed properly and/or wrong alignment and therefore these very large RMSD values.

Protein and ligands:
https://github.com/OpenFreeEnergy/protein-ligand-benchmark/tree/changes_plb/data/tnks2

Ligand COM drift, Ligand RMSD and Protein 2D RMSD: