Mutations. In this vein, a mutations module allows to introduce standard amino acid mutations to the topology without the need to go through the full process of topology generation. This has proven particularly useful in the study of heavily glycosylated systems, such as the SARS-CoV-2 Spike , where ready-made topologies and systems were often shared publicly but introducing even minor changes (such as a point mutation) would entail going through the same complicated server-based pipeline, risking introducing additional errors at this stage. This idea is also extended to protonation states, so that individual titratable residues can be protonated or deprotonated easily and in a consistent manner. As long as standard atom name conventions are followed, the mutation module is force-field agnostic, and the user can point to a specific .rtp file containing the respective residue definitions.