# System preparation

A focused tutorial set on preparing biomolecular systems for simulation: protonation, non-standard residues, custom residues from SMILES, and mutation/gap-closing/segmentation.

```{toctree}
:maxdepth: 1

01-basic-protonation
02-non-standard-residues
03-custom-residues-from-smiles
04-mutation-gap-closing-segmentation
```