System preparation

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

• Basic protonation
• Non-standard residues and covalent modifications
• Custom residues from SMILES
• Mutation, gap closing, and auto-segmentation
• Filling missing loops from a homologous structure