System building

Build solvated, parameterized systems ready for production MD. Each tutorial is a working end-to-end build for a different class of system, in order of increasing complexity:

• Build a protein
• Build a protein with a ligand
• Build a protein with a ligand using OpenFF
• Build a stapled peptide
• Build a cyclic peptide
• Build a bicyclic peptide
• Build a membrane-embedded protein
• Build a protein-RNA complex

The system-building overview lays out the conceptual pipeline these tutorials walk through; the API reference for htmd.builder and htmd.builder.nonstandard has the full argument lists.