I am frequently asked to set up and parameterize difficult systems for molecular dynamics simulation, and thought I would make it easier for others to do the same in the future by writing some tutorials.
Here, we will set up a diubiquitin system with a K11 isopeptide linkage joining two chains. The info here can be applied to any systems that have residues that join in ways different from the usual peptide sequence.
Here we will use the AMBER forcefield, parameters, and file types. You’ll learn about how AMBER defines new resides in perhaps more detail than is necessary. You should have basic experience preparing PDB structures for MD simulation (tutorials here) and have a general understanding of what atom types and forcefields are (helpful review article).