This is where replacing the GAFF atom types with the equivalent AMBER protein atom types would help (see my earlier email). AMBER has no built-in parameters for (GAFF atom)-(non-GAFF atom) bonds, so the backbone connections to neighboring residues will be unrestrained.

On Fri, 18 Apr 2025 at 11:38, Yang Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Addendum: some odd mainchain behaviour as a result of the residue not being recognised as a regular peptide, but nothing a few restraints can't shoehorn and keep under control. In particular, secondary structure restraints still seem to hold.
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