How to deal with the error: Too many tries in fill_missing_atoms? about pyrosetta.notebooks HOT 1 CLOSED

IAS is L-aspartic acid, but linked as a beta amino acid. Right now, Rosetta is trying to load the residue parameterization from the wwPDB's Chemical Components Dictionary, but it's having issues with the beta connectivity annotation.

If you want to use the residue as-is, you're likely going to have to generate your own parameter file for it. Failing that, you could potentially use one of the other B-amino acid parameters which are already in the database (e.g. database/chemical/residue_type_sets/fa_standard/residue_types/beta-peptide/B3D.params), either as a template for the params file, or just as is. For the latter you would likely have to edit the input PDB to change atom name and residue specifications.

from pyrosetta.notebooks.