Question: does the Rosetta force field incorporate amino acid post-translational modifications such as hydroxyproline and C-terminal amidation? If yes, where can I see this in the database? If not, how can I parameterize these PTMs?
I think MOE from CCG should be able to help you study the impact of PTMs likes oxidation, deamidation and Asp isomerization on protein conformation and stability using AMBER10:EHT. EHT part will parameter-ize the non-standard amino acids. In past, I have used MOE and AMBER:EHT to model Antibody drug conjugates (ADCs). The linkers and small molecule payloads involved needed to be parameterized in that case.