Member Site Forums Rosetta 3 Rosetta 3 – General Using D-amino acids in Rosetta docking Reply To: Using D-amino acids in Rosetta docking


    The unknown atom name error is not occuring when Rosetta is reading in your PDB file, it is occuring when other code in the program is trying to access the H atom on that residue. Proline doesn’t have a amide hydrogen, so trying to look it up is a pretty legitimate failure.

    I think in both cases these failures are likely caused somewhere in the scorefunction. The standard scorefunctions make many assumptions about having normal protein; the scorefunctions used for noncanonicals (and Ds) do not. I’ve emailed the noncanonicals guy for advice on which scorefunction to use.