I am currently trying to analyze a crystal structure that has various N-linked Glycans attached and would like to be able to work with these glycans in PyRosetta. However, if I try to work with the structure without cleaning it I receive the error message:
>>>pose = pose_from_pdb("my_molecule.pdb")
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 9172 residue types
ERROR: unrecognized aa NAG
ERROR:: Exit from: src/core/io/pdb/file_data.cc line: 1424
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
RuntimeError: unidentifiable C++ exception
Is there currently defined residue types that I can add to my pyrosetta library that define these glycans or ways to work with uncleaned pdb files?
Any help or suggestions would be greatly appreciated.