I've been trying to incorporate a noncanonical selenium-containing residue into my protein sequence, however, when running molefile_to_params_polymer.py I keep getting an error saying "unknown element SE." I've tried looking at the code where the error occurs, and it seems there are a series of elif statements that specify some atoms that are allowed. That being said, I swapped selenium out for xenon (not listed in the code) in the sdf file and the function ran to completion. I've attached a screenshot of my SDF.
Thank you in advance for your help!
Here is the error message:
Traceback (most recent call last):
File "./molfile_to_params_polymer.py", line 1995, in <module>
File "./molfile_to_params_polymer.py", line 1932, in main
File "./molfile_to_params_polymer.py", line 255, in assign_rosetta_types
else: raise ValueError("Unknown element '%s'" % a.elem)
ValueError: Unknown element 'SE'