I am struggling with generating params files to represent a new linear polymer in rosetta. I am using the general idea employed for the already implemented polymers (such as CAAs, NCAAs or nucleic acids) in which you define a params file containing the lower and upper atom connect entries. I also have set up the internal coordinate entries for these upper and lower connections, which are needed to generate meaningful connections between the polymer's residues. Additionally, I've created upper and lower terminus variants as separated params files, changing their atoms and charges and setting their lower or upper connections accordingly as none.
My problem is when I try to read the PDB file containing a ten residues version of the polymer. I am reading all the (three) params files with -extra_res_fa option; however, it complains about:
ERROR: Unable to find desired residue 'PET' with variant 'UPPER_TERMINUS_VARIANT'. Attempted to add target variant(s) to ResidueType using both ResidueType base name 'PET' and base ResidueType. Was attempting to add new variant type 'UPPER_TERMINUS_VARIANT'
I tried to find how Rosetta interprets the upper and lower terminus variants, but I could not find much information about this. I looked at the database and found the param files for protein caps (i.e., ACE and NME residues) and, copying that idea, I set up my upper and lower variants as different cap residues; however, the error continued to be the same.
Is there any way I can make rosetta aware of the polymer residue's upper and lower terminus variants? or is my problem laying somewhere else entirely?
I am attaching all my params files.
(I apologise for putting this in the Non-Canonical Peptides category; I could not find anything more adequate).