On the matter of using GenKIC to model a loop of noncanonical groups like beta-peptides or peptoids, the GenKIC program falters due to lack of centroid data.
The requirements for centroids is confirmed by removal of the ALA.params file from: database/chemical/residue_type_sets/centroid/residue_types
This causes the same error as it does for sequences of beta-peptides and peptoids for which there are all-atom params files in: database/chemical/residue_type_sets/fa_standard/residue_types/
So there are two possible approaches I see right away:
(1) Modify the GenKIC code to allow for all-atom residues to be assessed at the first pass, or
(2) Generate centroid .params files for the noncanonical (non-protein) residues of interest.
I am hoping to do the latter as this would allow the continued use of GenKIC for non-protein residues and permit modelling of hybrid loops.
Does anyone know how to create a centroid params file from scratch?