Recently I'm stumbling with rosetta RAbD application (version 2020.08.61146) in hope to modify an antibody whose antigen containing a non-canonical,N-term, and PRO-like aa ,namely the pyroglutamic acid in its epitope.
I generated params file according tutorials in :https://new.rosettacommons.org/demos/latest/public/design_with_ncaa/README,with input mol file below.
the product params runs properly during dock,relax,and RAbD's seq_design mode (except for wrong number in N-term hydrogen adding). but when doing graft design ,the application failed during CCDEndsGraftMover with a segmentation fault.
I had a series of attempts to solve the problem:
I fixed the patch file in database/chemical/residue_type_sets/fa_standard( and centroid ) /patches .
I tried to use Pro's centroid Params for this one. I tried to modify the ICOOR_INTERNAL lines so as to make the fold tree grows from CA (rather than from N , as the python script generated) ,adding virtual N and cut_bonds(as Pro's params does) .
I tried to change the value of NBR_RADIUS.
I even tried to modifying the params directly from PRO's by adding an acyl-oxgen atoms.
Below are two files I finally got. Sadly neither of them works. Due to limit error message, it's quite hard for me to debug the 'segmentation fault'.
Can anyone give it a look and help me out ?
thank you very much.