I have been succesfully used ROSIE for the generation of Ab Fab models, but now I am having problems with one of them and I don't really understand why.
I run ROSIE with the H3 loop model option and the server generated the 10 model models as usual, but when I openened the pdb files the structure seemed wrong. The N-terminal of the main VL chain goes into the core of the Ig domain and there is a weird turn (instead of a b-strand) before the CDRL3 which is affecting the proper folding of the VL chain. I have attached the .pdb file for the lowest energy model so you guys can take a look at the VL folding and hopefully give a hand with this problem.
Any help/suggestion would be greatly appreaciated
Thanks in advance