As referred in http://antibody.graylab.jhu.edu/antibody/doc/, the command of rosetta antibody in stage of CDR H3 modeling and VL-VH optimization options has the option ~~#FF0000:-relax_dock -snug_fit~~ .
When I applied these options, the log threw some warnings like:
^pose_minimize:: Big score_delta when turning off the nblist: 45246.6
This probably means the structure moved too far during
minimization. If you are minimizing rigid-body translations you
may need to damp the repulsive initially or change the step-size
======================================================
======================================================
DANGER!!!! DANGER!!!! DANGER!!!! DANGER!!!! DANGER!!!!
======================================================
======================================================
======================================================
======================================================
DANGER!!!! DANGER!!!! DANGER!!!! DANGER!!!! DANGER!!!!
======================================================
^
But if I use those options: ~~#FF0000:-relax_cdrs~~ but __NO__ ~~#FF0000:-relax_dock -snug_fit~~, there are no such warnings in log.
I want to know what 's the differences of the two options and why they introduce such differences.
many thanks.
-Jarod