I'm folding a protein which is a trimeric long helix bundle. I started from the main/demos/public/symmetry_examples/fold-and-dock/ and added my info (sequence, fragments etc). This basically works but a lot of the resulting folds are globular not long - the helixes fold over on themselves. I'd like to constrain this to extended conformations only.
I looked at constraints in the Rosetta docs, and tried creating input_files/constraints.cst to give a penalty to any structure which has less than 50-70 A distance between residues 1 and 63:
AtomPair CA 1A CA 63A FADE 50 1000 20 -100 100
AtomPair CA 1B CA 63B FADE 50 1000 20 -100 100
AtomPair CA 1C CA 63C FADE 50 1000 20 -100 100
I also added this to inputs/fold-and-dock-flags to turn on the constraints:
However this has no effect; most of the resulting structures are compact, same as before.
How do I turn on constraints for fold-and-dock with symmetry? Is there a problem with how I'm specifying the constraints?
(My normal fold-and-dock flags before the constraints are attached; Environment is Rosetta 2020.11 on Ubuntu 18.04 on AWS)