I'd like to fold a protein in Rosetta which is known to be a long helix bundle. It is a homo-trimer, so I'm using the fold-and-dock method with symmetry. I started from the main/demos/public/symmetry_examples/fold-and-dock/ example and made some changes for my protein (fasta, fragments etc).
This basically works in that it produces symmetric structures, and they are mostly helixes, but they tend to be fairly globular - the helixes fold over on themselves to form a sort of big ball. From what is known about the structure, the helixes should not fold over - they are expected to coil around each other, and may have some (small) loops, but the overall shape is extended not globular.
How do I restrict Rosetta to only consider extended conformations during docking?
I looked at constraints in the Rosetta docs, and tried creating input_files/constraints.cst like this:
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
(this is intended to add a penalty if the distance between first and last CA atom on each chain is less than 50 Angstroms)
I also added to inputs/fold-and-dock-flags:
-constraints:cst_fa_file ./input_files/constraints.cst
-constraints:cst_fa_weight 2.0
However, this appears to have no effect, and the resulting structures certainly bring the first and last residues closer than 50 A. Why are the constraints not working?
Also, is this a good constraints strategy to "stretch out" the protein?
Environment: Rosetta 2020.11.61179, Ubuntu 18.04 on AWS
