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:
-constraints:cst_fa_file ./input_files/constraints.cst
-constraints:cst_fa_weight 2.0
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?
Many thanks!
(My normal fold-and-dock flags before the constraints are attached; Environment is Rosetta 2020.11 on Ubuntu 18.04 on AWS)
| Attachment | Size |
|---|---|
 fold-and-dock-flags.txt | 1.73 KB |
EDIT: I did not read your question well enough and thought you were aiming for a range between 50 and 70, but now I notice you mentioned you do want the upper limit huge and was done on purpose. So my message was all wrong. But I would suggest trying BOUNDED. And adding the weight to the centroid scorefunction (cen) in addition to the full-atom (fa) one.
The problem is your bounds I reckon.
The upper should be 70, while the d is how quickly you get the bonus. That is the function has a pontential well shape, which starts decreasing at lower and reaches full depth at lower + distance and starts going up at upper + distance, to be fully up at upper.
So FADE 45 75 5 -100 100 would be better. That is at 45 Å you pay 2 * 100 kcal/mol, while with 50-70 Å you gain -200 kcal/mol (those are mad high numbers btw!).
I personally unimaginatively would have gone with FLAT_HARMONIC centered at 60 Å ± 5 with tollerance 10 and have not used this, so I may be reading this wrong.
The FADE function is less common than BOUNDED or FLAT_HARMONIC, but has the feature you get a bonus in addition to a penalty. So makes total sense here.
Thank you very much! I think you solved it - fold-and-dock uses centroids, so the constraints probably weren't being applied because of that.
I will try and report back.
Btw it seems like the centroid constraints are set with -constraints:cst_file and fullatom with -constraints:cst_fa_file? Does my syntax look okay except for that? It would be good to add this to the documentation at https://www.rosettacommons.org/docs/latest/application_documentation/analysis/Constraint-Info - now it doesn't explain about the difference between the two.
FLAT_HARMONIC or BOUNDED would both work - I should probably use a more common type of function. I wanted to essentially rule out any compact conformations, hence the high numbers :)
I should mention that for amino acids in centroid the side chain is shrunk down to the beta carbon and a lot of atoms would not be there, here is phenylalanine in centroid:
So the _fa_ to _cen_ works in your case, but no for other cases.
About the confusingness, it makes a bit more sense with pyrosetta where you explicitly apply the constraints to the pose and set the weight to the scorefunction. And a centroid pose is different than a full atom one.