I have been trying to dock 2 peptides together, one of them phosphorylated at the serine. It seems that only the docking_local_refine option recognizes the phosphorylated group and generates an output. From what I understand, this option is used only when biological relevant information is available for the interaction interface. In the case where it is absent, is there other ways for the other docking options to work?
Greatly appreciate any help in this! =)
Your problem is likely to be that most docking protocols pass through a centroid phase; Rosetta has no way to represent phosphoserine in the centroid phase and probably converts it to serine. The local_refine method is all fullatom, so the phosphoserine is maintained.
You could try a few things:
A) hack together a centroid parameter file for phosphoserine (um...try just copying serine and changing the name? This is not that valid w/r/t electrostatics or sterics, but centroid mode is pretty vague anyway)
B) perform centroid docking only, get fullatom outputs of the centroid-docked poses, use a script to patch the phosphate back on, and continue to full atom refinement
Thanks for the suggestions!
For (A) do you mean editing the residue types SER.params in the centroid folder in the database?
If the centroid phase is vague, then if I start a run without the phosphate group and finally adding the PO4 group and starting the dockinglocalrefine should be the same as B?
For A, it's more of a duplicate-and-edit, not edit SER directly (surely you have normal serines around).
For B...yes, I think that will work.
Thanks aplenty =)!
I have used option B, then add in the PO4 group for full atom docking, the structures converge nicely into a funnel with less then 5A rmsd from native.