I'm trying to dock a symmetrical trimer of the transmebrane helix domain of SARS-CoV-2 spike protein: https://web.expasy.org/cgi-bin/protparam/protparam1?P0DTC2@1214-1234@ using Rosetta (2020.08).
The docking seems to work, and produces reasonably packed triple helix bundles which are symmetric. However, since this entire domain is supposed to be in the membrane, I'd like to not have a penalty for exposed hydrophobic side chains.
How do I change the options to do that?
The command I'm running is:
rosetta/main/source/bin/SymDock.static.linuxgccrelease @flags
and flags is:
-in:file:s input/robetta_job_23994_model01.pdb
-in:file:fasta input/robetta_job_23994_model01.fasta
-symmetry:symmetry_definition input/c3_denovo.sym
-packing:ex1
-packing:ex2aro
-out:nstruct 100
-out:file:fullatom
-symmetry:initialize_rigid_body_dofs
-symmetry:symmetric_rmsd
-ignore_unrecognized_res
-docking:dock_mcm_trans_magnitude 0.1
-docking:dock_mcm_rot_magnitude 1
-ex1
-ex2
-symmetry:perturb_rigid_body_dofs 3 8
Please also let me know if the flags look reasonable for this problem.
The input pdb file is a simple helix as predicted here: http://new.robetta.org/domain.php?id=23556
P.S. Now that the docking job has generated a few hundred structures and I've had a chance to look at them, I notice that many of them have the helixes far too steeply tilted, and with too small a contact area, to be realistic. I'm not sure why Rosetta is doing that - there should be some kind of term that favors tight packing (entropy-driven?) but it doesn't seem to be working here.
