Hi Rosetta Users,
I have been trying out the "UBQ chemically conjugated docking" protocol with a multicomponent system including protein+DNA as the input. I used the UBQ_Gp_LYX-Cterm application to attach the ubiquitin to a lysine residue in one of the protein chains in the protein/DNA complex. The options file is basically the same as provided in the demo. I added the DNA molecule as well as other protein chains (except the target chain to be ubiquitinated) using the flag -chemically_conjugated_docking:extra_bodies. But the following error occurred:
apps.public.scenarios.chemically_conjugated_docking.UBQ_Gp_LYX-Cterm: Current Low total cycles =100 apps.public.scenarios.chemically_conjugated_docking.UBQ_Gp_LYX-Cterm: 1 122031 122031 core.mm.MMTorsionLibrary: MM torsion sets added fully assigned: 766; wildcard: 43 and 1 virtual parameter. core.mm.MMTorsionLibrary: No parameters for CN7-ON2-P-ON3
ERROR: COULD NOT FIND TORSION PARAMS FOR 18 78 84 79
ERROR:: Exit from: src/core/scoring/mm/MMTorsionLibrary.cc line: 221
I guess it means there are missing parameters for the DNA molecule in the system, because when I removed the DNA, the program ran smoothly. Any idea how to fix this issue? Thanks.