Hello. I am trying to get my RNA as a ligand in Remodel and according to rosetta documentation it should be read directly but my format is somehow off.
Flags:
-in:file:s protein.pdb
-remodel:blueprint protein.blp
-remodel:num_trajectory 150
-remodel:save_top 50
-overwrite
-remodel:checkpoint
-out:file:scorefile protein.sc
-remodel:use_pose_relax
-constrain_relax_to_start_coords
-score:set_weights coordinate_constraint 4.0
-coord_constrain_sidechains
-ramp_constraints false
-ex1
-ex2
-use_input_sc
-extra_res_cen rna.pdb
tried in:file:extra_res_fa. Same just error thrown earlier.
I tried getting RNA as a param file but i get stuck at splitting P-O3' bonds (rotable bonds definitions, torsions,etc.)
Format:
ATOM 1 P RGU B1138 50.994 77.831 92.006 1.00 76.88 P
i really need help on this. I just need it to sit as a rigid body so pose relax works properly. RGU is GUA for RNA according to res_fa