I am trying to model a loop (using kinematic loop modeling) that is in close proximity to a ligand. So I included the ligand by converting the HETATMs into Rosetta atom types and including centroid (for remodel) and all-atom (for refine) parameter files via the -extra_res_cen and -extra_res_fa command lines. I used the script molfile_to_params.py to create the parameter files (both centroid and all-atom) and the ligand.pdb file.
[I made them from a .mol file using the .pdb file of the ligand using openbabel.... maybe there is a problem here..]
The final score of the design is ~700, 400 of which are the score of the ligand alone (after scoring using .../bin/score_jd2.linuxrelease -s design.pdb -database path -extra_res_fa fa.params) . Is it normal for the ligand to have a high score like this or am I doing something wrong here?
I also tried scoring the input pdb (which has the ligand.pdb generated from the script inserted), and the 'ligand residue' also had a high score by itself which was also ~400.
any help is very much appreciated.