Dear Rosetta Users,
I'm using the "residue_energy_breakdown" utility in order to obtain a per-residue energy breakdown of the residues that interact with the ligand in my protein-ligand complex generated by the RosettaLigand application.
In the POSE_ENERGIES_TABLE at the end of the docked model I read quite reasonable energy terms :
but when I try to breakdown the energy on a per-residue basis, I get these values for the residue-ligand interaction :
I can't figure out why the Lennard-Jones repulsive force is so high. There are no evident clashes in the .pdb input.
I'm trying to relax the protein-ligand complex by using the default relax utility or the all-atom harmonic-restrained relax protocol (even though I think that it should be well suited for the Rosetta "residue_energy_breakdown" utility, since it has been generated in the RosettaLigand scorefunction), but I'm not sure how to handle the ligand, as the ligand bonds become totally distorted.
Thanks everyone in advance!