Hello Rosetta people,
I performed a protein protein docking of a protain A + ligand A (74 atoms) noted as binary_complex to protein B, and got warning of missing atoms, still could get docked P-P poses, however, the ligand is not intact, some atoms missed in the output binary_complex. I also added the -ignore_unrecognized_res flag in the command.
Then I parameterized my ligand using molfile_to_params.py to generate LIG.pdb and LIG.params, copied and pasted the coordiantes of LIG.pdb to my binary_complex. I also added the flag "-extra_res_fa LIG.params" in the commond line while performing docking_protocol.static.linuxgccrelease, then I got error massge for missing atoms. (all atoms of my ligand) and calculation killed. No poses were generated at this time.
Can someone instruct how to solve this issue?