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?
Answered at https://rosettacommons.org/node/11750