Hi, I'm minimizing structures in a list of PDB's using the -l option. Some structures have different ligands which I'd like to ignore or skip. The -ignore_unrecognized_res doesn't work. Minimize got bumped out trying to fill in missing atoms. Apparently it did not see or understand the flag.
Try also adding "-load_pdb_components false"
A few years ago we added the wwPDB's chemical components dictionary so that Rosetta can auto-create parameters for ligands that appear in the PDB / files downloaded from that source. Not all of them work cleanly. This flag will tell Rosetta to NOT try keeping those ligands via that data source and it will much more aggressively ignore nonprotein residues.
Hi smlewis, Thanks a lot for the tip. The combination worked! However, minimize spits out another error: "Error, no reference ligand for RMSD calculation". Is there a flag to tell it to skip RMSD calculation for that particular structure that has been ignored/skipped?
Another question is minimize doesn't write out the score.sc file. I use -l pdb.list and -out:file:scorefile score.sc but it would write out score.sc. It would when I use -s filename.pdb but not -l pdb.list. The -s flag doesn't work with a list.