I have tested the new option -auto_setup_metals ( https://www.rosettacommons.org/docs/latest/Metals.html ) when relaxing an enzyme containing a Zinc ion, corrdinated by four cysteine residues. The weekly build version used for test was downloaded at the end of 2014 from Rosettacommon website.
The relax program finished successfully. However, the extract_pdb program fails to read the silent file generated by relax with -auto_setup_metals. It complains:
[ERROR] EXCN_utility_exit has been thrown from: src/core/chemical/ResidueTypeSet.cc line: 397
ERROR: unrecognized residue name 'CYSSG_connect'
In the silent file, the sequence contains cysteine residues followed by the unknown "residue" CYSSG_connect:
Obviously, the annotation tells Rosetta that the cysteine residues coordinate the Zinc ion. But extract_pdbs program does not understant that and does not find a residue type CYSSG_connect in the res_types directory (I could not find any file with such a name or containing such a term).
I added -auto_setup_metals to the extract_pdb program, same error.
I added -ignore_unrecognized_res true to the command line, same error.
Of course a temp solution is to ask relax to output only pdb files. But is there any way to read the silent files? Was it because the residue type files are missing from the new weekly build? Was it because the residue type CYSSG_connect was not decomposed correctly by the extract_pdbs program?