This is the command I am trying to execute (taken from here: https://www.rosettacommons.org/docs/latest/application_documentation/ana..., in the Preminimization of the Input Structures paragraph, in High Resolution Protocol):
minimize_with_cst.linuxgccrelease \
-in:file:s "input.pdb" -in:file:fullatom -ignore_unrecognized_res \
-fa_max_dis 9.0 -ddg::harmonic_ca_tether 0.5 -score:weights standard \
-ddg::constraint_weight 1.0 -ddg::out_pdb_prefix min_cst_0.5 \
-ddg::sc_min_only false \
-score:patch $ROSETTA3_DB/scoring/weights/score12.wts_patch > mincst.log
I get the following error:
ERROR: Rosetta does not recognize the property: SIDECHAIN_THIOL; has it been added to general_properties.list?
The "input.pdb" file was obtained by running tools/protein_tools/scripts/clean_pdb.py on a crystallographic pdb files, selecting a single chain.
I have no idea what this error means. What can I do to fix this?
I am using Rosetta 2015.31.
This error is normally due to a version mismatch between your executable and database. (That is, residue information in the database has "SIDECHAIN_THIOL" properties annotated, but the version of Rosetta you're using is an older one which doesn't recognize that property.)
Double check your paths and versions you're using, both of the executable and of the database, to make sure they're compatible. Try explicitly giving the path to the correct database on the commandline with the "-database" flag.
If all else fails, try re-compiling your Rosetta installation. (Just re-run the same command you used originally.) To be safe, I'd recommend deleting the contents of the bin/ directory (but *not* the build directory, at least not at this point) to make sure you don't have links to older versions of the programs hanging around/mis-linked.
Also, if you're using a weekly release, the scorefunctions are set up with talaris2013 as the defaults. This is generally incompatible with the older score12 settings. If you want to go back to score12, you should add the "-restore_pre_talaris_2013_behavior" flag to your commands.