Hi everybody!
I'm trying to learn how to use Rosetta in de novo protein design. I use this article as a manual: https://www.ncbi.nlm.nih.gov/pubmed/23744289
It doesn't work for me at some point. Namely, when I go to step 13 (Running the comparative modeling job), I try to execute the following command in the terminal:
./loopmodel.default.linuxgccrelease @modeling.options -database rosetta_database -nstruct 100
But the response is:
ERROR: ERROR: Option matching -loops:fa_input not found in command line top-level context
It seems rather strange, because Rosetta modeling option contains the description of this parameter: https://www.rosettacommons.org/manuals/rosetta3.1_user_guide/opt_loops.html
My rosetta version is rosetta_bin_linux_2017.08.59291_bundle
I performed search of this error on the forum but didn't find anything.
Thank you in advance!
Nick.
The documentation page you're looking at is for Rosetta 3.1, which is old (released late 2009). The manual for recent versions of Rosetta can be found here: https://www.rosettacommons.org/docs/latest/Home
That particular option (-loops:fa_input) hasn't been used in a while. I don't belive it's necessary for most current loop modeling applications. In a pinch you can try '-in:file:fullatom' to tell Rosetta that your input structures are in fullatom format, but that's likely not going to be necessary.
Thank you very much for the link!