-loops:fa_input not found in command line top-level context

[Anonymous]

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.

[Anonymous]

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.

[Anonymous]

Thank you very much for the link!

[Author]

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