first run of abinitio in rosetta 3.2 produces an error right away

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    • #814

        I just got Rosetta 3.2 built on linux and I’m trying to run abinitio for the first time. I am getting this error when I run AbinitioRelax.linuxgccrelease.

        ERROR: [ERROR] Unable to open kill_hairpins file
        ERROR:: Exit from: src/core/scoring/ line: 344

        In the command I have “-kill_hairpins 1l2y_.psipred_ss2” but when I search for the file I can’t find it. Where should this file be and how do I set-up this command line option to get it to run? I am completely new to Rosetta so maybe this is something stupid/easy, but I can’t figure it out. Let me know if you need more information. Thanks for the help.

      • #5121

          So…why did you put kill_hairpins in your command line? Was it in an example or something? Perhaps 1l2y_prispred_ss2 was also in the same example folder (where you found the input fasta, etc.) Surely you aren’t trying to fold 1l2y on purpose (since it IS one of our common example proteins…)

        • #5127

            I don’t have a clue what it does either. I’d just skip it. If you find yourself with a psipred_2 file later doing your actual modeling, you can always try it then! You may collect one as a side effect of generating fragments.

            Psipred_2 is a secondary structure prediction algorithm; I’m guessing the file contains hints telling Rosetta where beta-hairpins are likely to occur.

          • #5123

              I was following the manual and it had that listed as a command line option to use for optimal performance. I really don’t know much about this and I’m just trying to figure out how to get rosetta to run. I’m a freshman undergrad and I work in a molecular bio lab. I recently took on the task of getting rosetta installed on one of the computers in the lab and to workout how to run rosetta. I was trying to run the demo that came in the bundle for abinitio but couldn’t find that file in the folder. So is the kill-hairpins option not needed? To be honest I don’t really even know what kill-hairpins does. I’ve only been working on this for just a few days. Thanks for the help.

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