ERROR:: Exit from: src/core/fragment/ line: 116

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    • #2027

        Dear all,
        when I run the ab_initio Flexpepdock protocol, I got this error :src/core/fragment/ line: 116
        Can someone give me some comments?
        this is my flag:
        -s eq_1_0001.pdb
        -database /home/tuongvy/SW/rosetta3.4/rosetta_database

        -out:file:silent decoys.silent
        -out:file:silent_struct_type binary

        -rep_ramp_cycles 10

        -jran 12456

        -frag3 ../NullFragments0/output_files/frags.200.3mers

        -frag5 ../NullFragments0/output_files/frags.200.5mers

        -nstruct 2000

        Thank in advance

      • #10428

          You’re getting that error because one of the fragment files you’re attempting to read can’t be read. Which file is giving you the problem should be being written to the standard error stream, in a message like “”Open failed for file: FILENAME”

          Apropos of nothing, my guess is that the relative path you’re giving for -frag3 and -frag5 aren’t working because the path isn’t correct from the directory you’re running from. (The paths would need to be relative to the directory from which you start Rosetta, not the directory where the option file lives.) Try changing the paths, or better yet, turning them into absolute paths, and see if that fixes your issue.

        • #10446

            Thank you a lot rmoretti
            Phan Vy

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