the problem in making fragments

Member Site Forums Rosetta 3 Rosetta 3 – General the problem in making fragments

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    • #398

        Hi I’m new user in this wiki page

        I have problem in making fragament step using rosetta3.0 in CS-rosetta

        which is developed in bax group for nmr structure determination

        when I invoked the command ( nearly same as

        make excep the vall database and compiled pNNMAKE.gnu)

        I got the following error message at the final step of fragment file making

        read_vall (unit= 20): /usr/local/csrosetta/vall.dat.apr24
        vall_size 2330105
        read homolog 18 ./t000_.homolog_vall
        WARNING:: unable to find/open homolog file
        read homolog 18 ./t000_.homolog_nr
        WARNING:: unable to open/find homolog-nr file
        make_dat 16./t000.dat
        not reading pdb file for t000
        size 3inserts 115
        size 9inserts 109
        merging fragments
        inserts stuck at 3mer pos: 8 inserts: 23
        shockingly low fragment diversity for 3mers at pos: 8 inserts: 23
        nnmake failed!

        I treid with several other fasta file also..

        but the result was same.

        what could be the problem?

      • #4265

          I don’t have a clue how to fix this fragments issue, but the Robetta fragment server might work better for you:

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