Fragment files for membrane_abinitio application

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    • February 16, 2011 at 1:23 am #789
      Anonymous

        Hi

        I am trying to make fragment files for membrane_abinitio application. I have secondary structure prediction results (*.rdb files) from SAM secondary structure server. I am trying to run the command:
        make_fragments.pl -nojufo -nopsipred -noprof -samfile HRG3_all_X.t2k.str2.rdb HRG3.fasta

        The program is generating all the files (.cst, .a2m) but somehow its not generating fragment (frag3, frag9) files at all.

        Could anyone please help in this matter ?

      • February 16, 2011 at 2:20 am #5034
        Anonymous

          You don’t need to generate .rdb file on the SAM server – just generate fragments using the following command:
          ~tex/src/nnmake/make_fragments.pl -id test_ -nopsipred -nojufo -verbose test.fasta

        • February 17, 2011 at 6:47 pm #5045
          Anonymous

            Hi I tried running the same command but and still I am not getting the results:

            [sdeshpande@titan sdeshpande]$ /bigstor1/sumukh/sdeshpande/rosetta-3.2/rosetta_fragments/nnmake/make_fragments.pl -id her1_ -nojufo -nopsipred HERG3.fasta > log_prof_fragments.txt
            [blastpgp] WARNING: a standard checkpoint file should have extension “.chk”.

            /usr/lib64/python2.4/whrandom.py:38: DeprecationWarning: the whrandom module is deprecated; please use the random module
            DeprecationWarning)
            /usr/lib64/python2.4/whrandom.py:38: DeprecationWarning: the whrandom module is deprecated; please use the random module
            DeprecationWarning)
            prof failed.

            I also tried running command with -noprof added. Here is the command which I ran:

            /bigstor1/sumukh/sdeshpande/rosetta-3.2/rosetta_fragments/nnmake/make_fragments.pl -id herg_ -nojufo -noprof -nopsipred HERG3.fasta > log_fragments.txt

            But still I am not able to get the results as its is asking for the file ‘overrep-3617-IDaa13-7-10-11-10-11-7-7-ebghtl-seeded3-stride-trained.net’. also it not generating the fragment files, instead it is generating some her1_.pssm, her1_.check, her1_.checkpoint, her1_.blast files. I am attaching the log files so that it will become much more clear. Please anyone help me in this matter. Thanks.

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