Error in using “loopmodel” for selective rebuilding

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    • July 14, 2014 at 6:57 pm #1947
      Anonymous

        Hi,

        I am new to rosetta. I am trying to build the missing residue loops in 4hna sturcture. But I am getting error while generating the input file for the loopmodel application.

        My input command is: loops_from_density.linuxgccrelease -database /util/rosetta/rosetta-3.2/rosetta_database/ -in:file:fullatom 4hna_9_his.pdb -edensity::mapfile apo_cut12.mrc -edensity::whole_structure_allatom_wt 1.0 -edensity::realign min -edensity::sliding_window 9 -edensity::mapreso 8.9 -edensity::grid_spacing 2.12 -max_helix_melt 1 -max_strand_melt 1 -frac_loop 0.026

        I am getting the error message: —> ERROR: Unused “free” argument specified: 4hna_9_his.pdb

        But this is just my input pdb structure not any library function. Any suggestion is welcome. Please help.

        Thanks
        Sushree.

      • July 16, 2014 at 2:48 pm #10160
        Anonymous

          -in:file:fullatom is a Booloean flag – it’s either on or off, and doesn’t take a filename. To pass an input PDB file in, you’d use the -in:file:s option, so your commandline should be “… -in:file:fullatom -in:file:s 4hna_9_his.pdb …”

        • August 26, 2014 at 8:02 pm #10237
          Anonymous

            Thanks for your reply. Now the problem is with flags -max_helix_melt and -max_strand_melt. If I take the default values (-1), it is creating the loopfile with no LOOP information. How should I determine this to get the correct loopfile.

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