Reply To: Is it possible to do Abinitio folding from a linear structure.?

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April 21, 2011 at 5:17 am #5474
Anonymous

    Okie, my cmd-line is FlexPepDocking.linuxgccrelease @flags.basic > dock.log &. Anyway, I just read the manual again and I realise that the starting structure is to be an approximate of the final complex structure that I’m expecting. If that’s the case, then it defeats my purpose in docking a linear peptide to the protein and hoping to see what and where would my final conformation of my peptide be like. So is it true that way or did I misinterpret anything.? Btw, I have added the extend_peptide flag but it seems to have no changes in the results at all.

    Filename: flags.basic

    -s input/complex.pdb
    -native input/complex.pdb
    -rbMCM
    -torsionsMCM
    #-lowres_preoptimize
    -flexpep_prepack
    #-flexPepDockingMinimizeOnly
    -ex1
    -ex2aro
    -use_input_sc
    -nstruct 20
    #-unboundrot input/unbound.pdb
    -database /home/u1/Programs/rosetta3.2.1_bundles/rosetta_database
    -rep_ramp_cycles 10
    -mcm_cycles 8
    -smove_angle_range 6.0
    -extend_peptide true