Reply To: energy minimization of loop only

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January 13, 2011 at 3:51 am #4827
Anonymous

    I have an easy way to do this.

    A)
    Add the options below to your looprelax flag file:
    -loops::refine refine_kic
    -loops::outer_cycles 1
    -loops::max_inner_cycles 1

    The looprelax will do a initial repack and minimization followed by JUST 2 times of KIC perturbation and a final full repack.
    This will make a small change of your loop backbone conformation, and you can generate 20 decoys or more and select the one which have the lowest energy or the minimal loop backbone changes.

    B) I think loop_backrub_mover can refine your loops and make a smaller scale conformation changes of backbone than KIC/CCD, but it was not included in looprelax in Rosetta3.1.