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PredesignPerturbMover randomly perturbs a ligand in a protein active site. The input protein will be transformed to a polyalanine context for residues surrounding the ligand. A number of random rotation+translation moves are made and then accepted/rejected based on the Boltzmann criteria with a modified (no attractive) score function (enzdes_polyA_min.wts).

PredesignPerturbMover currently will perturb only the last ligand in the pose (the last jump).

<PredesignPerturbMover name="(&string)" trans_magnitude="(0.1 &real)" rot_magnitude="(2.0 &real)" dock_trials="(100 &integer)" task_operations="(&string,&string)"/>
  • dock_trials - the number of Monte Carlo steps to attempt
  • trans_magnitude - how large (stdev of a gaussian) a random translation step to take in each of x, y, and z (angstrom)
  • rot_magnitude - how large (stdev of a gaussian) a random rotational step to take in each of the Euler angles (degrees)
  • task_operations - comma separated list of task operations to specify which residues (specified as designable in the resulting task) are converted to polyAla