Docking Options

Here is the list of options used in Docking protocol

-docking:view			Decide whether to use the viewer (graphical) or not.
				Default='false'. [Boolean]
-docking:fake_native		Decide whether to use low res docking filters after
				centroid mode. Default='false' [Boolean]
-docking:partners		Defines docking partners by ChainID.
				Example: docking chains L+H with A is -partners LH_A',
          			Default='_'. [String]
-docking:docking_local_refine	Do a local refinement of the docking position(high resolution)
			        Default='false'. [Boolean]
-docking:randomize1		Randomize the first docking partner.Default='false'
				[Boolean]
-docking:randomize2		Randomize the second docking partner.Default='false'
				[Boolean]
-docking:spin			Spin a second docking partner around axes from center of mass
				of partner1 to partner2. Default='false'. [Boolean]
-docking:dock_pert		Do a small perturbation with partner two: -dock_pert DEGREES ANGSTROMS.
				Good values for protein docking are 3 deg and 8 A.', n='2'
				[RealVector]
-docking:uniform_trans		Uniform random repositioning within a sphere of the given radius.
				[Real]
-docking:docking_centroid_outer_cycles
				Outer cycles during docking rigid body adaptive moves.
        			Default='10' [Integer]
-docking:docking_centroid_inner_cycles
				Inner cycles during docking rigid body adaptive moves.
        			Default='50' [Integer]
-docking:dock_mcm		Do a monte-carlo minimize search.Default='true'
				[Boolean]
-docking:dock_min		Minimize the final êÏΩfullatom structure.Default='false'
				[Boolean]
-docking:dock_mcm_trans_magnitude
				The magnitude of the translational perturbation during mcm in docking.
        			Default='0.1'. [Real]
-docking:dock_mcm_rot_magnitude	The magnitude of the rotational perturbation during mcm in docking.
			        Default='5.0'. [Real]
-docking:norepack1		Do not repack the side-chains of partner 1.
           			Default='false' [Boolean]
-docking:norepack2		Do not repack the side-chains of partner 2.
           			Default='false' [Boolean]
-docking:dock_ppk		Docking prepack mode'. Default='false' [Boolean]
-docking:dock_lowres_filter	Manually sets the lowres docking filter:
				-dock_lowres_filter <INTERCHAIN_CONTACT CUTOFF> <INTERCHAIN_VDW CUTOFF>.
				Default values for protein docking are 10.0 and 1.0',n='2' [RealVector]

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