# by editing this file, you can customize the Rosetta run
# the format and content of this file is specified here:
# http://www.rosettacommons.org/manuals/rosetta3_user_guide/command_options.html
# note that here we format using indentation, alternately semicolons could have been used

-in
 -file
	# contains a protein PDB with header and solvent atoms removed. A ligand PDB with HETATM 
	# records has been appended.
  -s 7cpa_7cpa_input.pdb
	# Since we have an experimentally determined structure for this complex, this docking study
	# can be used to benchmark the quality of RosettaLigand predictions.  The native structure
	# will be used to calculate RMSD deviation for our predicted models.
  -native 7cpa_7cpa_native.pdb
	# params files for amino acid residues are found in the rosetta_database.  Extra params
	# files should be created using molfile_2_params.py, and specified here.
  -extra_res_fa 7cpa.params ZN1.params
 -path
	# edit this path to point to your rosetta3 databases
  -database /programs/l/rosetta/3.1-x86_64/rosetta_database
-out
 # number of output structures to produce.  Generally 1000s of models are made.
 -nstruct 5 
 -file
  # name of the output file
  -silent silent.out
-packing
 # If your PDB file does not have hydrogens in the right place, use this:
 #-no_optH false
 # otherwise use
 -no_optH 
 # use additional protein rotamers (can take much longer)
 -ex1
 -ex1aro
 -ex2
-docking
 # Random perturbation of up to N Angstroms in X, Y, and Z, drawn from a uniform 
 # distribution. This gives a cube, but points outside the sphere of radius N are 
 # discarded, resulting in uniform positional sampling within the sphere.
 -uniform_trans 5
 # Randomize the starting orientation and conformer (respectively) of the
 # ligand.  Unnecessary if using -improve_orientation.
 #-randomize2
 -ligand
  # Instead of choosing an orientation and conformer at random,  try all
  # available conformers in N random orientations, and try to maximize
  # shape complementarity to the protein 
  # We find this *significantly* improves search, and costs just a few seconds.
  -improve_orientation 1000
  # the starting point for the ligand, prior to random translation
  -start_from  -1.731  32.589  -5.039
	# Let ligand rotatable bonds minimize, with harmonic restraints
	# where one standard deviation is 10 degrees:
  -minimize_ligand
  -harmonic_torsions 10 
	# In the final minimization, let the backbone minimize with harmonic restraints on 
	# the Calphas (stddev = 0.3 A). Only stretches of residues near the ligand are 
	# minimized, typically 20 - 40 in total.  (40 - 80 residues are repacked.)
	#-minimize_backbone
	#-harmonic_Calphas 0.3

-mute core.util.prof ## dont show timing info
-mute core.io.database ## dont show database reading info
