# 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.

#-relax
 #-fast
   # This flag will result in 5X-10X speed up, and gives nearly as good results
 #-constrain_relax_to_start_coords 1
 #-ramp_constraints 1
   # these two flags can be useful if the intial structure has bad contacts, 
   # resulting in very high unfavorable initial energy and "blowing up" behavior

-in
 -file
  -s 1ubi.pdb
   # this specifies the starting (input) file

 -path .
  -database /sb/meiler/rosetta/rosetta-3.0/rosetta3_database
   # The path to your rosetta3 databases is required

-out
 #-path output_files
  # Path where PDB output files will be written to, default '.'
  # if you specify a directory name here, it must exist
 -nstruct 1
   # The number of output decoys to produce
 -pdb 
  # output PDB files, default=false [Boolean]
 -prefix aa
  # beginning part of output filename like old -series code
 -file
  #-fullatom
   # Low-resolution or "centroid" folding mode is the default; you must specify
   # fullatom output if you want to match -relax, above
  #-silent folding_silent.out
   # Enable "silent file" output with filename after this flag, default=default.out
  -o relax.fasc
   # The "full-atom score" file
 -mute core.util.prof 
   # don't show timing info
