Rosetta ddg_monomer 사용법

-in:file:s min_cst_0.5.WT_0001.pdb # the PDB file of the structure on which point mutations should be made -ddg::mut_file Y176A.resfile # the list of point mutations to consider in this run -ddg:weight_file soft_rep_design # Use soft-repulsive weights for the initial sidechain optimization stage -ddg:minimization_scorefunction <weights file> # optional -- the weights file to use, if not given, then the current default scorefunction will be used. -ddg::minimization_patch <weights patch file > # optional -- the weight-patch file to apply to the weight file; does not have to be given -database /path/to/rosetta/main/database #the full oath to the database is required -fa_max_dis 9.0 # optional -- if not given, the default value of 9.0 Angstroms is used. -ddg::iterations 50 # 50 is the recommended number of iterations -ddg::dump_pdbs true # write out PDB files for the structures, one for the wildtype and one for the pointmutant for each iteration -ignore_unrecognized_res # optional -- if there are residues in the input PDB file that Rosetta cannot recognize, ignore them instead of quitting with an error message -ddg::local_opt_only false # recommended: local optimization restricts the sidechain optimization to only the 8 A neighborhood of the mutation (equivalent to row 13) -ddg::min_cst true # use distance restraints (aka constraints) during the backbone minimization phase -constraints::cst_file <cbeta-distance-constraint-file> # the set of constraints to use during minimization which should reflect distances in the original (non-pre-relaxed) structure -ddg::suppress_checkpointing true # don't checkpoint LIZ DOES CHECKPOINTING WORK AT ALL? -in::file::fullatom # read the input PDB file as a fullatom structure -ddg::mean false # do not report the mean energy -ddg::min true # report the minimum energy -ddg::sc_min_only false # do not minimize only the backbone during the backbone minimization phase -ddg::ramp_repulsive true # perform three rounds of minimization (and not just the default 1 round) where the weight on the repulsive term is increased from 10% to 33% to 100% -mute all # optional -- silence all of the log-file / stdout output generated by this protocol -unmute core.optimization.LineMinimizer # optional -- unsilence a particular tracer -ddg::output_silent true # write output to a silent file