Rosetta 3.1 Release Manual

"RNA Structual Modeling Options"

Here is a list of options used in RNA Structual Modeling.
-minimize_rna                  Minimize RNA after fragment assembly. default='false' [Boolean]
-relax_rna                     Relax RNA after fragment assembly. default='false' [Boolean]
-simple_relax                  Relax by minimizing after any fragment insertion. default='false' [Boolean]
-ignore_secstruct              Ignore sec struct in input file.  default='false' [Boolean]
-filter_lores_base_pairs       Filter for models that satisfy structure parameters. default='false' [Boolean]
-cycles                        Default number of Monte Carlo cycles. default=10000 [Integer]
-vall_torsions                 Torsions file. default='1jj2.torsions' [String]
-temperature                   Temperature. default='0.3' [Real]
-jump_change_frequency         Jump change frequency. default='0.1' [Real]
-close_loops                   Close loops during frag insertion and jump mover.  default='false' [Boolean]
-output_lores_silent_file      Output lores stuff.  default='false' [Boolean]
-heat                          Heat (random frag insertions). default='false' [Boolean]
-dump	                         Dump pdb. default='false' [Boolean]
-jump_library_file             Input file for jumps. default='1jj2_RNA_jump_library.dat' [String]
-params_file                   Input file for pairings. default='default.prm' [String]
-cst_file                      Input file for constraints. default='default.constraints' [String]

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