- This topic has 4 replies, 2 voices, and was last updated 16 years, 5 months ago by
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> If you have a rosetta.xxx successfully generated, you can run a simple test with “-s xxx.pdb -design -fixbb -natrot” to get native structure energy information
[tru@sillage samplerun]$ pwd
/rosetta_documentation/docking/tutorial/examples/samplerun[tru@sillage samplerun]$ ../../../../../rosetta++/rosetta.intel32-intel9-32bits.stripped -s test.pdb -design -fixbb -natrot
command executed: ../../../../../rosetta++/rosetta.intel32-intel9-32bits.stripped -s test.pdb -design -fixbb -natrot
[T/F OPT]Default FALSE value for [-no_option_display]
[T/F OPT]Default FALSE value for [-args_file]
[STR OPT]Default value for [-paths] paths.txt.
[T/F OPT]Default FALSE value for [-version]
[T/F OPT]Default FALSE value for [-score]
[T/F OPT]Default FALSE value for [-abinitio]
[T/F OPT]Default FALSE value for [-refine]
[T/F OPT]Default FALSE value for [-assemble]
[T/F OPT]Default FALSE value for [-idealize]
[T/F OPT]Default FALSE value for [-relax]
[T/F OPT]Default FALSE value for [-abrelax]
[T/F OPT]Default FALSE value for [-abrelax_mode]
[T/F OPT]New TRUE value for [-design]
[T/F OPT]Default FALSE value for [-onlypack]
[T/F OPT]New TRUE value for [-fixbb]
[T/F OPT]Default FALSE value for [-pack_in_parallel]
[T/F OPT]Default FALSE value for [-directed_design]
[REAL OPT]Default value for [-interface_electrostatic_complementarity_shift] 0
[T/F OPT]Default FALSE value for [-reverse_comp]
[INT OPT]Default value for [-conv_limit_mod] 3
[STR OPT]Default value for [-chain_in_preferred_state] none.
[STR OPT]Default value for [-chain_in_ref_state] none.
[T/F OPT]Default FALSE value for [-rotamerize]
[T/F OPT]Default FALSE value for [-point_mutation]
[T/F OPT]Default FALSE value for [-mcmin_trials]
[T/F OPT]Default FALSE value for [-output_design_movie]
[T/F OPT]Default FALSE value for [-no_new_CG]
[T/F OPT]Default FALSE value for [-multistate]
[T/F OPT]Default FALSE value for [-dna_motifs]
[REAL OPT]Default value for [-motifs_close_enough] 1.20000005
[REAL OPT]Default value for [-motifs_far_dist] 5
[REAL OPT]Default value for [-Motifs_bump_value] 100
[REAL OPT]Default value for [-motifs_match_weight] 1
[INT OPT]Default value for [-motifs_rots_required] 2
….
[REAL OPT]Default value for [-mod_hhrep_height] 1
[REAL OPT]Default value for [-mod_hhrep_width] 1
[REAL OPT]Default value for [-mod_hhrep_center] 2.79999995
[REAL OPT]Default value for [-mod_hhrep_exponent] 4
[REAL OPT]Default value for [-smooth_etable_ljweight] 1.15999997
[REAL OPT]Default value for [-smooth_etable_solvweight] 1.5
[STR OPT]New value for [-s] test.pdb.
Starting structure: test
Reading ../../../../../rosetta_database/Rama_smooth_dyn.dat_ss_6.4
Reading ../../../../../rosetta_database/phi.theta.36.HS.resmooth
Reading ../../../../../rosetta_database/phi.theta.36.SS.resmooth
[STR OPT]Default value for [-atom_vdw_set] default.
[T/F OPT]Default FALSE value for [-IUPAC]
Atom_mode set to all
[STR OPT]Default value for [-paircutoffs] paircutoffs.
Reading ../../../../../rosetta_database/paircutoffs
[T/F OPT]Default FALSE value for [-interface_ds]
[T/F OPT]Default FALSE value for [-decoystats]
set_decoystats_flag: from,to F F
[T/F OPT]Default FALSE value for [-decoyfeatures]
[T/F OPT]Default FALSE value for [-t32s3]
[T/F OPT]Default FALSE value for [-evolution]
[T/F OPT]Default FALSE value for [-evol_recomb]
[T/F OPT]Default FALSE value for [-profile]
[T/F OPT]Default FALSE value for [-dummy_model]
[T/F OPT]Default FALSE value for [-saxs_model]
Profile defined from q = 0 to 1.
ERROR:: Can’t find starting structure: ../prepack/test.pdb
ERROR:: Exit from: input_pdb.cc line: 3028-> *** Can’t find starting structure: ../prepack/test.pdb ***
I guess I need another command to generate the “prepacked” pdb
Tru
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