when i do that, what is here
https://boinc.bakerlab.org/rosetta/rah_view_predictions.php
the file S_XXXX_XXXX.pdb or F_XXXX_XXXX.pdb will not be created

here are logs

****stderr.txt****
Can't set up shared mem: -1
Will run in standalone mode.
# cpu_run_time_pref: 7200
Too many restarts with no progress. Keep application in memory while preempted.
======================================================
DONE :: 1 starting structures built 10 (nstruct) times
This process generated 0 decoys from 0 attempts
======================================================


BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down...

****stdout.txt****
[STR OPT]Default value for [-description_file] rosetta_description.txt.
[REAL OPT]Default value for [-cpu_frac] 10
[REAL OPT]Default value for [-frame_rate] 10
[INT OPT]Default value for [-cpu_run_time] 28800
command executed: rosetta_5.45_windows_intelx86.exe -extract -all -s aaz029.out
[T/F OPT]Default FALSE value for [-args_file]
[STR OPT]Default value for [-paths] paths.txt.
[T/F OPT]Default FALSE value for [-unix_paths]
--------------------------------------------
WARNING:: paths.txt file not found!!
Setting all paths to .
Using default fragment file names:
aa*****03_05.200_v1_3
aa*****03_05.200_v1_3
--------------------------------------------
[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]Default FALSE value for [-design]
[T/F OPT]Default FALSE value for [-dock]
[T/F OPT]Default FALSE value for [-membrane]
[T/F OPT]Default FALSE value for [-loops]
[T/F OPT]Default FALSE value for [-pdbstats]
[T/F OPT]Default FALSE value for [-interface]
[T/F OPT]Default FALSE value for [-barcode_stats]
[T/F OPT]Default FALSE value for [-pKa]
[T/F OPT]Default FALSE value for [-pose_looping]
[T/F OPT]Default FALSE value for [-domain_insertion]
[T/F OPT]Default FALSE value for [-pose1]
[T/F OPT]Default FALSE value for [-bk_min]
[T/F OPT]Default FALSE value for [-adna]
[T/F OPT]Default FALSE value for [-pdna]
[T/F OPT]Default FALSE value for [-prna]
[T/F OPT]Default FALSE value for [-jumping]
[T/F OPT]Default FALSE value for [-pose_abinitio]
[T/F OPT]Default FALSE value for [-pose_rhiju]
[T/F OPT]New TRUE value for [-extract]
[T/F OPT]Default FALSE value for [-jump_relax]
[T/F OPT]Default FALSE value for [-cst_mode]
[T/F OPT]Default FALSE value for [-mj_min]
Rosetta mode: pose1
[T/F OPT]Default FALSE value for [-chain]
[T/F OPT]Default FALSE value for [-protein]
[T/F OPT]Default FALSE value for [-series]
[INT OPT]Default value for [-nstruct] 10
[T/F OPT]Default FALSE value for [-read_all_chains]
[T/F OPT]Default FALSE value for [-preserve_header]
[T/F OPT]Default FALSE value for [-use_pdb_numbering]
[T/F OPT]Default FALSE value for [-flip_symmetric_sidechains]
[T/F OPT]Default FALSE value for [-fa_input]
[T/F OPT]Default FALSE value for [-overwrite]
[T/F OPT]Default FALSE value for [-no_filters]
[T/F OPT]Default FALSE value for [-output_pdb_gz]
[T/F OPT]Default FALSE value for [-output_silent_gz]
[T/F OPT]Default FALSE value for [-output_scorefile_gz]
[T/F OPT]Default FALSE value for [-pose_silent_out]
[T/F OPT]Default FALSE value for [-sasapack_bvalues]
[T/F OPT]Default FALSE value for [-cenlist_values]
[T/F OPT]Default FALSE value for [-termini]
[T/F OPT]Default FALSE value for [-Nterminus]
[T/F OPT]Default FALSE value for [-Cterminus]
[T/F OPT]Default FALSE value for [-use_trie]
[T/F OPT]Default FALSE value for [-no_trie]
[T/F OPT]Default FALSE value for [-use_conformer]
[T/F OPT]Default FALSE value for [-use_bbind_conformer]
[T/F OPT]Default FALSE value for [-trials_trie]
[T/F OPT]Default FALSE value for [-no_trials_trie]
[T/F OPT]Default FALSE value for [-pose_relax]
[T/F OPT]Default FALSE value for [-output_interaction_graph_memory_usage]
[T/F OPT]Default FALSE value for [-read_interaction_graph]
[T/F OPT]Default FALSE value for [-write_interaction_graph]
[STR OPT]Default value for [-ig_file] .
[T/F OPT]Default FALSE value for [-packer_precompute_only]
[T/F OPT]Default FALSE value for [-tight_memory_restrictions]
[T/F OPT]Default FALSE value for [-lazy_ig]
[T/F OPT]Default FALSE value for [-linmem_ig]
[T/F OPT]Default FALSE value for [-minimalist_ig]
[T/F OPT]Default FALSE value for [-use_sasa_pack_score]
[T/F OPT]Default FALSE value for [-output_dot_kinemage]
[T/F OPT]Default FALSE value for [-pack_low_temp_annealing]
[T/F OPT]Default FALSE value for [-multi_cool_annealer]
[T/F OPT]Default FALSE value for [-no_his_his_pairE]
[T/F OPT]Default FALSE value for [-silent_input]
[T/F OPT]Default FALSE value for [-timer]
[T/F OPT]Default FALSE value for [-count_attempts]
[T/F OPT]Default FALSE value for [-status]
[T/F OPT]Default FALSE value for [-decoy_status]
[T/F OPT]Default FALSE value for [-ise_movie]
[T/F OPT]Default FALSE value for [-output_all]
[T/F OPT]Default FALSE value for [-output_chi_silent]
[T/F OPT]Default FALSE value for [-accept_all]
[T/F OPT]Default FALSE value for [-skip_missing_residues]
[STR OPT]Default value for [-cst] cst.
[STR OPT]Default value for [-dpl] dpl.
[STR OPT]Default value for [-resfile] none.
[STR OPT]Default value for [-equiv_resfile] none.
[T/F OPT]Default FALSE value for [-auto_resfile]
[T/F OPT]Default FALSE value for [-chain_inc]
[T/F OPT]Default FALSE value for [-full_filename]
[T/F OPT]Default FALSE value for [-map_sequence]
[INT OPT]Default value for [-max_frags] 200
[T/F OPT]Default FALSE value for [-output_centroids]
[STR OPT]Default value for [-protein_name_prefix] .
[STR OPT]Default value for [-frags_name_prefix] .
[T/F OPT]Default FALSE value for [-protein_name_prefix_homolog]
[T/F OPT]Default FALSE value for [-use_homolog_env_stats]
[T/F OPT]Default FALSE value for [-use_homolog_pair_stats]
[T/F OPT]Default FALSE value for [-use_homolog_env_stats_in_farlx]
[T/F OPT]Default FALSE value for [-use_homolog_pair_stats_in_farlx]
[T/F OPT]Default FALSE value for [-output_hbond_info]
[REAL OPT]Default value for [-vdw_reweight] 1
[REAL OPT]Default value for [-env_reweight] 1
[REAL OPT]Default value for [-pair_reweight] 1
[REAL OPT]Default value for [-cb_reweight] 1
[REAL OPT]Default value for [-sheet_reweight] 1
[REAL OPT]Default value for [-ss_reweight] 1
[REAL OPT]Default value for [-hs_reweight] 1
[REAL OPT]Default value for [-rsigma_reweight] 1
[REAL OPT]Default value for [-rg_reweight] 1
[REAL OPT]Default value for [-pc_reweight] 1
[REAL OPT]Default value for [-fa_atr_reweight] 1
[REAL OPT]Default value for [-fa_rep_reweight] 1
[REAL OPT]Default value for [-fa_dun_reweight ] 1
[REAL OPT]Default value for [-fa_pair_reweight] 1
[REAL OPT]Default value for [-fa_plane_reweight] 1
[REAL OPT]Default value for [-fa_solv_reweight] 1
[REAL OPT]Default value for [-fa_ref_reweight ] 1
[REAL OPT]Default value for [-fa_pH_reweight] 1
[REAL OPT]Default value for [-fa_h2o_reweight] 1
[REAL OPT]Default value for [-fa_prob1b_reweight] 1
[REAL OPT]Default value for [-fa_gb_elec_reweigh] 1
[REAL OPT]Default value for [-hb_srbb_reweight] 1
[REAL OPT]Default value for [-hb_lrbb_reweight] 1
[REAL OPT]Default value for [-hb_sc_reweight] 1
[REAL OPT]Default value for [-chainbreak_reweight] 1
[REAL OPT]Default value for [-dummy_model_reweight] 1
[REAL OPT]Default value for [-saxs_model_reweight] 1
[REAL OPT]Default value for [-Wplane_total] 0
[T/F OPT]Default FALSE value for [-fa_max_dis]
[T/F OPT]Default FALSE value for [-hydrogen_interaction_cutoff]
[T/F OPT]Default FALSE value for [-find_disulf]
[T/F OPT]Default FALSE value for [-fix_disulf]
[T/F OPT]Default FALSE value for [-enable_dna]
[T/F OPT]Default FALSE value for [-enable_rna]
[T/F OPT]Default FALSE value for [-dna_interface]
[T/F OPT]Default FALSE value for [-enable_ligand_aa]
[T/F OPT]Default FALSE value for [-phospho_ser]
[T/F OPT]Default FALSE value for [-surface]
[T/F OPT]Default FALSE value for [-loops]
[T/F OPT]Default FALSE value for [-taboo]
[T/F OPT]Default FALSE value for [-vary_omega]
[T/F OPT]Default FALSE value for [-fine_hb_categories]
[T/F OPT]Default FALSE value for [-geometric_sol]
[T/F OPT]Default FALSE value for [-multi_chain]
[T/F OPT]Default FALSE value for [-ex1]
[T/F OPT]Default FALSE value for [-ex2]
[T/F OPT]Default FALSE value for [-ex3]
[T/F OPT]Default FALSE value for [-ex4]
[T/F OPT]Default FALSE value for [-ex1aro]
[T/F OPT]Default FALSE value for [-ex1aro_half]
[T/F OPT]Default FALSE value for [-ex2aro_only]
[T/F OPT]Default FALSE value for [-exOH]
[INT OPT]Default value for [-extrachi_cutoff] 18
[T/F OPT]Default FALSE value for [-rot_pert]
[T/F OPT]Default FALSE value for [-rot_pert_input]
[T/F OPT]Default FALSE value for [-exdb]
[T/F OPT]Default FALSE value for [-use_electrostatic_repulsion]
[T/F OPT]Default FALSE value for [-explicit_h2o]
[T/F OPT]Default FALSE value for [-solvate]
[T/F OPT]Default FALSE value for [-pH]
[T/F OPT]Default FALSE value for [-try_both_his_tautomers]
[T/F OPT]Default FALSE value for [-hydrate_dna]
[T/F OPT]Default FALSE value for [-ex_dna_waters]
[T/F OPT]Default FALSE value for [-minimize_rot]
[T/F OPT]Default FALSE value for [-read_hetero_h2o]
[T/F OPT]Default FALSE value for [-Wint_score_only]
[T/F OPT]Default FALSE value for [-Wint_repack_only]
[T/F OPT]Default FALSE value for [-ligand]
[T/F OPT]Default FALSE value for [-enzyme_design]
[T/F OPT]Default FALSE value for [-score_contact_flag]
[T/F OPT]Default FALSE value for [-score_contact_weight]
[T/F OPT]Default FALSE value for [-score_contact_threshold]
[T/F OPT]Default FALSE value for [-scorefxn]
default centroid scorefxn: 4
default fullatom scorefxn: 12
[INT OPT]Default value for [-run_level] 0
[T/F OPT]Default FALSE value for [-silent]
[T/F OPT]Default FALSE value for [-output_silent_gz]
[T/F OPT]Default FALSE value for [-verbose]
[T/F OPT]Default FALSE value for [-gush]
[T/F OPT]Default FALSE value for [-yap]
[T/F OPT]Default FALSE value for [-chat]
[T/F OPT]Default FALSE value for [-inform]
[T/F OPT]Default FALSE value for [-quiet]
run level: 0
[T/F OPT]Default FALSE value for [-benchmark]
[T/F OPT]Default FALSE value for [-debug]
[INT OPT]Default value for [-sym_des_units] 1
[T/F OPT]Default FALSE value for [-mj_min]
[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] aaz029.out.
Starting structure: aaz029.out
Reading .Rama_smooth_dyn.dat_ss_6.4.gz
Reading .phi.theta.36.HS.resmooth.gz
Reading .phi.theta.36.SS.resmooth.gz
[STR OPT]Default value for [-atom_vdw_set] default.
[T/F OPT]Default FALSE value for [-IUPAC]
Atom_mode set to all
Reading .paircutoffs.gz
[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 [-evolution]
[T/F OPT]Default FALSE value for [-evol_recomb]
[T/F OPT]Default FALSE value for [-profile]
BOINC :: [2007-02-06 04:02:10] :: mode: pose1 :: nstartnum: 1 :: number_of_output: 10 :: num_decoys: 0 :: pct_complete: 0.01
======================================================
DONE :: 1 starting structures built 10 (nstruct) times
This process generated 0 decoys from 0 attempts
======================================================

thanx for help

---

You have to remove the rosetta_init_cnt.txt file. You also may need to add -termini in the arguments for some work units. We'll modify the app in the next release so you will no longer have to remove the init_cnt file if running in standalone mode. The file prevents the app from restarting over and over again without producing any results.

You have to remove the rosetta_init_cnt.txt file. You also may need to add -termini in the arguments for some work units. We'll modify the app in the next release so you will no longer have to remove the init_cnt file if running in standalone mode. The file prevents the app from restarting over and over again without producing any results.

rosetta_init_cnt.txt is in the folder.

***rosetta_init_cnt.txt***
54 0

and when will be the next release???

---

you can either remove the file or edit it by changing 54 to 0.

Then try extracting the models. What particular work unit are you trying to extract from?

you can either remove the file or edit it by changing 54 to 0.

Then try extracting the models. What particular work unit are you trying to extract from?

Oooo
I channged 54 to 0.
And it is all ok..
After each extract is the number higher by 1.
So, somewhere in the program is a bug...

And i try it with cca 10 out files and all is ok...

thanx a lot...

---