/projects/compbio/experiments/protein-predict/casp7/starter-directory/Make.main:646: SECONDARY_TARGET = T0300.t04.str2 /usr/bin/gmake -k decoys/T0300.try12-opt2.pdb.gz \ decoys/T0300.try12-opt2.repack-nonPC.pdb.gz \ decoys/grep-best-rosetta \ decoys/T0300.try12-opt2.gromacs0.pdb.gz \ decoys/score-all.try12.rdb decoys/score-all.try12.pretty gmake[1]: Entering directory `/projects/compbio/experiments/protein-predict/casp7/T0300' /projects/compbio/experiments/protein-predict/casp7/starter-directory/Make.main:646: SECONDARY_TARGET = T0300.t04.str2 mkdir -p decoys nice -5 /projects/compbio/programs/undertaker/undertaker < try12.under > try12.log 2>&1 gzip -f decoys/T0300.try12*pdb gzip -9f try12.log Template.atoms gzip: Template.atoms: No such file or directory gmake[1]: [decoys/T0300.try12-opt2.pdb.gz] Error 1 (ignored) /projects/compbio/experiments/protein-predict/casp7/scripts/make-repack-res-file -start_col 1 < T0300.a2m > T0300.repack.res Read 102 residues, have 102 chain ids and 102 pdb_nums Printing 1 copies of 1 chains gunzip -c decoys/T0300.try12-opt2.pdb.gz > XXXX.pdb gunzip -c guide.a2m.gz > XXXXA.fasta /projects/compbio/bin/i686/rosetta aa XXXX A \ -s ./XXXX.pdb \ -scorefile T0300.try12-opt2 \ -read_all_chains \ -design -fixbb -resfile T0300.repack.res \ -fa_output -fa_input \ -ex1 -ex2 -ex34 \ -use_input_sc \ -find_disulf -norepack_disulf \ -nstruct 1 command executed: /projects/compbio/bin/i686/rosetta aa XXXX A -s ./XXXX.pdb -scorefile T0300.try12-opt2 -read_all_chains -design -fixbb -resfile T0300.repack.res -fa_output -fa_input -ex1 -ex2 -ex34 -use_input_sc -find_disulf -norepack_disulf -nstruct 1 [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]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 [-mcmin_trials] [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] 0.5 [REAL OPT]Default value for [-motifs_far_dist] 5 [REAL OPT]Default value for [-motifs_bump_value] 100 [INT OPT]Default value for [-motifs_rots_required] 2 [T/F OPT]Default FALSE value for [-design_loops_dock] [REAL OPT]Default value for [-multi_offset] 0 [T/F OPT]Default FALSE value for [-mut_list] [T/F OPT]Default FALSE value for [-cluster_design] [T/F OPT]Default FALSE value for [-rotamerize] [T/F OPT]Default FALSE value for [-rot_opt] [T/F OPT]Default FALSE value for [-design_trials] [T/F OPT]Default FALSE value for [-mvbb] [T/F OPT]Default FALSE value for [-desock] [T/F OPT]Default FALSE value for [-fixseq] [T/F OPT]Default FALSE value for [-tail] [T/F OPT]Default FALSE value for [-tail_fix_helix] [T/F OPT]Default FALSE value for [-use_bw] [T/F OPT]Default FALSE value for [-use_aw] [T/F OPT]Default FALSE value for [-design_inter] [T/F OPT]Default FALSE value for [-repack_inter] [T/F OPT]Default FALSE value for [-alter_spec] [T/F OPT]Default FALSE value for [-mutate_cluster] [T/F OPT]Default FALSE value for [-output_pdb] [T/F OPT]Default FALSE value for [-design_in_pieces] [T/F OPT]Default FALSE value for [-rotamer_explosion] [T/F OPT]Default FALSE value for [-dna_interface] [T/F OPT]Default FALSE value for [-dna_minimize] [T/F OPT]Default FALSE value for [-analyze_dna_interface] [T/F OPT]Default FALSE value for [-force_basepair_muts] [T/F OPT]Default FALSE value for [-natrot] [T/F OPT]Default FALSE value for [-optE] [T/F OPT]Default FALSE value for [-optE_ctsa] [T/F OPT]Default FALSE value for [-optE_inter] [T/F OPT]Default FALSE value for [-optE_ctsa] [T/F OPT]Default FALSE value for [-optE_inter] [STR OPT]Default value for [-ms_comp_list] default. [STR OPT]Default value for [-ms_out_name] best_fit.pdb. [STR OPT]Default value for [-Eout] default. [STR OPT]Default value for [-sqc] none. [STR OPT]Default value for [-pdbout] des. [INT OPT]Default value for [-ndruns] 1 [INT OPT]Default value for [-begin] 0 [INT OPT]Default value for [-end] 0 [STR OPT]Default value for [-alter_spec_mutlist] mutlist. [STR OPT]Default value for [-point_mut_energies] none. [STR OPT]Default value for [-mut_mut_energies] none. [STR OPT]Default value for [-design_mutlist] none. [T/F OPT]Default FALSE value for [-safety] [T/F OPT]Default FALSE value for [-design_dock] [T/F OPT]Default FALSE value for [-favor_native_residue] [T/F OPT]Default FALSE value for [-favor_polar] [T/F OPT]Default FALSE value for [-favor_nonpolar] [T/F OPT]Default FALSE value for [-favor_charged] [T/F OPT]Default FALSE value for [-favor_aromatic] Rosetta mode: design [T/F OPT]Default FALSE value for [-chain] [T/F OPT]Default FALSE value for [-protein] [T/F OPT]Default FALSE value for [-series] series_code = aa :: protein_name is XXXX:: chain_id is A. [INT OPT]New value for [-nstruct] 1 [T/F OPT]New TRUE value for [-read_all_chains] [T/F OPT]Default FALSE value for [-use_pdb_numbering] [T/F OPT]Default FALSE value for [-repack] [T/F OPT]Default FALSE value for [-overwrite] [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 [-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 [-trials_trie] [T/F OPT]Default FALSE value for [-no_trials_trie] [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 [-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 [-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 [-skip_missing_residues] [T/F OPT]New TRUE value for [-use_input_sc] [T/F OPT]Default FALSE value for [-use_input_cb] [STR OPT]Default value for [-cst] cst. [STR OPT]Default value for [-dpl] dpl. [STR OPT]New value for [-resfile] T0300.repack.res. [T/F OPT]Default FALSE value for [-auto_resfile] [T/F OPT]Default FALSE value for [-chain_inc] WARNING:: nstruct > 0 but output_coord F no pdb files will be output [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 [-enable_dna] [T/F OPT]Default FALSE value for [-phospho_ser] [T/F OPT]Default FALSE value for [-loops] [T/F OPT]Default FALSE value for [-taboo] [T/F OPT]Default FALSE value for [-multi_chain] [T/F OPT]New TRUE value for [-ex1] [T/F OPT]New TRUE 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] [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 [-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] [STR OPT]New value for [-s] ./XXXX.pdb. Starting structure: ./XXXX Reading /projects/compbio/programs/rosetta/rosetta_database/Rama_smooth_dyn.dat_ss_6.4 Reading /projects/compbio/programs/rosetta/rosetta_database/phi.theta.36.HS.resmooth Reading /projects/compbio/programs/rosetta/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 Reading /projects/compbio/programs/rosetta/rosetta_database/paircutoffs [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] Searching for dat file: ./XXXX.dat Searching for dat file: ./XXXX.dat WARNING!! .dat file not found! Looking for fasta file: ./XXXXA.fasta [T/F OPT]New TRUE value for [-find_disulf] [T/F OPT]Default FALSE value for [-fix_disulf] Using extra cysteine rotamers...excys=True [T/F OPT]New TRUE value for [-norepack_disulf] [T/F OPT]Default FALSE value for [-use_disulf_logfile] Looking for psipred file: ./XXXXA.psipred_ss2 Looking for psipred file: ./XXXXA.psipred_ss2 Looking for psipred file: ./XXXXA.jones Looking for psipred file: ./XXXXA.psipred Looking for psipred file: ./XXXXA.jones Looking for psipred file: ./XXXXA.psipred WARNING :: Unable to find psipred file! XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX WARNING: CONSTRAINT FILE NOT FOUND Searched for: ./XXXXA.cst Running without distance constraints XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX WARNING: DIPOLAR CONSTRAINT FILE NOT FOUND Searched for: ./XXXXA.dpl Dipolar constraints will not be used XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX [T/F OPT]Default FALSE value for [-barcode_mode] disabling all filters [REAL OPT]Default value for [-co] -1 [REAL OPT]Default value for [-rms] -1 Searching for pdb...: ./XXXX.pdb [T/F OPT]Default FALSE value for [-use_native_centroid] initializing full atom functions [T/F OPT]Default FALSE value for [-soft_rep] [T/F OPT]Default FALSE value for [-soft_rep_design] [T/F OPT]Default FALSE value for [-gen_born] [T/F OPT]Default FALSE value for [-small_radii] [STR OPT]Default value for [-fa_lj_rep_slope] highres. Reading /projects/compbio/programs/rosetta/rosetta_database/bbdep02.May.sortlib Reading /projects/compbio/programs/rosetta/rosetta_database/plane_data_table_1015.dat Reading /projects/compbio/programs/rosetta/rosetta_database/pdbpairstats_fine Reading /projects/compbio/programs/rosetta/rosetta_database/Paa Reading /projects/compbio/programs/rosetta/rosetta_database/Paa_n Reading /projects/compbio/programs/rosetta/rosetta_database/Paa_pp generating Etable... Starting energy table calculation Energy table parameter set: polh_aroh Revision: 7252 Date: 2006-01-10 14:07:37 -0800 (Tue, 10 Jan 2006) Finished calculating energy tables. Reading /projects/compbio/programs/rosetta/rosetta_database/avgE_from_pdb Filling missing atoms optimizing missing atoms optimizing hydrogen positions [T/F OPT]Default FALSE value for [-constant_seed] [INT OPT]Default value for [-seed_offset] 0 # ===================================== # random seed: 1294441 # ===================================== Looking for dssp file: ./XXXX.dssp dssp file not found Looking for secondary structure assignment file: ./XXXXA.ssa ssa file not found calculating secondary structure from torsion angles [REAL OPT]Default value for [-parallel_weight] 1 [REAL OPT]Default value for [-antiparallel_weight] 1 [T/F OPT]Default FALSE value for [-vary_omega] [T/F OPT]Default FALSE value for [-new_centroid_packing] [REAL OPT]Default value for [-cb_weight] 1 [T/F OPT]Default FALSE value for [-separate_centroid_pack_score] Reading /projects/compbio/programs/rosetta/rosetta_database/SASA-masks.dat Reading /projects/compbio/programs/rosetta/rosetta_database/SASA-angles.dat ======================================== Reading /projects/compbio/programs/rosetta/rosetta_database/sasa_offsets.txt Reading /projects/compbio/programs/rosetta/rosetta_database/sasa_prob_cdf.txt Constraints Scores viol stage res1 atom1 res2 atom2 dist upper delta aa1 aa2 score Constraints: 0 Scores Total 0 [T/F OPT]Default FALSE value for [-repeatin] [T/F OPT]Default FALSE value for [-repeatout] [T/F OPT]Default FALSE value for [-clnt] reading starting structure: ././XXXX.pdb Filling missing atoms optimizing missing atoms optimizing hydrogen positions WARNING:: end of pdb file reached: angle, secstruct, & res info not found Looking for dssp file: ././XXXX.dssp dssp file not found Looking for secondary structure assignment file: ././XXXX.ssa ssa file not found calculating secondary structure from torsion angles [T/F OPT]Default FALSE value for [-use_input_bond] [T/F OPT]Default FALSE value for [-regions] [T/F OPT]Default FALSE value for [-knot_filter] [T/F OPT]Default FALSE value for [-poke_filter] [T/F OPT]Default FALSE value for [-rand_envpair_res_wt] [T/F OPT]Default FALSE value for [-rand_SS_wt] [T/F OPT]Default FALSE value for [-random_parallel_antiparallel] [T/F OPT]Default FALSE value for [-rand_cst_res_wt] Constraints Scores viol stage res1 atom1 res2 atom2 dist upper delta aa1 aa2 score Constraints: 0 Scores Total 0 [T/F OPT]Default FALSE value for [-movie] [T/F OPT]Default FALSE value for [-trajectory] Start of design structure designing with this many rotamers 2272 [T/F OPT]Default FALSE value for [-profile] ====================================================== DONE :: 1 starting structures built 1 (nstruct) times This process generated 1 decoys from 1 attempts 0 starting pdbs were skipped ====================================================== rm XXXX.pdb XXXXA.fasta mv decoys/XXXX_0001.pdb decoys/T0300.try12-opt2.repack-nonPC.pdb gzip -9f decoys/T0300.try12-opt2.repack-nonPC.pdb gmake[1]: Warning: File `decoys' has modification time 0.1 s in the future /projects/compbio/experiments/protein-predict/casp7/scripts/sort-by-rosetta gunzip -c decoys/T0300.try12-opt2.pdb.gz \ | /projects/compbio/experiments/protein-predict/casp7/scripts/run-gromacs -force_field 0 \ -nokeeptmp -tmp /tmp \ | gzip -9 \ > decoys/T0300.try12-opt2.gromacs0.pdb.gz run-gromacs running in /tmp/run-gromacs-bort-24960-49357441 Running 'echo 0 | pdb2gmx -f tmp.pdb -p tmp.top -o tmp.gro' Running 'editconf -f tmp -o -d 0.5 -c' Running 'genbox -cp out -cs -p tmp -o tmp.b4em' Running 'grompp -v -f em -c tmp.b4em -o tmp -p tmp' Running 'mdrun -v -s tmp -o tmp -c tmp.after_em -g tmp.emlog' Running 'echo 1 | trjconv -f tmp.after_em.gro -s tmp.tpr -o tmp.raw_gromacs.pdb' mkdir -p decoys rm decoys/read-pdb.under cd decoys; for x in *.pdb* ; do echo ReadConformPDB $x >> read-pdb.under ; done chgrp protein decoys/read-pdb.under chmod g+w decoys/read-pdb.under mv -f decoys/score-all.try12.rdb decoys/score-all.try12.rdb.old mv: cannot stat `decoys/score-all.try12.rdb': No such file or directory gmake[1]: [decoys/score-all.try12.rdb] Error 1 (ignored) rm -f decoys/all.clashes* rm -f decoys/all.breaks* cat /projects/compbio/experiments/protein-predict/casp7/starter-directory/score-all.under \ | sed s/START_COL/1/g \ | sed -e s/XXX0000/T0300/ -e s/try1/try12/ \ | nice -2 /projects/compbio/programs/undertaker/undertaker # command:# Seed set to 1150392275 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading monomeric-50pc.atoms # trans (non-proline) backbone unit: # CA= -2.2088 1.0126 -0.0031 # O= -0.1499 2.2440 0.0017 # C= -0.6889 1.1368 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 0.0000 0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2099 1.0634 -0.0014 # O= -0.1233 2.2459 0.0075 # C= -0.6871 1.1518 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading monomeric-50pc.atoms have 448 chains in training database # Count of chains,residues,atoms: 448,112605,876684 # 109826 residues have no bad marker # 665 residues lack atoms needed to compute omega # 322 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 6 # HAS_OXT 325 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 523 # HAS_UNKNOWN_ATOMS 2 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 208 # NON_PLANAR_PEPTIDE 143 # BAD_PEPTIDE 1959 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Reading spots from monomeric-50pc-dry-5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-5.hist # created burial cost function dry5 with radius 5 with spots at monomeric-50pc-dry-5.spot # command:# Reading spots from monomeric-50pc-wet-6.5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-wet-6.5.hist # created burial cost function wet6.5 with radius 6.5 with spots at monomeric-50pc-wet-6.5.spot # command:# Reading spots from monomeric-50pc-dry-6.5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-6.5.hist # created burial cost function dry6.5 with radius 6.5 with spots at monomeric-50pc-dry-6.5.spot # command:# Reading spots from monomeric-50pc-generic-6.5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-generic-6.5.hist # created burial cost function gen6.5 with radius 6.5 with spots at monomeric-50pc-generic-6.5.spot # command:# Reading spots from near-backbone-center.spot # reading histogram from smoothed-near-backbone-2spot.hist # Reading spots from near-backbone-count.spot # created burial cost function near_backbone with radius 9.65 with spots at near-backbone-center.spot counting only near-backbone-count.spot # command:# Reading spots from way-back-center.spot # reading histogram from smoothed-way-back-2spot.hist # Reading spots from way-back-count.spot # created burial cost function way_back with radius 8.9 with spots at way-back-center.spot counting only way-back-count.spot # command:# Reading spots from monomeric-50pc-dry-8.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-8.hist # created burial cost function dry8 with radius 8 with spots at monomeric-50pc-dry-8.spot # command:# Reading spots from monomeric-50pc-dry-10.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-10.hist # created burial cost function dry10 with radius 10 with spots at monomeric-50pc-dry-10.spot # command:# Reading spots from monomeric-50pc-dry-12.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-12.hist # created burial cost function dry12 with radius 12 with spots at monomeric-50pc-dry-12.spot # command:# reading histogram from dunbrack-2191-alpha.hist # created alpha cost function alpha with offset 0 and 360 bins # command:# reading histogram from dunbrack-2191-alpha-1.hist # created alpha cost function alpha_prev with offset -1 and 360 bins # command:CPU_time= 5.61515 sec, elapsed time= 6.53549 sec) # command:# Prefix for input files set to # command:# Making conformation for sequence T0300 numbered 1 through 102 Created new target T0300 from T0300.a2m # command:# command:# No conformations to remove in PopConform # command:# Prefix for input files set to /projects/compbio/lib/alphabet/ # command:# Read 3 alphabets from alpha.alphabet # command:CPU_time= 7.75682 sec, elapsed time= 8.68386 sec) # command:# Prefix for input files set to # command:# reading script from file try12.costfcn # reading predictions from T0300.t2k.alpha.rdb # created predicted alpha cost function pred_alpha2k with 360 bins smoothing outer_iter=2 inner_iter=1 width=7 # reading predictions from T0300.t04.alpha.rdb # created predicted alpha cost function pred_alpha04 with 360 bins smoothing outer_iter=2 inner_iter=1 width=7 # reading predictions from T0300.t06.alpha.rdb # created predicted alpha cost function pred_alpha06 with 360 bins smoothing outer_iter=2 inner_iter=1 width=7 # SetCost created cost = # ( 15 * wet6.5(6.5, /log(length)) + 5 * near_backbone(9.65) + 5 * way_back(8.9) + 15 * dry5(5) + 25 * dry6.5(6.5) + 15 * dry8(8) + 5 * dry12(12) + 1 * phobic_fit + 3 * sidechain + 5 * n_ca_c + 10 * bad_peptide + 5 * bystroff + 20 * soft_clashes + 2 * backbone_clashes + 50 * break + 2 * pred_alpha2k + 2 * pred_alpha04 + 2 * pred_alpha06 + 20 * constraints + 5 * hbond_geom + 10 * hbond_geom_backbone + 50 * hbond_geom_beta + 100 * hbond_geom_beta_pair + 1 * missing_atoms ) # HelixConstraint # Added 76 helix constraints for (T0300)Y10 through (T0300)K32 # HelixConstraint # Added 108 helix constraints for (T0300)A46 through (T0300)A76 # HelixConstraint # Added 13 helix constraints for (T0300)E82 through (T0300)Q90 # StrandConstraint # Added 2 Strand constraints for (T0300)L94 through (T0300)D97 # Constraint # added constraint: constraint((T0300)I68.CB, (T0300)L92.CB) [> -10 = 5 < 9] w=0.8 # Constraint # added constraint: constraint((T0300)V72.CB, (T0300)L92.CB) [> -10 = 4 < 8] w=0.8 # Constraint # added constraint: constraint((T0300)V31.CB, (T0300)I53.CB) [> -10 = 5 < 9] w=0.9 # Constraint # added constraint: constraint((T0300)V72.CB, (T0300)L88.CB) [> -10 = 4 < 8] w=0.9 # Constraint # added constraint: constraint((T0300)M13.CB, (T0300)L88.CB) [> -10 = 7 < 13] w=0.5 # Constraint # added constraint: constraint((T0300)A64.CB, (T0300)L92.CB) [> -10 = 7 < 14] w=0.7 # Constraint # added constraint: constraint((T0300)I68.CB, (T0300)L89.CB) [> -10 = 7 < 14] w=0.7 # Constraint # added constraint: constraint((T0300)I68.CB, (T0300)L88.CB) [> -10 = 7 < 12] w=0.7 # Constraint # added constraint: constraint((T0300)V72.CB, (T0300)L85.CB) [> -10 = 7 < 12] w=0.7 # Constraint # added constraint: constraint((T0300)V31.CB, (T0300)S51.CB) [> -10 = 7 < 14] w=0.8 # Constraint # added constraint: constraint((T0300)R75.CB, (T0300)L85.CB) [> -10 = 7 < 14] w=0.7 # command:CPU_time= 7.8718 sec, elapsed time= 8.83436 sec) # command:# Prefix for input files set to decoys/ # command:# reading script from file read-pdb.under # ReadConformPDB reading from PDB file georgesuggestion.renum.pdb looking for model 1 # choosing archetypes in rotamer library # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file rotateFromTry2attempt1.renum.pdb looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file rotateFromTry2attempt2.renum.pdb looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file rotateFromTry3attempt1.renum.pdb looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file rotateFromTry3attempt2.renum.pdb looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file rotateFromTry3attempt3.fix.pdb looking for model 1 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file rotateFromTry3attempt3.renum.pdb looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try10-opt1.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try10-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try10-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 1 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try10-opt2.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try10-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try11-opt1.pdb.gz looking for model 1 # Found a chain break before 66 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try11-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 66 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try11-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try11-opt2.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try11-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try12-opt1.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try12-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try12-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try12-opt2.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try12-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try1-opt1.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try1-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try1-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 61 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try1-opt2.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try1-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try2-opt1.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try2-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try2-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try2-opt2.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try2-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try3-opt1.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try3-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try3-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try3-opt2.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try3-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try4-opt1.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try4-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try4-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try4-opt2.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try4-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try5-opt1.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try5-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try5-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try5-opt2.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try5-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try6-opt1.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try6-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try6-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try6-opt2.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try6-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try7-opt1.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try7-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try7-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try7-opt2.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try7-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try8-opt1.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try8-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try8-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 10 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try8-opt2.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try8-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try9-opt1.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try9-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try9-opt2.gromacs0.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file T0300.try9-opt2.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0300.try9-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # command:CPU_time= 11.5932 sec, elapsed time= 12.6607 sec) # command:# Prefix for output files set to decoys/ # command:# Will now start reporting costs to decoys/score-all.try12.rdb # command:# CostConform T0300.try9-opt2.repack-nonPC.pdb.gz costs 179.561 T0300.try9-opt2.pdb.gz costs 173.109 T0300.try9-opt2.gromacs0.pdb.gz costs 178.192 T0300.try9-opt1-scwrl.pdb.gz costs 187.815 T0300.try9-opt1.pdb.gz costs 185.654 T0300.try8-opt2.repack-nonPC.pdb.gz costs 195.548 T0300.try8-opt2.pdb.gz costs 191.349 T0300.try8-opt2.gromacs0.pdb.gz costs 197.963 T0300.try8-opt1-scwrl.pdb.gz costs 197.487 T0300.try8-opt1.pdb.gz costs 195.979 T0300.try7-opt2.repack-nonPC.pdb.gz costs 200.075 T0300.try7-opt2.pdb.gz costs 197.625 T0300.try7-opt2.gromacs0.pdb.gz costs 204.131 T0300.try7-opt1-scwrl.pdb.gz costs 203.623 T0300.try7-opt1.pdb.gz costs 202.757 T0300.try6-opt2.repack-nonPC.pdb.gz costs 184.285 T0300.try6-opt2.pdb.gz costs 179.316 T0300.try6-opt2.gromacs0.pdb.gz costs 188.181 T0300.try6-opt1-scwrl.pdb.gz costs 190.244 T0300.try6-opt1.pdb.gz costs 186.517 T0300.try5-opt2.repack-nonPC.pdb.gz costs 188.646 T0300.try5-opt2.pdb.gz costs 184.712 T0300.try5-opt2.gromacs0.pdb.gz costs 193.316 T0300.try5-opt1-scwrl.pdb.gz costs 191.508 T0300.try5-opt1.pdb.gz costs 187.962 T0300.try4-opt2.repack-nonPC.pdb.gz costs 206.012 T0300.try4-opt2.pdb.gz costs 201.923 T0300.try4-opt2.gromacs0.pdb.gz costs 207.354 T0300.try4-opt1-scwrl.pdb.gz costs 211.558 T0300.try4-opt1.pdb.gz costs 208.179 T0300.try3-opt2.repack-nonPC.pdb.gz costs 190.66 T0300.try3-opt2.pdb.gz costs 187.067 T0300.try3-opt2.gromacs0.pdb.gz costs 194.268 T0300.try3-opt1-scwrl.pdb.gz costs 194.007 T0300.try3-opt1.pdb.gz costs 190.967 T0300.try2-opt2.repack-nonPC.pdb.gz costs 259.474 T0300.try2-opt2.pdb.gz costs 257.105 T0300.try2-opt2.gromacs0.pdb.gz costs 263.495 T0300.try2-opt1-scwrl.pdb.gz costs 264.895 T0300.try2-opt1.pdb.gz costs 262.491 T0300.try1-opt2.repack-nonPC.pdb.gz costs 199.282 T0300.try1-opt2.pdb.gz costs 193.645 T0300.try1-opt2.gromacs0.pdb.gz costs 203.357 T0300.try1-opt1-scwrl.pdb.gz costs 203.922 T0300.try1-opt1.pdb.gz costs 198.75 T0300.try12-opt2.repack-nonPC.pdb.gz costs 186.877 T0300.try12-opt2.pdb.gz costs 181.959 T0300.try12-opt2.gromacs0.pdb.gz costs 190.017 T0300.try12-opt1-scwrl.pdb.gz costs 192.949 T0300.try12-opt1.pdb.gz costs 191 T0300.try11-opt2.repack-nonPC.pdb.gz costs 200.611 T0300.try11-opt2.pdb.gz costs 196.65 T0300.try11-opt2.gromacs0.pdb.gz costs 203.206 T0300.try11-opt1-scwrl.pdb.gz costs 206.063 T0300.try11-opt1.pdb.gz costs 203.877 T0300.try10-opt2.repack-nonPC.pdb.gz costs 181.445 T0300.try10-opt2.pdb.gz costs 177.002 T0300.try10-opt2.gromacs0.pdb.gz costs 183.222 T0300.try10-opt1-scwrl.pdb.gz costs 185.746 T0300.try10-opt1.pdb.gz costs 183.037 rotateFromTry3attempt3.renum.pdb costs 230.403 rotateFromTry3attempt3.fix.pdb costs 232.864 rotateFromTry3attempt2.renum.pdb costs 204.536 rotateFromTry3attempt1.renum.pdb costs 200.487 rotateFromTry2attempt2.renum.pdb costs 248.305 rotateFromTry2attempt1.renum.pdb costs 220.154 georgesuggestion.renum.pdb costs 215.187 # command:CPU_time= 12.906 sec, elapsed time= 14.356 sec) # command:# command:# ClashConform Computing clashes for 67 conformations # command:CPU_time= 13.189 sec, elapsed time= 15.2425 sec) # command:rm -f sort.tmp /projects/compbio/bin/sorttbl cost < decoys/score-all.try12.rdb > sort.tmp mv -f sort.tmp decoys/score-all.try12.rdb gzip -9f decoys/all.clashes gzip -9f decoys/all.breaks mv -f decoys/score-all.try12.pretty decoys/score-all.try12.pretty.old mv: cannot stat `decoys/score-all.try12.pretty': No such file or directory gmake[1]: [decoys/score-all.try12.pretty] Error 1 (ignored) /projects/compbio/experiments/protein-predict/casp7/scripts/prettyscore -terse -targpfx -decpoint < decoys/score-all.try12.rdb > decoys/score-all.try12.pretty gmake[1]: warning: Clock skew detected. Your build may be incomplete. rm T0300.repack.res gmake[1]: Leaving directory `/projects/compbio/experiments/protein-predict/casp7/T0300' gzip -9f decoys/T0300.try12*.pdb gzip: decoys/T0300.try12*.pdb: No such file or directory make: [T0300.do12] Error 1 (ignored)