DAlphaBall missing #39
Comments
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While you can possibly find it elsewhere, DAlphaBall is also included within the regular Rosetta distribution. If you go to |
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Thanks. but I have checked and path is correct. core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_nov16.wts core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.64 seconds. basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/hydroxyl_torsion_preference.txt core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb protocols.jd2.parser.ScoreFunctionLoader: defined score function "sfxn" with weights "beta_nov16" core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_nov16.wts protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "chain1only" of type SwitchChainOrder protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "move_chainA_far_away" of type RollMover protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "pack_long" of type ProteinInterfaceDesign core.pack.task.xml_util: Object min reading the following task_operations: Adding the following task operations pack_long protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "min" of type TaskAwareMinMover core.select.residue_selector.util: [ WARNING ] Selector name is empty! protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "res_count_all" of type ResidueCount protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "buried_npsa_FAMILYVW" of type BuriedSurfaceArea protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "buried_npsa" of type BuriedSurfaceArea protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "interface_buried_sasa" of type Sasa protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "exposed_hydrophobics" of type ExposedHydrophobics protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "buried_npsa_per_res" of type CalculatorFilter protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "buried_npsa_FAMILYVW_per_res" of type CalculatorFilter protocols.filters.Filter: Setting MoveBeforeFilter for mover 'chain1only' and filter 'buried_npsa_FAMILYVW' protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "buried_npsa_FAMILYVW_monomer" of type MoveBeforeFilter protocols.filters.Filter: Setting MoveBeforeFilter for mover 'chain1only' and filter 'buried_npsa' protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "buried_npsa_monomer" of type MoveBeforeFilter protocols.filters.Filter: Setting MoveBeforeFilter for mover 'chain1only' and filter 'exposed_hydrophobics' protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "exposed_hydrophobics_monomer" of type MoveBeforeFilter protocols.filters.Filter: Setting MoveBeforeFilter for mover 'chain1only' and filter 'buried_npsa_per_res' protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "buried_npsa_per_res_monomer" of type MoveBeforeFilter protocols.filters.Filter: Setting MoveBeforeFilter for mover 'chain1only' and filter 'buried_npsa_FAMILYVW_per_res' protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "buried_npsa_FAMILYVW_per_res_monomer" of type MoveBeforeFilter protocols.filters.Filter: Setting MoveBeforeFilter for mover 'move_chainA_far_away' and filter 'buried_npsa_FAMILYVW' protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "buried_npsa_FAMILYVW_apo" of type MoveBeforeFilter protocols.filters.Filter: Setting MoveBeforeFilter for mover 'move_chainA_far_away' and filter 'buried_npsa' protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "buried_npsa_apo" of type MoveBeforeFilter protocols.filters.Filter: Setting MoveBeforeFilter for mover 'move_chainA_far_away' and filter 'exposed_hydrophobics' protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "exposed_hydrophobics_apo" of type MoveBeforeFilter protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "delta_buried_npsa_FAMILYVW" of type CalculatorFilter protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "delta_buried_npsa" of type CalculatorFilter protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "delta_exposed_hydrophobics" of type CalculatorFilter protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molecular_surface_ap_target" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molec_sq5_ap_target" of type ContactMolecularSurfPyRosetta-4 2022 [Rosetta PyRosetta4.Release.python310.linux 2022.39+release.d8d9982120b445e65d19d1e63ccc663cc1d639e8 2022-09-28T17:13:34] retrieved from: http://www.pyrosetta.org (C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team. Using 2 cores sh: DAlphaBall.gcc: No such file or directory sh: DAlphaBall.gcc: No such file or directory ace protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molecular_surface_apap_target" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molec_sq5_apap_target" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molecular_surface" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molecular_surface_ap_binder" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molec_sq5_ap_binder" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molecular_surface_apap_binder" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molec_sq5_apap_binder" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "buns_heavy_ball_1.1D" of type BuriedUnsatHbonds protocols.simple_filters.DdgFilter: ddg filter with threshold -10 and threshold_min -999999 repeats=5 and scorefxn sfxn extreme_value_removal: 1 and repack 1 protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "ddg" of type Ddg protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "pre_mismatch_probability" of type SSPrediction protocols.filters.Filter: Setting MoveBeforeFilter for mover 'chain1only' and filter 'pre_mismatch_probability' protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "mismatch_probability" of type MoveBeforeFilter protocols.simple_filters.ShapeComplementarityFilter: Structures with shape complementarity < 0.55, interface area < 0 A^2, median distance > 0 will be filtered. protocols.simple_filters.ShapeComplementarityFilter: Ignoring residue range selection since residues2 is empty. protocols.simple_filters.ShapeComplementarityFilter: Using Jump Selector to define surfaces. protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "interface_sc" of type ShapeComplementarity protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following settings protocols.rosetta_scripts.ParsedProtocol: Added filter "contact_molecular_surface_ap_target" protocols.rosetta_scripts.ParsedProtocol: Added filter "contact_molecular_surface_apap_target" protocols.rosetta_scripts.ParsedProtocol: Added filter "contact_molec_sq5_apap_target" protocols.rosetta_scripts.ParsedProtocol: Added filter "interface_sc" protocols.rosetta_scripts.ParsedProtocol: Added filter "interface_buried_sasa" protocols.rosetta_scripts.ParsedProtocol: Added filter "contact_molecular_surface" protocols.rosetta_scripts.ParsedProtocol: Added filter "mismatch_probability" core.simple_metrics.util: Added simple metric SapScoreMetric. protocols.rosetta_scripts.ParsedProtocol: Added metrics: "sap_score" core.simple_metrics.util: Added simple metric SapScoreMetric. protocols.rosetta_scripts.ParsedProtocol: Added metrics: "sap_score_target" core.simple_metrics.util: Added simple metric SapScoreMetric. protocols.rosetta_scripts.ParsedProtocol: Added metrics: "binder_blocked_sap" core.simple_metrics.util: Added simple metric SapScoreMetric. protocols.rosetta_scripts.ParsedProtocol: Added metrics: "target_blocked_sap" protocols.rosetta_scripts.ParsedProtocol: Added filter "ddg" protocols.rosetta_scripts.ParsedProtocol: Added filter "buns_heavy_ball_1.1D" core.import_pose.import_pose: File 'output/run2/trf_relax/pd1_r1_3_r2_2.pdb' automatically determined to be of type PDB protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER contact_molecular_surface_ap_target======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER contact_molecular_surface_ap_target======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER contact_molecular_surface_apap_target======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER contact_molecular_surface_apap_target======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER contact_molec_sq5_apap_target======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER contact_molec_sq5_apap_target======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER interface_sc======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER interface_sc======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER interface_buried_sasa======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER interface_buried_sasa======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER contact_molecular_surface======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER contact_molecular_surface======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER mismatch_probability======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER mismatch_probability======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN METRIC sap_score======================= basic.io.database: Database file opened: scoring/score_functions/sap_sasa_calib.dat ace protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molecular_surface_apap_target" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molec_sq5_apap_target" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molecular_surface" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molecular_surface_ap_binder" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molec_sq5_ap_binder" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molecular_surface_apap_binder" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molec_sq5_apap_binder" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "buns_heavy_ball_1.1D" of type BuriedUnsatHbonds protocols.simple_filters.DdgFilter: ddg filter with threshold -10 and threshold_min -999999 repeats=5 and scorefxn sfxn extreme_value_removal: 1 and repack 1 protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "ddg" of type Ddg protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "pre_mismatch_probability" of type SSPrediction protocols.filters.Filter: Setting MoveBeforeFilter for mover 'chain1only' and filter 'pre_mismatch_probability' protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "mismatch_probability" of type MoveBeforeFilter protocols.simple_filters.ShapeComplementarityFilter: Structures with shape complementarity < 0.55, interface area < 0 A^2, median distance > 0 will be filtered. protocols.simple_filters.ShapeComplementarityFilter: Ignoring residue range selection since residues2 is empty. protocols.simple_filters.ShapeComplementarityFilter: Using Jump Selector to define surfaces. protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "interface_sc" of type ShapeComplementarity protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following settings protocols.rosetta_scripts.ParsedProtocol: Added filter "contact_molecular_surface_ap_target" protocols.rosetta_scripts.ParsedProtocol: Added filter "contact_molecular_surface_apap_target" protocols.rosetta_scripts.ParsedProtocol: Added filter "contact_molec_sq5_apap_target" protocols.rosetta_scripts.ParsedProtocol: Added filter "interface_sc" protocols.rosetta_scripts.ParsedProtocol: Added filter "interface_buried_sasa" protocols.rosetta_scripts.ParsedProtocol: Added filter "contact_molecular_surface" protocols.rosetta_scripts.ParsedProtocol: Added filter "mismatch_probability" core.simple_metrics.util: Added simple metric SapScoreMetric. protocols.rosetta_scripts.ParsedProtocol: Added metrics: "sap_score" core.simple_metrics.util: Added simple metric SapScoreMetric. protocols.rosetta_scripts.ParsedProtocol: Added metrics: "sap_score_target" core.simple_metrics.util: Added simple metric SapScoreMetric. protocols.rosetta_scripts.ParsedProtocol: Added metrics: "binder_blocked_sap" core.simple_metrics.util: Added simple metric SapScoreMetric. protocols.rosetta_scripts.ParsedProtocol: Added metrics: "target_blocked_sap" protocols.rosetta_scripts.ParsedProtocol: Added filter "ddg" protocols.rosetta_scripts.ParsedProtocol: Added filter "buns_heavy_ball_1.1D" core.import_pose.import_pose: File 'output/run2/trf_relax/pd1_r1_3_r2_0.pdb' automatically determined to be of type PDB protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER contact_molecular_surface_ap_target======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER contact_molecular_surface_ap_target======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER contact_molecular_surface_apap_target======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER contact_molecular_surface_apap_target======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER contact_molec_sq5_apap_target======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER contact_molec_sq5_apap_target======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER interface_sc======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER interface_sc======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER interface_buried_sasa======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER interface_buried_sasa======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER contact_molecular_surface======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER contact_molecular_surface======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER mismatch_probability======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER mismatch_probability======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN METRIC sap_score======================= basic.io.database: Database file opened: scoring/score_functions/sap_sasa_calib.dat WARNING!! DALPHABALL output nan at index WARNING!! DALPHABALL output nan at index 9449927794875294499277949472 |
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I encountered the same error. Did you find a solution later on? |
When running the get_interface_metrics.py? I get the following error
sh: /software/rosetta/DAlphaBall.gcc: No such file or directory
sh: /software/rosetta/DAlphaBall.gcc: No such file or directory
From where should Iget the DAlphaBall?
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