Rosetta Enzyme Design Error: std::out_of_range Exception

(my-rdkit-env) sun@wp:/media/sun/yingpan/linux/enzds/enzdes/design_again$ /media/sun/yingpan/linux/rosetta_bin_linux_2021.16.61629_bundle/main/source/bin/enzyme_design.linuxgccrelease @design.flags core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: rosetta.binary.linux.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:52:25.363712 core.init: command: /media/sun/yingpan/linux/rosetta_bin_linux_2021.16.61629_bundle/main/source/bin/enzyme_design.linuxgccrelease @design.flags basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=817267485 seed_offset=0 real_seed=817267485 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=817267485 RG_type=mt19937 core.init: found database environment variable ROSETTA3_DB: /media/sun/yingpan/linux/rosetta_bin_linux_2021.16.61629_bundle/main/database 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/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 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/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 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 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. core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.50124 seconds. core.scoring.ScoreFunctionFactory: [ WARNING ] **************************************************************************

talaris2013_cst may be a 'talaris' scorefunction, but ScoreFunctionFactory thinks the -restore_talaris_behavior flags weren't set. Your scorefunction may be garbage!

basic.io.database: Database file opened: scoring/score_functions/envsmooth/envdata.txt basic.io.database: Database file opened: scoring/score_functions/carbon_hbond/ch_o_bond_potential.dat basic.io.database: Database file opened: scoring/score_functions/custom_pair_distance/pos_charge_repulsion basic.io.database: Database file opened: scoring/score_functions/custom_pair_distance/neg_charge_repulsion core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy: Added 8 AtomPairFuncList lists protocols.jobdist.JobDistributors: Looking for an available job: 1 1 /media/sun/yingpan/linux/enzds/enzdes/design_again/complex.pdb 1 apps.public.enzdes.enzyme_design: Starting complex_0001 ... core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'HIP' from the PDB components dictionary for residue type 'pdb_HIP' core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 1 in file /media/sun/yingpan/linux/enzds/enzdes/design_again/complex.pdb. Best match rsd_type: TYR:NtermProteinFull core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 50 in file /media/sun/yingpan/linux/enzds/enzdes/design_again/complex.pdb. Best match rsd_type: ASP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 165 in file /media/sun/yingpan/linux/enzds/enzdes/design_again/complex.pdb. Best match rsd_type: GLU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 255 in file /media/sun/yingpan/linux/enzds/enzdes/design_again/complex.pdb. Best match rsd_type: pdb_HIP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 421 in file /media/sun/yingpan/linux/enzds/enzdes/design_again/complex.pdb. Best match rsd_type: GLU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 429 in file /media/sun/yingpan/linux/enzds/enzdes/design_again/complex.pdb. Best match rsd_type: pdb_HIP core.conformation.Conformation: [ WARNING ] missing heavyatom: P on residue pdb_HIP 255 core.conformation.Conformation: [ WARNING ] missing heavyatom: OP1 on residue pdb_HIP 255 core.conformation.Conformation: [ WARNING ] missing heavyatom: OP2 on residue pdb_HIP 255 core.conformation.Conformation: [ WARNING ] missing heavyatom: O3P on residue pdb_HIP 255 core.conformation.Conformation: [ WARNING ] missing heavyatom: P on residue pdb_HIP 429 core.conformation.Conformation: [ WARNING ] missing heavyatom: OP1 on residue pdb_HIP 429 core.conformation.Conformation: [ WARNING ] missing heavyatom: OP2 on residue pdb_HIP 429 core.conformation.Conformation: [ WARNING ] missing heavyatom: O3P on residue pdb_HIP 429 core.pack.pack_missing_sidechains: packing residue number 255 because of missing atom number 9 atom name P core.pack.pack_missing_sidechains: packing residue number 429 because of missing atom number 9 atom name P core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /media/sun/yingpan/linux/rosetta_bin_linux_2021.16.61629_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/media/sun/yingpan/linux/rosetta_bin_linux_2021.16.61629_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.077284 seconds to load from binary core.pack.rotamers.SingleLigandRotamerLibrary: Read in 999 rotamers from /media/sun/yingpan/linux/enzds/enzdes/design_again/LIG_conformers.pdb ! core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_HIP core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_HIP core.pack.pack_rotamers: built 2 rotamers at 2 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.enzdes.EnzdesFixBBProtocol: starting apply function... protocols.toolbox.match_enzdes_util.MatchConstraintFileIfo: [ WARNING ] No appropriate atoms found for entry 2 in constraint 1 protocols.toolbox.match_enzdes_util.MatchConstraintFileIfo: [ WARNING ] No appropriate atoms found for entry 2 in constraint 1 protocols.toolbox.match_enzdes_util.MatchConstraintFileIfo: [ WARNING ] No appropriate atoms found for entry 2 in constraint 1 protocols.toolbox.match_enzdes_util.MatchConstraintFileIfo: [ WARNING ] No appropriate atoms found for entry 2 in constraint 1 core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'E' from the PDB components dictionary for residue type 'pdb_E' protocols.toolbox.match_enzdes_util.MatchConstraintFileIfo: [ WARNING ] No appropriate atoms found for entry 1 in constraint 1 protocols.toolbox.match_enzdes_util.MatchConstraintFileIfo: [ WARNING ] No appropriate atoms found for entry 2 in constraint 1 core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'GLH' from the PDB components dictionary for residue type 'pdb_GLH' protocols.toolbox.match_enzdes_util.MatchConstraintFileIfo: [ WARNING ] No appropriate atoms found for entry 1 in constraint 1 protocols.toolbox.match_enzdes_util.MatchConstraintFileIfo: [ WARNING ] No appropriate atoms found for entry 2 in constraint 1 protocols.toolbox.match_enzdes_util.EnzConstraintIO: read enzyme constraints from /media/sun/yingpan/linux/enzds/enzdes/design_again/LIG.cst ... done, 6 cst blocks were read. protocols.toolbox.match_enzdes_util.EnzConstraintIO: Generating constraints for pose...

AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.

terminate called after throwing an instance of 'std::out_of_range' what(): map::at 已放弃 (核心已转储)

如何解决内容：这个错误是由于程序中出现了一个std::out_of_range异常，导致程序终止。要解决这个问题，你可以尝试以下几个步骤：

1. 检查输入文件和参数是否正确。确保输入文件存在，并且参数设置正确。

2. 检查程序所需的所有文件和数据库是否正确加载。确保文件路径正确，并且数据库文件没有损坏。

3. 更新Rosetta软件到最新版本。有时，这种错误可能是由于软件版本不兼容或存在bug导致的。更新到最新版本可能会修复这个问题。

4. 查看Rosetta的官方文档和论坛。可能有其他用户遇到过类似的问题，并提供了解决方案或建议。

如果以上步骤都没有解决问题，你可以尝试联系Rosetta的开发团队，向他们报告这个问题，并提供详细的错误信息和复现步骤。他们可能能够提供更具体的解决方案或修复该问题的补丁。