global_properties: working_dir_path: biobb_wf_flexdyn can_write_console_log: False step0_extract_model: tool: extract_model paths: input_structure_path: /data/structure.pdb output_structure_path: structure_model.pdb properties: models: [1] step1_extract_chain: tool: extract_chain paths: input_structure_path: dependency/step0_extract_model/output_structure_path output_structure_path: structure_monomer.pdb properties: chains: ['A'] step2_cpptraj_mask: tool: cpptraj_mask paths: input_top_path: dependency/step1_extract_chain/output_structure_path input_traj_path: dependency/step1_extract_chain/output_structure_path output_cpptraj_path: structure_backbone.pdb properties: mask: backbone format: pdb step3_cpptraj_mask: tool: cpptraj_mask paths: input_top_path: dependency/step1_extract_chain/output_structure_path input_traj_path: dependency/step1_extract_chain/output_structure_path output_cpptraj_path: structure_ca.pdb properties: mask: c-alpha format: pdb step4_concoord_dist: tool: concoord_dist paths: input_structure_path: dependency/step1_extract_chain/output_structure_path output_pdb_path: structure_dist.pdb output_gro_path: structure_dist.gro output_dat_path: structure_dist.dat properties: retain_hydrogens: False cutoff: 4.0 env_vars_dict: CONCOORD_OVERWRITE: '1' CONCOORDLIB: /opt/conda/envs/biobb_wf_flexdyn/share/concoord/lib step5_concoord_disco: tool: concoord_disco paths: input_pdb_path: dependency/step4_concoord_dist/output_pdb_path input_dat_path: dependency/step4_concoord_dist/output_dat_path output_traj_path: structure_disco_traj.pdb output_rmsd_path: structure_disco_rmsd.dat output_bfactor_path: structure_disco_bfactor.pdb properties: vdw: 4 num_structs: 300 env_vars_dict: CONCOORD_OVERWRITE: '1' CONCOORDLIB: /opt/conda/envs/biobb_wf_flexdyn/share/concoord/lib step6_cpptraj_rms: tool: cpptraj_rms paths: input_top_path: dependency/step4_concoord_dist/output_pdb_path input_traj_path: dependency/step5_concoord_disco/output_traj_path input_exp_path: dependency/step1_extract_chain/output_structure_path output_cpptraj_path: structure_concoord_rmsd.dat properties: start: 1 end: -1 steps: 1 mask: c-alpha reference: experimental step7_cpptraj_convert: tool: cpptraj_convert paths: input_top_path: dependency/step4_concoord_dist/output_pdb_path input_traj_path: dependency/step5_concoord_disco/output_traj_path output_cpptraj_path: structure_concoord_disco_traj.trr properties: mask: c-alpha format: trr step8_prody_anm: tool: prody_anm paths: input_pdb_path: dependency/step1_extract_chain/output_structure_path output_pdb_path: structure_prody_anm_traj.pdb properties: selection: backbone num_structs: 300 rmsd: 2.0 step9_cpptraj_rms: tool: cpptraj_rms paths: input_top_path: dependency/step8_prody_anm/output_pdb_path input_traj_path: dependency/step8_prody_anm/output_pdb_path input_exp_path: dependency/step1_extract_chain/output_structure_path output_cpptraj_path: structure_prody_rmsd.dat properties: start: 1 end: -1 steps: 1 mask: c-alpha reference: experimental step10_cpptraj_convert: tool: cpptraj_convert paths: input_top_path: dependency/step2_cpptraj_mask/output_cpptraj_path input_traj_path: dependency/step8_prody_anm/output_pdb_path output_cpptraj_path: structure_prody_anm_traj.trr properties: mask: c-alpha format: trr step11_bd_run: tool: bd_run paths: input_pdb_path: dependency/step3_cpptraj_mask/output_cpptraj_path output_crd_path: structure_flexserv_bd_ensemble.mdcrd output_log_path: structure_flexserv_bd_ensemble.log properties: time: 30000 wfreq: 100 step12_cpptraj_rms: tool: cpptraj_rms paths: input_top_path: dependency/step3_cpptraj_mask/output_cpptraj_path input_traj_path: dependency/step11_bd_run/output_crd_path input_exp_path: dependency/step1_extract_chain/output_structure_path output_cpptraj_path: structure_flexserv_bd_rmsd.dat output_traj_path: structure_flexserv_bd_traj_fitted.trr properties: start: 1 end: -1 steps: 1 mask: c-alpha reference: experimental step13_dmd_run: tool: dmd_run paths: input_pdb_path: dependency/step3_cpptraj_mask/output_cpptraj_path output_crd_path: structure_flexserv_dmd_ensemble.mdcrd output_log_path: structure_flexserv_dmd_ensemble.log properties: frames: 300 step14_cpptraj_rms: tool: cpptraj_rms paths: input_top_path: dependency/step3_cpptraj_mask/output_cpptraj_path input_traj_path: dependency/step13_dmd_run/output_crd_path input_exp_path: dependency/step1_extract_chain/output_structure_path output_cpptraj_path: structure_flexserv_dmd_rmsd.dat output_traj_path: structure_flexserv_dmd_traj_fitted.trr properties: start: 1 end: -1 steps: 1 mask: c-alpha reference: experimental step15_nma_run: tool: nma_run paths: input_pdb_path: dependency/step3_cpptraj_mask/output_cpptraj_path output_crd_path: structure_flexserv_nma_ensemble.mdcrd output_log_path: structure_flexserv_nma_ensemble.log properties: frames: 300 step16_cpptraj_rms: tool: cpptraj_rms paths: input_top_path: dependency/step3_cpptraj_mask/output_cpptraj_path input_traj_path: dependency/step15_nma_run/output_crd_path input_exp_path: dependency/step1_extract_chain/output_structure_path output_cpptraj_path: structure_flexserv_nma_rmsd.dat properties: start: 1 end: -1 steps: 1 mask: c-alpha reference: experimental step17_cpptraj_convert: tool: cpptraj_convert paths: input_top_path: dependency/step3_cpptraj_mask/output_cpptraj_path input_traj_path: dependency/step15_nma_run/output_crd_path output_cpptraj_path: structure_flexserv_nma_ensemble.trr properties: mask: c-alpha format: trr step18_nolb_nma: tool: nolb_nma paths: input_pdb_path: dependency/step3_cpptraj_mask/output_cpptraj_path output_pdb_path: structure_nolb_ensemble.pdb properties: num_structs: 300 rmsd: 4 step19_cpptraj_rms: tool: cpptraj_rms paths: input_top_path: dependency/step3_cpptraj_mask/output_cpptraj_path input_traj_path: dependency/step18_nolb_nma/output_pdb_path input_exp_path: dependency/step1_extract_chain/output_structure_path output_cpptraj_path: structure_nolb_rmsd.dat properties: start: 1 end: -1 steps: 1 mask: c-alpha reference: experimental step20_cpptraj_convert: tool: cpptraj_convert paths: input_top_path: dependency/step3_cpptraj_mask/output_cpptraj_path input_traj_path: dependency/step18_nolb_nma/output_pdb_path output_cpptraj_path: structure_nolb_ensemble.trr properties: mask: c-alpha format: trr step21_imod_imode: tool: imod_imode paths: input_pdb_path: dependency/step1_extract_chain/output_structure_path output_dat_path: structure_imode_evecs.dat properties: cg: 2 step22_imod_imc: tool: imod_imc paths: input_pdb_path: dependency/step1_extract_chain/output_structure_path input_dat_path: dependency/step21_imod_imode/output_dat_path output_traj_path: structure_imc.pdb properties: num_structs: 300 num_modes: 10 amplitude: 6.0 step23_cpptraj_rms: tool: cpptraj_rms paths: input_top_path: dependency/step22_imod_imc/output_traj_path input_traj_path: dependency/step22_imod_imc/output_traj_path input_exp_path: dependency/step1_extract_chain/output_structure_path output_cpptraj_path: structure_imods_rmsd.dat properties: start: 1 end: -1 steps: 1 mask: c-alpha reference: experimental step24_cpptraj_convert: tool: cpptraj_convert paths: input_top_path: dependency/step22_imod_imc/output_traj_path input_traj_path: dependency/step22_imod_imc/output_traj_path output_cpptraj_path: structure_imods_ensemble.trr properties: mask: c-alpha format: trr step25_trjcat: tool: trjcat paths: input_trj_zip_path: concat_trr.zip output_trj_path: structure_concat_traj.trr step26_make_ndx: tool: make_ndx paths: input_structure_path: dependency/step3_cpptraj_mask/output_cpptraj_path output_ndx_path: structure_gmx_ndx.ndx properties: selection: 3 step27_gmx_cluster: tool: gmx_cluster paths: input_structure_path: dependency/step3_cpptraj_mask/output_cpptraj_path input_traj_path: dependency/step25_trjcat/output_trj_path input_index_path: dependency/step26_make_ndx/output_ndx_path output_pdb_path: structure_concat_cluster.pdb properties: fit_selection: System output_selection: System method: linkage cutoff: 0.12 step28_cpptraj_rms: tool: cpptraj_rms paths: input_top_path: dependency/step3_cpptraj_mask/output_cpptraj_path input_traj_path: dependency/step27_gmx_cluster/output_pdb_path input_exp_path: dependency/step3_cpptraj_mask/output_cpptraj_path output_cpptraj_path: structure_meta_traj_rmsd.dat output_traj_path: structure_meta_traj_fitted.crd properties: start: 1 end: -1 steps: 1 mask: c-alpha reference: experimental step29_pcz_zip: tool: pcz_zip paths: input_pdb_path: dependency/step3_cpptraj_mask/output_cpptraj_path input_crd_path: dependency/step28_cpptraj_rms/output_traj_path output_pcz_path: structure_concat_ensemble.pcz properties: variance: 90 neigenv: 10 step30_pcz_zip: tool: pcz_zip paths: input_pdb_path: dependency/step3_cpptraj_mask/output_cpptraj_path input_crd_path: dependency/step28_cpptraj_rms/output_traj_path output_pcz_path: structure_concat_ensemble_gaussian.pcz properties: variance: 90 neigenv: 10 gauss_rmsd: True step31_pcz_info: tool: pcz_info paths: input_pcz_path: dependency/step29_pcz_zip/output_pcz_path output_json_path: structure_pcz_report.json step32_pcz_evecs: tool: pcz_evecs paths: input_pcz_path: dependency/step29_pcz_zip/output_pcz_path output_json_path: structure_pcz_evecs.json properties: eigenvector: 1 step33_pcz_animate: tool: pcz_animate paths: input_pcz_path: dependency/step29_pcz_zip/output_pcz_path output_crd_path: structure_pcz_proj1.crd properties: eigenvector: 1 step34_cpptraj_convert: tool: cpptraj_convert paths: input_top_path: dependency/step3_cpptraj_mask/output_cpptraj_path input_traj_path: dependency/step33_pcz_animate/output_crd_path output_cpptraj_path: structure_pcz_proj1.dcd properties: format: dcd step35_pcz_bfactor: tool: pcz_bfactor paths: input_pcz_path: dependency/step29_pcz_zip/output_pcz_path output_dat_path: structure_bfactor_all.dat output_pdb_path: structure_bfactor_all.pdb properties: eigenvector: 0 pdb: True step36_pcz_hinges: tool: pcz_hinges paths: input_pcz_path: dependency/step30_pcz_zip/output_pcz_path output_json_path: structure_hinges_bfactor_report.json properties: eigenvector: 0 method: Bfactor_slope step37_pcz_hinges: tool: pcz_hinges paths: input_pcz_path: dependency/step30_pcz_zip/output_pcz_path output_json_path: structure_hinges_dyndom_report.json properties: eigenvector: 0 method: Dynamic_domain step38_pcz_hinges: tool: pcz_hinges paths: input_pcz_path: dependency/step30_pcz_zip/output_pcz_path output_json_path: structure_hinges_fcte_report.json properties: eigenvector: 0 method: Force_constant step39_pcz_stiffness: tool: pcz_stiffness paths: input_pcz_path: dependency/step29_pcz_zip/output_pcz_path output_json_path: structure_pcz_stiffness.json properties: eigenvector: 0 step40_pcz_collectivity: tool: pcz_collectivity paths: input_pcz_path: dependency/step29_pcz_zip/output_pcz_path output_json_path: structure_pcz_collectivity.json properties: eigenvector: 0