global_properties: working_dir_path: biobb_wf_amber_md_setup can_write_console_log: False step00_reduce_remove_hydrogens: tool: reduce_remove_hydrogens paths: input_path: /data/structure.pdb output_path: structure.noH.pdb step0_extract_molecule: tool: extract_molecule paths: input_structure_path: dependency/step00_reduce_remove_hydrogens/output_path output_molecule_path: protein.pdb step000_cat_pdb: tool: cat_pdb paths: input_structure1: dependency/step0_extract_molecule/output_molecule_path input_structure2: /data/ions.pdb output_structure_path: protein.ions.pdb step1_pdb4amber_run: tool: pdb4amber_run paths: input_pdb_path: dependency/step000_cat_pdb/output_structure_path output_pdb_path: structure.pdb4amber.pdb step2_leap_gen_top: tool: leap_gen_top paths: input_pdb_path: dependency/step1_pdb4amber_run/output_pdb_path output_pdb_path: structure.leap.pdb output_top_path: structure.leap.top output_crd_path: structure.leap.crd properties: forcefield: ["protein.ff14SB","DNA.bsc1","RNA.OL3","water.tip3p"] step3_sander_mdrun_minH: tool: sander_mdrun paths: input_top_path: dependency/step2_leap_gen_top/output_top_path input_crd_path: dependency/step2_leap_gen_top/output_crd_path input_ref_path: dependency/step2_leap_gen_top/output_crd_path output_traj_path: sander.h_min.x output_rst_path: sander.h_min.rst output_log_path: sander.h_min.log properties: simulation_type: min_vacuo mdin : maxcyc: 500 ntwx: 100 ntpr: 5 ntr: 1 restraintmask: "\":*&!@H=\"" restraint_wt: 50.0 step4_process_minout_minH: tool: process_minout paths: input_log_path: dependency/step3_sander_mdrun_minH/output_log_path output_dat_path: sander.h_min.energy.dat properties: terms : [ENERGY] step5_sander_mdrun_min: tool: sander_mdrun paths: input_top_path: dependency/step2_leap_gen_top/output_top_path input_crd_path: dependency/step3_sander_mdrun_minH/output_rst_path input_ref_path: dependency/step3_sander_mdrun_minH/output_rst_path output_traj_path: sander.n_min.x output_rst_path: sander.n_min.rst output_log_path: sander.n_min.log properties: simulation_type: min_vacuo mdin : maxcyc: 500 ntwx: 100 ntpr: 5 ntr: 1 restraintmask: "\":*&!@H=\"" restraint_wt: 50.0 step6_process_minout_min: tool: process_minout paths: input_log_path: dependency/step5_sander_mdrun_min/output_log_path output_dat_path: sander.n_min.energy.dat properties: terms : [ENERGY] step7_amber_to_pdb: tool: amber_to_pdb paths: input_top_path: dependency/step2_leap_gen_top/output_top_path input_crd_path: dependency/step5_sander_mdrun_min/output_rst_path output_pdb_path: structure.ambpdb.pdb step8_leap_solvate: tool: leap_solvate paths: input_pdb_path: dependency/step7_amber_to_pdb/output_pdb_path output_pdb_path: structure.solv.pdb output_top_path: structure.solv.parmtop output_crd_path: structure.solv.crd properties: forcefield: ["protein.ff14SB","DNA.bsc1","RNA.OL3","water.tip3p"] water_type: TIP3PBOX distance_to_molecule: 9 box_type: truncated_octahedron step9_leap_add_ions: tool: leap_add_ions paths: input_pdb_path: dependency/step8_leap_solvate/output_pdb_path output_pdb_path: structure.ions.pdb output_top_path: structure.ions.parmtop output_crd_path: structure.ions.crd properties: forcefield: ["protein.ff14SB","DNA.bsc1","RNA.OL3","water.tip3p"] neutralise: True positive_ions_type: Na+ negative_ions_type: Cl- ionic_concentration: 150 box_type: truncated_octahedron step10_sander_mdrun_energy: tool: sander_mdrun paths: input_top_path: dependency/step9_leap_add_ions/output_top_path input_crd_path: dependency/step9_leap_add_ions/output_crd_path input_ref_path: dependency/step9_leap_add_ions/output_crd_path output_traj_path: sander.min.x output_rst_path: sander.min.rst output_log_path: sander.min.log properties: simulation_type: minimization mdin : maxcyc: 500 ntwx: 100 ntr: 1 restraintmask: "\"!:WAT,Cl-,Na+\"" restraint_wt: 50.0 step11_process_minout_energy: tool: process_minout paths: input_log_path: dependency/step10_sander_mdrun_energy/output_log_path output_dat_path: sander.min.energy.dat properties: terms : [ENERGY] step12_sander_mdrun_warm: tool: sander_mdrun paths: input_top_path: dependency/step9_leap_add_ions/output_top_path input_crd_path: dependency/step10_sander_mdrun_energy/output_rst_path input_ref_path: dependency/step10_sander_mdrun_energy/output_rst_path output_traj_path: sander.heat.netcdf output_rst_path: sander.heat.rst output_log_path: sander.heat.log properties: simulation_type: heat mdin : maxcyc: 50000 ntwx: 100 ntr: 1 restraintmask: "\"!:WAT,Cl-,Na+\"" restraint_wt: 10.0 step13_process_mdout_warm: tool: process_mdout paths: input_log_path: dependency/step12_sander_mdrun_warm/output_log_path output_dat_path: sander.md.temp.dat properties: terms : [TEMP] step14_sander_mdrun_nvt: tool: sander_mdrun paths: input_top_path: dependency/step9_leap_add_ions/output_top_path input_crd_path: dependency/step12_sander_mdrun_warm/output_rst_path input_ref_path: dependency/step12_sander_mdrun_warm/output_rst_path output_traj_path: sander.nvt.netcdf output_rst_path: sander.nvt.rst output_log_path: sander.nvt.log properties: simulation_type: nvt mdin : nstlim: 25000 ntwx: 100 ntr: 1 restraintmask: "\"!:WAT,Cl-,Na+ & !@H=\"" restraint_wt: 5.0 step15_process_mdout_nvt: tool: process_mdout paths: input_log_path: dependency/step14_sander_mdrun_nvt/output_log_path output_dat_path: sander.md.nvt.temp.dat properties: terms : [TEMP] step16_sander_mdrun_npt: tool: sander_mdrun paths: input_top_path: dependency/step9_leap_add_ions/output_top_path input_crd_path: dependency/step14_sander_mdrun_nvt/output_rst_path input_ref_path: dependency/step14_sander_mdrun_nvt/output_rst_path output_traj_path: sander.npt.netcdf output_rst_path: sander.npt.rst output_log_path: sander.npt.log properties: simulation_type: npt mdin : nstlim: 25000 ntwx: 100 ntr: 1 restraintmask: "\"!:WAT,Cl-,Na+ & !@H=\"" restraint_wt: 2.5 step17_process_mdout_npt: tool: process_mdout paths: input_log_path: dependency/step16_sander_mdrun_npt/output_log_path output_dat_path: sander.md.npt.dat properties: terms : [PRES, DENSITY] step18_sander_mdrun_md: tool: sander_mdrun paths: input_top_path: dependency/step9_leap_add_ions/output_top_path input_crd_path: dependency/step16_sander_mdrun_npt/output_rst_path output_traj_path: sander.free.netcdf output_rst_path: sander.free.rst output_log_path: sander.free.log properties: simulation_type: free mdin : nstlim: 250000 ntwx: 500 step19_rmsd_first: tool: cpptraj_rms paths: input_top_path: dependency/step9_leap_add_ions/output_top_path input_traj_path: dependency/step18_sander_mdrun_md/output_traj_path output_cpptraj_path: setup.rms_first.dat properties: mask : backbone reference: first step20_rmsd_exp: tool: cpptraj_rms paths: input_top_path: dependency/step9_leap_add_ions/output_top_path input_traj_path: dependency/step18_sander_mdrun_md/output_traj_path input_exp_path: dependency/step2_leap_gen_top/output_pdb_path output_cpptraj_path: setup.rms_exp.dat properties: mask : backbone reference: experimental step21_cpptraj_rgyr: tool: cpptraj_rgyr paths: input_top_path: dependency/step9_leap_add_ions/output_top_path input_traj_path: dependency/step18_sander_mdrun_md/output_traj_path output_cpptraj_path: setup.rgyr.dat properties: mask : backbone step22_cpptraj_image: tool: cpptraj_image paths: input_top_path: dependency/step9_leap_add_ions/output_top_path input_traj_path: dependency/step18_sander_mdrun_md/output_traj_path output_cpptraj_path: setup.imaged_traj.xtc properties: mask : all-atoms format: xtc