global_properties:
  working_dir_path: biobb_wf_amber_abc_setup
  can_write_console_log: False

step1_leap_gen_top:
  tool: leap_gen_top
  paths:
    input_pdb_path:  /data/sequence.pdb
    output_pdb_path: structure.leap.pdb
    output_top_path: structure.leap.top
    output_crd_path: structure.leap.crd
  properties:
    forcefield: ["DNA.bsc1"]

step2_leap_solvate:
  tool: leap_solvate
  paths:
    input_pdb_path:  dependency/step1_leap_gen_top/output_pdb_path
    output_pdb_path: structure.solv.pdb
    output_top_path: structure.solv.parmtop
    output_crd_path: structure.solv.crd
  properties:
    forcefield: ["DNA.bsc1"]
    water_type: OPCBOX
    ions_type : ionsjc_tip4pew
    box_type: truncated_octahedron
    distance_to_molecule : 15
    neutralise : True
    iso : True
    closeness : 0.97
    positive_ions_type : K+

step3_leap_add_ions:
  tool: leap_add_ions
  paths:
    input_pdb_path:  dependency/step2_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: ["DNA.bsc1"]
    water_type: OPCBOX
    ions_type : ionsjc_tip4pew
    box_type: truncated_octahedron
    ionic_concentration : 100
    positive_ions_type : K+

step4_cpptraj_randomize_ions:
  tool: cpptraj_randomize_ions
  paths:
    input_top_path:  dependency/step3_leap_add_ions/output_top_path
    input_crd_path:  dependency/step3_leap_add_ions/output_crd_path
    output_pdb_path: structure.randIons.pdb
    output_crd_path: structure.randIons.crd
  properties:
    distance : 6.0
    overlap : 4.0

step5_parmed_hmassrepartition:
  tool: parmed_hmassrepartition
  paths:
    input_top_path:  dependency/step3_leap_add_ions/output_top_path
    output_top_path: structure.leap.4fs.top

step6_sander_mdrun_eq1:
  tool: sander_mdrun
  paths:
    input_top_path: dependency/step5_parmed_hmassrepartition/output_top_path
    input_mdin_path: /data/ABCix_config_files/step1.in
    input_crd_path: dependency/step4_cpptraj_randomize_ions/output_crd_path
    input_ref_path: dependency/step4_cpptraj_randomize_ions/output_crd_path
    output_traj_path: sander.eq1.nc
    output_rst_path: sander.eq1.ncrst
    output_log_path: sander.eq1.log
    output_mdinfo_path: sander.eq1.mdinfo
  properties:
    mdin: 
      maxcyc: 1000
      restraintmask: ":DA,DC,DG,DT,D=3,D=5&!@H="

step7_process_minout_eq1:
  tool: process_minout
  paths:
    input_log_path:  dependency/step6_sander_mdrun_eq1/output_log_path
    output_dat_path: sander.eq1.energy.dat
  properties:
    terms: [ENERGY]

step8_sander_mdrun_eq2:
  tool: sander_mdrun
  paths:
    input_top_path: dependency/step5_parmed_hmassrepartition/output_top_path
    input_mdin_path: /data/ABCix_config_files/step2.in
    input_crd_path: dependency/step6_sander_mdrun_eq1/output_rst_path
    input_ref_path: dependency/step6_sander_mdrun_eq1/output_rst_path
    output_traj_path: sander.eq2.nc
    output_rst_path: sander.eq2.ncrst
    output_log_path: sander.eq2.log
    output_mdinfo_path: sander.eq2.mdinfo
  properties:
    mdin: 
      nstlim: 15000
      restraintmask: ":DA,DC,DG,DT,D=3,D=5&!@H="

step9_process_mdout_eq2:
  tool: process_mdout
  paths:
    input_log_path:  dependency/step8_sander_mdrun_eq2/output_log_path
    output_dat_path: sander.eq2.energy.dat
  properties:
    terms: [TEMP]

step10_sander_mdrun_eq3:
  tool: sander_mdrun
  paths:
    input_top_path: dependency/step5_parmed_hmassrepartition/output_top_path
    input_mdin_path: /data/ABCix_config_files/step3.in
    input_crd_path: dependency/step8_sander_mdrun_eq2/output_rst_path
    input_ref_path: dependency/step8_sander_mdrun_eq2/output_rst_path
    output_traj_path: sander.eq3.nc
    output_rst_path: sander.eq3.ncrst
    output_log_path: sander.eq3.log
    output_mdinfo_path: sander.eq3.mdinfo
  properties:
    mdin: 
      maxcyc: 1000
      restraintmask: ":DA,DC,DG,DT,D=3,D=5&!@H="

step11_process_minout_eq3:
  tool: process_minout
  paths:
    input_log_path:  dependency/step10_sander_mdrun_eq3/output_log_path
    output_dat_path: sander.eq3.energy.dat
  properties:
    terms: [ENERGY]

step12_sander_mdrun_eq4:
  tool: sander_mdrun
  paths:
    input_top_path: dependency/step5_parmed_hmassrepartition/output_top_path
    input_mdin_path: /data/ABCix_config_files/step4.in
    input_crd_path: dependency/step10_sander_mdrun_eq3/output_rst_path
    input_ref_path: dependency/step10_sander_mdrun_eq3/output_rst_path
    output_traj_path: sander.eq4.nc
    output_rst_path: sander.eq4.ncrst
    output_log_path: sander.eq4.log
    output_mdinfo_path: sander.eq4.mdinfo
  properties:
    mdin: 
      maxcyc: 1000
      restraintmask: ":DA,DC,DG,DT,D=3,D=5&!@H="

step13_process_minout_eq4:
  tool: process_minout
  paths:
    input_log_path:  dependency/step12_sander_mdrun_eq4/output_log_path
    output_dat_path: sander.eq4.energy.dat
  properties:
    terms: [ENERGY]

step14_sander_mdrun_eq5:
  tool: sander_mdrun
  paths:
    input_top_path: dependency/step5_parmed_hmassrepartition/output_top_path
    input_mdin_path: /data/ABCix_config_files/step5.in
    input_crd_path: dependency/step12_sander_mdrun_eq4/output_rst_path
    input_ref_path: dependency/step12_sander_mdrun_eq4/output_rst_path
    output_traj_path: sander.eq5.nc
    output_rst_path: sander.eq5.ncrst
    output_log_path: sander.eq5.log
    output_mdinfo_path: sander.eq5.mdinfo
  properties:
    mdin: 
      maxcyc: 1000

step15_process_minout_eq5:
  tool: process_minout
  paths:
    input_log_path:  dependency/step14_sander_mdrun_eq5/output_log_path
    output_dat_path: sander.eq5.energy.dat
  properties:
    terms: [ENERGY]

step16_sander_mdrun_eq6:
  tool: sander_mdrun
  paths:
    input_top_path: dependency/step5_parmed_hmassrepartition/output_top_path
    input_mdin_path: /data/ABCix_config_files/step6.in
    input_crd_path: dependency/step14_sander_mdrun_eq5/output_rst_path
    input_ref_path: dependency/step14_sander_mdrun_eq5/output_rst_path
    output_traj_path: sander.eq6.nc
    output_rst_path: sander.eq6.ncrst
    output_log_path: sander.eq6.log
    output_mdinfo_path: sander.eq6.mdinfo
  properties:
    mdin: 
      nstlim: 5000
      restraintmask: ":DA,DC,DG,DT,D=3,D=5&!@H="

step17_process_mdout_eq6:
  tool: process_mdout
  paths:
    input_log_path:  dependency/step16_sander_mdrun_eq6/output_log_path
    output_dat_path: sander.eq6.pressure_and_density.dat
  properties:
    terms: [PRES]

step18_sander_mdrun_eq7:
  tool: sander_mdrun
  paths:
    input_top_path: dependency/step5_parmed_hmassrepartition/output_top_path
    input_mdin_path: /data/ABCix_config_files/step7.in
    input_crd_path: dependency/step16_sander_mdrun_eq6/output_rst_path
    input_ref_path: dependency/step16_sander_mdrun_eq6/output_rst_path
    output_traj_path: sander.eq7.nc
    output_rst_path: sander.eq7.ncrst
    output_log_path: sander.eq7.log
    output_mdinfo_path: sander.eq7.mdinfo
  properties:
    mdin: 
      nstlim: 5000
      restraintmask: ":DA,DC,DG,DT,D=3,D=5&!@H="

step19_process_mdout_eq7:
  tool: process_mdout
  paths:
    input_log_path:  dependency/step18_sander_mdrun_eq7/output_log_path
    output_dat_path: sander.eq7.pressure_and_density.dat
  properties:
    terms: [PRES, DENSITY]

step20_sander_mdrun_eq8:
  tool: sander_mdrun
  paths:
    input_top_path: dependency/step5_parmed_hmassrepartition/output_top_path
    input_mdin_path: /data/ABCix_config_files/step8.in
    input_crd_path: dependency/step18_sander_mdrun_eq7/output_rst_path
    input_ref_path: dependency/step18_sander_mdrun_eq7/output_rst_path
    output_traj_path: sander.eq8.nc
    output_rst_path: sander.eq8.ncrst
    output_log_path: sander.eq8.log
    output_mdinfo_path: sander.eq8.mdinfo
  properties:
    mdin: 
      nstlim: 10000
      restraintmask: ":DA,DC,DG,DT,D=3,D=5&@P,O5=,C5=,C4=,C3=,O3="

step21_process_mdout_eq8:
  tool: process_mdout
  paths:
    input_log_path:  dependency/step20_sander_mdrun_eq8/output_log_path
    output_dat_path: sander.eq8.pressure_and_density.dat
  properties:
    terms: [PRES, DENSITY]

step22_sander_mdrun_eq9:
  tool: sander_mdrun
  paths:
    input_top_path: dependency/step5_parmed_hmassrepartition/output_top_path
    input_mdin_path: /data/ABCix_config_files/step9.in
    input_crd_path: dependency/step20_sander_mdrun_eq8/output_rst_path
    input_ref_path: dependency/step20_sander_mdrun_eq8/output_rst_path
    output_traj_path: sander.eq9.nc
    output_rst_path: sander.eq9.ncrst
    output_log_path: sander.eq9.log
    output_mdinfo_path: sander.eq9.mdinfo
  properties:
    mdin: 
      nstlim: 10000

step23_process_mdout_eq9:
  tool: process_mdout
  paths:
    input_log_path:  dependency/step22_sander_mdrun_eq9/output_log_path
    output_dat_path: sander.eq9.pressure_and_density.dat
  properties:
    terms: [PRES, DENSITY]

step24_sander_mdrun_eq10:
  tool: sander_mdrun
  paths:
    input_top_path: dependency/step5_parmed_hmassrepartition/output_top_path
    input_mdin_path: /data/ABCix_config_files/step10.in
    input_crd_path: dependency/step22_sander_mdrun_eq9/output_rst_path
    input_ref_path: dependency/step22_sander_mdrun_eq9/output_rst_path
    output_traj_path: sander.eq10.nc
    output_rst_path: sander.eq10.ncrst
    output_log_path: sander.eq10.log
    output_mdinfo_path: sander.eq10.mdinfo
  properties:
    mdin: 
      nstlim: 10000
      ntpr: 50

step25_process_mdout_eq10:
  tool: process_mdout
  paths:
    input_log_path:  dependency/step24_sander_mdrun_eq10/output_log_path
    output_dat_path: sander.eq10.pressure_and_density.dat
  properties:
    terms: [PRES, DENSITY]

step26_sander_mdrun_md:
  tool: sander_mdrun
  paths:
    input_top_path: dependency/step5_parmed_hmassrepartition/output_top_path
    input_mdin_path: /data/ABCix_config_files/md.in
    input_crd_path: dependency/step24_sander_mdrun_eq10/output_rst_path
    input_ref_path: dependency/step24_sander_mdrun_eq10/output_rst_path
    output_traj_path: sander.md.netcdf
    output_rst_path: sander.md.ncrst
    output_mdinfo_path: sander.md.mdinfo
    output_log_path: sander.md.log
  properties:
    mdin: 
      nstlim: 25000
      ntpr: 50
      ntwx: 50

step27_rmsd_first:
  tool: cpptraj_rms
  paths:
    input_top_path: dependency/step3_leap_add_ions/output_top_path
    input_traj_path: dependency/step26_sander_mdrun_md/output_traj_path
    output_cpptraj_path: setup.rms_first.dat
  properties:
    mask : backbone
    reference: first

step28_rmsd_exp:
  tool: cpptraj_rms
  paths:
    input_top_path: dependency/step3_leap_add_ions/output_top_path
    input_traj_path: dependency/step26_sander_mdrun_md/output_traj_path
    input_exp_path: dependency/step1_leap_gen_top/output_pdb_path
    output_cpptraj_path: setup.rms_exp.dat
  properties:
    mask : backbone
    reference: experimental

step29_cpptraj_rgyr:
  tool: cpptraj_rgyr
  paths:
    input_top_path: dependency/step3_leap_add_ions/output_top_path
    input_traj_path: dependency/step26_sander_mdrun_md/output_traj_path
    output_cpptraj_path: setup.rgyr.dat
  properties:
    mask : backbone

step30_cpptraj_image:
  tool: cpptraj_image
  paths:
    input_top_path: dependency/step3_leap_add_ions/output_top_path
    input_traj_path: dependency/step26_sander_mdrun_md/output_traj_path
    output_cpptraj_path: setup.imaged_traj.xtc
  properties:
    mask : solute
    format: xtc