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BioExcel AMBER MD Setup - Lysozyme 1AKI

W-05 · AMBER MD Setup

v123 stages0 clones0

The pipeline

Every stage picks its own compute target. Temple Compute OS resolves the dependencies between them and moves the data across each boundary.

  1. 01Download 1AKI structure from PDB
    Consumes
    fetch_pdb_config, src_conda_env_yaml
    Produces
    downloaded_pdb
  2. 02Prepare PDB for AMBER (pdb4amber)
    Consumes
    downloaded_pdb
    Produces
    pdb4amber_pdb
  3. 03Create protein system topology (leap)
    Consumes
    gen_top_config, pdb4amber_pdb
    Produces
    top_pdb, top_top, top_crd
  4. 04Minimize hydrogens in vacuo (sander)
    Consumes
    sander_h_min_config, top_top, top_crd
    Produces
    h_min_traj, h_min_rst, h_min_log
  5. 05Extract hydrogen minimization energy (process_minout)
    Consumes
    process_energy_config, h_min_log
    Produces
    h_min_dat
  6. 06Minimize system in vacuo (sander)
    Consumes
    sander_n_min_config, top_top, h_min_rst
    Produces
    n_min_traj, n_min_rst, n_min_log
  7. 07Extract system minimization energy (process_minout)
    Consumes
    process_energy_config, n_min_log
    Produces
    n_min_dat
  8. 08Convert minimized structure to PDB (ambpdb)
    Consumes
    top_top, n_min_rst
    Produces
    ambpdb_pdb
  9. 09Create solvent box and solvate system (leap)
    Consumes
    leap_solvate_config, ambpdb_pdb
    Produces
    solv_pdb, solv_top, solv_crd
  10. 10Neutralize and add ions (leap)
    Consumes
    leap_add_ions_config, solv_pdb
    Produces
    ions_pdb, ions_top, ions_crd
  11. 11Energy minimize the system (sander)
    Consumes
    sander_min_config, ions_top, ions_crd
    Produces
    min_traj, min_rst, min_log
  12. 12Extract system minimization energy (process_minout)
    Consumes
    process_energy_config, min_log
    Produces
    min_dat
  13. 13Heat the system 0 to 300 K (sander)
    Consumes
    sander_heat_config, ions_top, min_rst
    Produces
    heat_traj, heat_rst, heat_log
  14. 14Extract heating temperature (process_mdout)
    Consumes
    process_temp_config, heat_log
    Produces
    heat_dat
  15. 15Equilibrate the system NVT (sander)
    Consumes
    sander_nvt_config, ions_top, heat_rst
    Produces
    nvt_traj, nvt_rst, nvt_log
  16. 16Extract NVT temperature (process_mdout)
    Consumes
    process_temp_config, nvt_log
    Produces
    nvt_dat
  17. 17Equilibrate the system NPT (sander)
    Consumes
    sander_npt_config, ions_top, nvt_rst
    Produces
    npt_traj, npt_rst, npt_log
  18. 18Extract NPT pressure and density (process_mdout)
    Consumes
    process_npt_config, npt_log
    Produces
    npt_dat
  19. 19Free MD simulation (sander)
    Consumes
    sander_free_config, ions_top, npt_rst
    Produces
    free_traj, free_rst, free_log
  20. 20RMSd vs first snapshot (cpptraj)
    Consumes
    cpptraj_rms_first_config, ions_top, free_traj, src_conda_env_yaml
    Produces
    rms_first_dat
  21. 21RMSd vs experimental structure (cpptraj)
    Consumes
    cpptraj_rms_exp_config, ions_top, free_traj, downloaded_pdb, src_conda_env_yaml
    Produces
    rms_exp_dat
  22. 22Radius of gyration (cpptraj)
    Consumes
    cpptraj_rgyr_config, ions_top, free_traj, src_conda_env_yaml
    Produces
    rgyr_dat
  23. 23Image trajectory and strip solvent (cpptraj)
    Consumes
    cpptraj_image_config, ions_top, free_traj, src_conda_env_yaml
    Produces
    imaged_traj

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