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BioExcel AMBER MD Setup - Protein-Ligand Complex (T4 Lysozyme 3HTB + JZ4)

W-15 · AMBER Protein-Ligand Complex MD Setup

v130 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 3HTB structure from PDB
    Consumes
    fetch_pdb_config, src_conda_env_yaml
    Produces
    downloaded_pdb
  2. 02Remove crystallographic water molecules
    Consumes
    downloaded_pdb, src_conda_env_yaml
    Produces
    nowat_pdb
  3. 03Remove PO4 ligand from structure
    Consumes
    remove_ligand_po4_config, nowat_pdb, src_conda_env_yaml
    Produces
    nopo4_pdb
  4. 04Remove BME ligand from structure
    Consumes
    remove_ligand_bme_config, nopo4_pdb, src_conda_env_yaml
    Produces
    nobme_pdb
  5. 05Prepare PDB for AMBER (pdb4amber)
    Consumes
    nobme_pdb
    Produces
    pdb4amber_pdb
  6. 06Extract JZ4 ligand structure
    Consumes
    extract_heteroatoms_config, pdb4amber_pdb, src_conda_env_yaml
    Produces
    ligand_pdb
  7. 07Add hydrogen atoms to ligand (Reduce)
    Consumes
    reduce_add_hydrogens_config, ligand_pdb, src_conda_env_yaml
    Produces
    ligand_h_pdb
  8. 08Energetically minimize ligand hydrogens (OpenBabel GAFF)
    Consumes
    babel_minimize_config, ligand_h_pdb, src_conda_env_yaml
    Produces
    ligand_min_mol2
  9. 09Generate AMBER ligand topology parameters (ACPype)
    Consumes
    acpype_params_ac_config, ligand_min_mol2, src_conda_env_yaml
    Produces
    acpype_inpcrd, acpype_frcmod, acpype_lib, acpype_prmtop
  10. 10Create protein-ligand complex system topology (leap)
    Consumes
    leap_gen_top_config, pdb4amber_pdb, acpype_lib, acpype_frcmod
    Produces
    top_pdb, top_top, top_crd
  11. 11Minimize hydrogens in vacuo (sander)
    Consumes
    sander_h_min_config, top_top, top_crd
    Produces
    h_min_traj, h_min_rst, h_min_log
  12. 12Extract hydrogen minimization energy (process_minout)
    Consumes
    process_energy_config, h_min_log
    Produces
    h_min_dat
  13. 13Minimize system in vacuo with ligand restraints (sander)
    Consumes
    sander_n_min_config, top_top, h_min_rst
    Produces
    n_min_traj, n_min_rst, n_min_log
  14. 14Extract system minimization energy (process_minout)
    Consumes
    process_energy_config, n_min_log
    Produces
    n_min_dat
  15. 15Convert minimized structure to PDB (ambpdb)
    Consumes
    top_top, n_min_rst
    Produces
    ambpdb_pdb
  16. 16Create solvent box and solvate system (leap)
    Consumes
    leap_solvate_config, ambpdb_pdb, acpype_lib, acpype_frcmod
    Produces
    solv_pdb, solv_top, solv_crd
  17. 17Neutralize and add ions (leap)
    Consumes
    leap_add_ions_config, solv_pdb, acpype_lib, acpype_frcmod
    Produces
    ions_pdb, ions_top, ions_crd
  18. 18Energy minimize the solvated system (sander)
    Consumes
    sander_min_config, ions_top, ions_crd
    Produces
    min_traj, min_rst, min_log
  19. 19Extract system minimization energy (process_minout)
    Consumes
    process_energy_config, min_log
    Produces
    min_dat
  20. 20Heat the system 0 to 300 K (sander)
    Consumes
    sander_heat_config, ions_top, min_rst
    Produces
    heat_traj, heat_rst, heat_log
  21. 21Extract heating temperature (process_mdout)
    Consumes
    process_temp_config, heat_log
    Produces
    heat_dat
  22. 22Equilibrate the system NVT (sander)
    Consumes
    sander_nvt_config, ions_top, heat_rst
    Produces
    nvt_traj, nvt_rst, nvt_log
  23. 23Extract NVT temperature (process_mdout)
    Consumes
    process_temp_config, nvt_log
    Produces
    nvt_dat
  24. 24Equilibrate the system NPT (sander)
    Consumes
    sander_npt_config, ions_top, nvt_rst
    Produces
    npt_traj, npt_rst, npt_log
  25. 25Extract NPT pressure and density (process_mdout)
    Consumes
    process_npt_config, npt_log
    Produces
    npt_dat
  26. 26Free MD simulation (sander)
    Consumes
    sander_free_config, ions_top, npt_rst
    Produces
    free_traj, free_rst, free_log
  27. 27RMSd vs first snapshot (cpptraj)
    Consumes
    cpptraj_rms_first_config, ions_top, free_traj, src_conda_env_yaml
    Produces
    rms_first_dat
  28. 28RMSd vs experimental structure (cpptraj)
    Consumes
    cpptraj_rms_exp_config, ions_top, free_traj, top_pdb, src_conda_env_yaml
    Produces
    rms_exp_dat
  29. 29Radius of gyration (cpptraj)
    Consumes
    cpptraj_rgyr_config, ions_top, free_traj, src_conda_env_yaml
    Produces
    rgyr_dat
  30. 30Image trajectory and strip solvent (cpptraj)
    Consumes
    cpptraj_image_config, ions_top, free_traj, src_conda_env_yaml
    Produces
    imaged_traj

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