All published workflows

Published workflow · Temple Compute

BioExcel CMIP - Classical Molecular Interaction Potentials

W-22 · Classical Molecular Interaction Potentials

v129 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 Lysozyme structure from PDB
    Consumes
    fetch_pdb_lysozyme_config, src_conda_env_yaml
    Produces
    downloaded_pdb_lysozyme
  2. 02Prepare Lysozyme PDB for CMIP (add charges and elements)
    Consumes
    downloaded_pdb_lysozyme
    Produces
    cmip_pdb_lysozyme
  3. 03Compute structural water molecules and ion positions (titration)
    Consumes
    cmip_titration_lysozyme_config, cmip_pdb_lysozyme
    Produces
    wat_ions_pdb, wat_ions_log
  4. 04Add structural water molecules and ions to Lysozyme PDB
    Consumes
    cmip_pdb_lysozyme, wat_ions_pdb, src_conda_env_yaml
    Produces
    tit_pdb
  5. 05Compute positive Molecular Interaction Potential (MIP+)
    Consumes
    cmip_run_mip_pos_config, cmip_pdb_lysozyme
    Produces
    mip_pos_log, mip_pos_cube
  6. 06Compute negative Molecular Interaction Potential (MIP-)
    Consumes
    cmip_run_mip_neg_config, cmip_pdb_lysozyme
    Produces
    mip_neg_log, mip_neg_cube
  7. 07Compute neutral Molecular Interaction Potential (MIPn)
    Consumes
    cmip_run_mip_neutral_config, cmip_pdb_lysozyme
    Produces
    mip_neutral_log, mip_neutral_cube
  8. 08Download 4HJO EGFR-Erlotinib complex structure from PDB
    Consumes
    fetch_pdb_complex_config, src_conda_env_yaml
    Produces
    complex_pdb
  9. 09Remove water molecules from EGFR complex structure
    Consumes
    complex_pdb, src_conda_env_yaml
    Produces
    nohoh_pdb
  10. 10Extract Erlotinib (AQ4) ligand from complex
    Consumes
    extract_heteroatoms_config, nohoh_pdb, src_conda_env_yaml
    Produces
    ligand_pdb
  11. 11Add hydrogen atoms to Erlotinib ligand
    Consumes
    ligand_pdb, src_conda_env_yaml
    Produces
    ligand_h_pdb
  12. 12Generate AMBER topology parameters for Erlotinib ligand (ACPype)
    Consumes
    acpype_params_ac_config, ligand_h_pdb, src_conda_env_yaml
    Produces
    acpype_inpcrd, acpype_frcmod, acpype_lib, acpype_prmtop
  13. 13Generate AMBER system topology for EGFR-Erlotinib complex (tleap)
    Consumes
    leap_gen_top_config, nohoh_pdb, acpype_lib, acpype_frcmod
    Produces
    system_pdb, system_top, system_crd
  14. 14Energy minimization of EGFR-Erlotinib complex (AMBER sander)
    Consumes
    sander_mdrun_config, system_top, system_crd
    Produces
    amber_traj, amber_rst, amber_log
  15. 15Convert minimized AMBER restart to PDB
    Consumes
    system_top, amber_rst
    Produces
    min_pdb
  16. 16Prepare EGFR-Erlotinib complex for CMIP using AMBER topology charges
    Consumes
    min_pdb, system_top
    Produces
    cmip_complex_pdb
  17. 17Extract isolated EGFR protein structure (remove Erlotinib)
    Consumes
    remove_ligand_config, cmip_complex_pdb, src_conda_env_yaml
    Produces
    no_lig_pdb
  18. 18Mark EGFR protein residues as dielectric for CMIP interaction
    Consumes
    cmip_ignore_residues_protein_config, cmip_complex_pdb
    Produces
    prot_ignored_pdb
  19. 19Compute EGFR-Erlotinib protein-ligand interaction energies
    Consumes
    cmip_run_egfr_interaction_config, prot_ignored_pdb, no_lig_pdb
    Produces
    egfr_energies_log, egfr_byat_out
  20. 20Prepare RBD-hACE2 MD structure for CMIP using MD topology charges
    Consumes
    md_pdb, md_top
    Produces
    md_cmip_pdb
  21. 21Extract hACE2 chain A from RBD-hACE2 complex
    Consumes
    extract_chain_hace2_config, md_cmip_pdb, src_conda_env_yaml
    Produces
    hace2_cmip_pdb
  22. 22Extract RBD chain B from RBD-hACE2 complex
    Consumes
    extract_chain_rbd_config, md_cmip_pdb, src_conda_env_yaml
    Produces
    rbd_cmip_pdb
  23. 23Compute 3D grid box enclosing the RBD monomer
    Consumes
    cmip_run_rbd_box_config, rbd_cmip_pdb
    Produces
    rbd_box_log, rbd_box_json
  24. 24Compute 3D grid box enclosing the hACE2 monomer
    Consumes
    cmip_run_hace2_box_config, hace2_cmip_pdb
    Produces
    hace2_box_log, hace2_box_json
  25. 25Compute 3D grid box enclosing the RBD-hACE2 complex
    Consumes
    cmip_run_complex_box_config, md_cmip_pdb
    Produces
    complex_box_log, complex_box_json
  26. 26Mark RBD residues (chain B) as dielectric for CMIP
    Consumes
    cmip_ignore_residues_rbd_config, md_cmip_pdb
    Produces
    rbd_ignored_pdb
  27. 27Compute RBD protein-protein interaction energies with hACE2
    Consumes
    cmip_run_rbd_interaction_config, rbd_ignored_pdb, rbd_cmip_pdb, rbd_box_json, complex_box_json
    Produces
    rbd_energies_log, rbd_byat_out, rbd_energies_box_json, complex_energies_box_json
  28. 28Mark hACE2 residues (chain A) as dielectric for CMIP
    Consumes
    cmip_ignore_residues_hace2_config, md_cmip_pdb
    Produces
    hace2_ignored_pdb
  29. 29Compute hACE2 protein-protein interaction energies with RBD
    Consumes
    cmip_run_hace2_interaction_config, hace2_ignored_pdb, hace2_cmip_pdb, hace2_box_json, complex_box_json
    Produces
    hace2_energies_log, hace2_byat_out, hace2_energies_box_json, complex_2_energies_box_json

Run this workflow

This release is frozen and self-contained: the pipeline definition, its input files, and its plugin environment. Open it in Temple Compute OS to clone it into your own account and run it on HPC or any cloud. Temple Compute OS is in private beta, so you will need an invitation first.

Run this in Temple Compute OSRequest an invitation