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PMX Mutation Free Energy Calculations - Staphylococcal nuclease I10A

W-10 · Mutation Free Energy Calculations

v123 stages1 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. 01Extract snapshots from stateA (WT) equilibrium trajectory
    Consumes
    gmx_trjconv_str_ens_stateA_config, stateA_traj, stateA_tpr, src_conda_env_yaml
    Produces
    stateA_frames
  2. 02Extract snapshots from stateB (Mutant) equilibrium trajectory
    Consumes
    gmx_trjconv_str_ens_stateB_config, stateB_traj, stateB_tpr, src_conda_env_yaml
    Produces
    stateB_frames
  3. 03Model stateA mutated structure (Ile10 -> Ala, WT->Mut)
    Consumes
    pmxmutate_stateA_config, stateA_frames
    Produces
    mutA_pdb
  4. 04Model stateB mutated structure (Ala10 -> Ile, Mut->WT)
    Consumes
    pmxmutate_stateB_config, stateB_frames
    Produces
    mutB_pdb
  5. 05Build GROMACS topology for stateA (pdb2gmx)
    Consumes
    pdb2gmx_stateA_config, mutA_pdb, src_conda_env_yaml
    Produces
    pdb2gmxA_gro, pdb2gmxA_top_zip
  6. 06Build GROMACS topology for stateB (pdb2gmx)
    Consumes
    pdb2gmx_stateB_config, mutB_pdb, src_conda_env_yaml
    Produces
    pdb2gmxB_gro, pdb2gmxB_top_zip
  7. 07Generate hybrid topology for stateA (pmxgentop)
    Consumes
    pmxgentop_stateA_config, pdb2gmxA_top_zip
    Produces
    pmxA_top_zip, pmxA_top_log
  8. 08Generate hybrid topology for stateB (pmxgentop)
    Consumes
    pmxgentop_stateB_config, pdb2gmxB_top_zip
    Produces
    pmxB_top_zip, pmxB_top_log
  9. 09Create FREEZE index for stateB dummy atoms (make_ndx)
    Consumes
    make_ndx_stateB_config, pdb2gmxB_gro, src_conda_env_yaml
    Produces
    indexB_ndx
  10. 10Compile stateB dummy-atom minimization run file (grompp)
    Consumes
    grompp_min_stateB_config, pdb2gmxB_gro, pmxB_top_zip, indexB_ndx, src_conda_env_yaml
    Produces
    min_stateB_tpr
  11. 11Energy minimization of stateB dummy atoms (mdrun)
    Consumes
    min_stateB_tpr, src_conda_env_yaml
    Produces
    min_stateB_gro, min_stateB_edr
  12. 12Extract potential energy from stateB minimization (gmx_energy)
    Consumes
    gmx_energy_min_stateB_config, min_stateB_edr, src_conda_env_yaml
    Produces
    min_stateB_ene_xvg
  13. 13Compile stateA equilibration run file (grompp)
    Consumes
    grompp_eq_stateA_config, pdb2gmxA_gro, pmxA_top_zip, src_conda_env_yaml
    Produces
    eq_stateA_tpr
  14. 14Compile stateB equilibration run file (grompp)
    Consumes
    grompp_eq_stateB_config, min_stateB_gro, pmxB_top_zip, src_conda_env_yaml
    Produces
    eq_stateB_tpr
  15. 15NPT equilibration for stateA (mdrun)
    Consumes
    eq_stateA_tpr, src_conda_env_yaml
    Produces
    eq_stateA_gro, eq_stateA_edr
  16. 16NPT equilibration for stateB (mdrun)
    Consumes
    eq_stateB_tpr, src_conda_env_yaml
    Produces
    eq_stateB_gro, eq_stateB_edr
  17. 17Extract pressure and density from stateA equilibration (gmx_energy)
    Consumes
    gmx_energy_eq_stateA_config, eq_stateA_edr, src_conda_env_yaml
    Produces
    eq_stateA_pd_xvg
  18. 18Extract pressure and density from stateB equilibration (gmx_energy)
    Consumes
    gmx_energy_eq_stateB_config, eq_stateB_edr, src_conda_env_yaml
    Produces
    eq_stateB_pd_xvg
  19. 19Compile stateA thermodynamic integration run file (grompp)
    Consumes
    grompp_ti_stateA_config, eq_stateA_gro, pmxA_top_zip, src_conda_env_yaml
    Produces
    ti_stateA_tpr
  20. 20Compile stateB thermodynamic integration run file (grompp)
    Consumes
    grompp_ti_stateB_config, eq_stateB_gro, pmxB_top_zip, src_conda_env_yaml
    Produces
    ti_stateB_tpr
  21. 21Thermodynamic integration simulation for stateA - WT->Mut (mdrun)
    Consumes
    ti_stateA_tpr, src_conda_env_yaml
    Produces
    ti_stateA_gro, ti_stateA_dhdl
  22. 22Thermodynamic integration simulation for stateB - Mut->WT (mdrun)
    Consumes
    ti_stateB_tpr, src_conda_env_yaml
    Produces
    ti_stateB_gro, ti_stateB_dhdl
  23. 23Compute free energy (CGI / BAR / Jarzynski) from dhdl work values (pmxanalyse)
    Consumes
    pmxanalyse_config, dhdlA_zip, dhdlB_zip
    Produces
    pmx_result, pmx_work_plot

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