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protein_md.cwl
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protein_md.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: Protein Ligand Complex MD Setup tutorial using BioExcel Building Blocks (biobb)
doc: |
Common Workflow Language example that illustrate the process of setting up a
simulation system containing a protein, step by step, using the BioExcel
Building Blocks library (biobb). The particular example used is the Lysozyme
protein (PDB code 1AKI).
inputs:
step1_pdb_name: string
step1_pdb_config: string
step4_editconf_config: string
step6_gppion_config: string
step7_genion_config: string
step8_gppmin_config: string
step10_energy_min_config: string
step10_energy_min_name: string
step11_gppnvt_config: string
step13_energy_nvt_config: string
step13_energy_nvt_name: string
step14_gppnpt_config: string
step16_energy_npt_config: string
step16_energy_npt_name: string
step17_gppmd_config: string
step19_rmsfirst_config: string
step19_rmsfirst_name: string
step20_rmsexp_config: string
step20_rmsexp_name: string
step21_rgyr_config: string
step22_image_config: string
step23_dry_config: string
outputs:
trr:
label: Trajectories - Raw trajectory
doc: |
Raw trajectory from the free simulation step
type: File
outputSource: step18_mdrun_md/output_trr_file
trr_imaged_dry:
label: Trajectories - Post-processed trajectory
doc: |
Post-processed trajectory, dehydrated, imaged (rotations and translations
removed) and centered.
type: File
outputSource: step22_image/output_traj_file
gro_dry:
label: Resulting protein structure
doc: |
Resulting protein structure taken from the post-processed trajectory, to
be used as a topology, usually for visualization purposes.
type: File
outputSource: step23_dry/output_str_file
gro:
label: Structures - Raw structure
doc: |
Raw structure from the free simulation step.
type: File
outputSource: step18_mdrun_md/output_gro_file
cpt:
label: Checkpoint file
doc: |
GROMACS portable checkpoint file, allowing to restore (continue) the
simulation from the last step of the setup process.
type: File
outputSource: step18_mdrun_md/output_cpt_file
tpr:
label: Topologies GROMACS portable binary run
doc: |
GROMACS portable binary run input file, containing the starting structure
of the simulation, the molecular topology and all the simulation parameters.
type: File
outputSource: step17_grompp_md/output_tpr_file
top:
label: GROMACS topology file
doc: |
GROMACS topology file, containing the molecular topology in an ASCII
readable format.
type: File
outputSource: step7_genion/output_top_zip_file
xvg_min:
label: System Setup Observables - Potential Energy
doc: |
Potential energy of the system during the minimization step.
type: File
outputSource: step10_energy_min/output_xvg_file
xvg_nvt:
label: System Setup Observables - Temperature
doc: |
Temperature of the system during the NVT equilibration step.
type: File
outputSource: step13_energy_nvt/output_xvg_file
xvg_npt:
label: System Setup Observables - Pressure and density
type: File
outputSource: step16_energy_npt/output_xvg_file
xvg_rmsfirst:
label: Simulation Analysis
doc: |
Root Mean Square deviation (RMSd) throughout the whole free simulation
step against the first snapshot of the trajectory (equilibrated system).
type: File
outputSource: step19_rmsfirst/output_xvg_file
xvg_rmsexp:
label: Simulation Analysis
doc: |
Root Mean Square deviation (RMSd) throughout the whole free simulation
step against the experimental structure (minimized system).
type: File
outputSource: step20_rmsexp/output_xvg_file
xvg_rgyr:
label: Simulation Analysis
doc: |
Radius of Gyration (RGyr) of the molecule throughout the whole free simulation step
type: File
outputSource: step21_rgyr/output_xvg_file
steps:
step1_pdb:
label: Fetch PDB Structure
doc: |
Download a protein structure from the PDB database
run: biobb/biobb_adapters/cwl/biobb_io/mmb_api/pdb.cwl
in:
output_pdb_path: step1_pdb_name
config: step1_pdb_config
out: [output_pdb_file]
step2_fixsidechain:
label: Fix Protein structure
doc: |
Fix the side chains, adding any side chain atoms missing in the
original structure.
run: biobb/biobb_adapters/cwl/biobb_model/model/fix_side_chain.cwl
in:
input_pdb_path: step1_pdb/output_pdb_file
out: [output_pdb_file]
step3_pdb2gmx:
label: Create Protein System Topology
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/pdb2gmx.cwl
in:
input_pdb_path: step2_fixsidechain/output_pdb_file
out: [output_gro_file, output_top_zip_file]
step4_editconf:
label: Create Solvent Box
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/editconf.cwl
in:
input_gro_path: step3_pdb2gmx/output_gro_file
out: [output_gro_file]
step5_solvate:
label: Fill the Box with Water Molecules
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/solvate.cwl
in:
input_solute_gro_path: step4_editconf/output_gro_file
input_top_zip_path: step3_pdb2gmx/output_top_zip_file
out: [output_gro_file, output_top_zip_file]
step6_grompp_genion:
label: Add Ions - part 1
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
in:
config: step6_gppion_config
input_gro_path: step5_solvate/output_gro_file
input_top_zip_path: step5_solvate/output_top_zip_file
out: [output_tpr_file]
step7_genion:
label: Add Ions - part 2
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/genion.cwl
in:
config: step7_genion_config
input_tpr_path: step6_grompp_genion/output_tpr_file
input_top_zip_path: step5_solvate/output_top_zip_file
out: [output_gro_file, output_top_zip_file]
step8_grompp_min:
label: Energetically Minimize the System - part 1
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
in:
config: step8_gppmin_config
input_gro_path: step7_genion/output_gro_file
input_top_zip_path: step7_genion/output_top_zip_file
out: [output_tpr_file]
step9_mdrun_min:
label: Energetically Minimize the System - part 2
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/mdrun.cwl
in:
input_tpr_path: step8_grompp_min/output_tpr_file
out: [output_trr_file, output_gro_file, output_edr_file, output_log_file]
step10_energy_min:
label: Energetically Minimize the System - part 3
run: biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_energy.cwl
in:
config: step10_energy_min_config
output_xvg_path: step10_energy_min_name
input_energy_path: step9_mdrun_min/output_edr_file
out: [output_xvg_file]
step11_grompp_nvt:
label: Equilibrate the System (NVT) - part 1
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
in:
config: step11_gppnvt_config
input_gro_path: step9_mdrun_min/output_gro_file
input_top_zip_path: step7_genion/output_top_zip_file
out: [output_tpr_file]
step12_mdrun_nvt:
label: Equilibrate the System (NVT) - part 2
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/mdrun.cwl
in:
input_tpr_path: step11_grompp_nvt/output_tpr_file
out: [output_trr_file, output_gro_file, output_edr_file, output_log_file, output_cpt_file]
step13_energy_nvt:
label: Equilibrate the System (NVT) - part 3
run: biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_energy.cwl
in:
config: step13_energy_nvt_config
output_xvg_path: step13_energy_nvt_name
input_energy_path: step12_mdrun_nvt/output_edr_file
out: [output_xvg_file]
step14_grompp_npt:
label: Equilibrate the System (NPT) - part 1
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
in:
config: step14_gppnpt_config
input_gro_path: step12_mdrun_nvt/output_gro_file
input_top_zip_path: step7_genion/output_top_zip_file
input_cpt_path: step12_mdrun_nvt/output_cpt_file
out: [output_tpr_file]
step15_mdrun_npt:
label: Equilibrate the System (NPT) - part 2
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/mdrun.cwl
in:
input_tpr_path: step14_grompp_npt/output_tpr_file
out: [output_trr_file, output_gro_file, output_edr_file, output_log_file, output_cpt_file]
step16_energy_npt:
label: Equilibrate the System (NPT) - part 3
run: biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_energy.cwl
in:
config: step16_energy_npt_config
output_xvg_path: step16_energy_npt_name
input_energy_path: step15_mdrun_npt/output_edr_file
out: [output_xvg_file]
step17_grompp_md:
label: Free Molecular Dynamics Simulation - part 1
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
in:
config: step17_gppmd_config
input_gro_path: step15_mdrun_npt/output_gro_file
input_top_zip_path: step7_genion/output_top_zip_file
input_cpt_path: step15_mdrun_npt/output_cpt_file
out: [output_tpr_file]
step18_mdrun_md:
label: Free Molecular Dynamics Simulation - part 2
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/mdrun.cwl
in:
input_tpr_path: step17_grompp_md/output_tpr_file
out: [output_trr_file, output_gro_file, output_edr_file, output_log_file, output_cpt_file]
step19_rmsfirst:
label: Post-processing Resulting 3D Trajectory - part 1
run: biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_rms.cwl
in:
config: step19_rmsfirst_config
output_xvg_path: step19_rmsfirst_name
input_structure_path: step17_grompp_md/output_tpr_file
input_traj_path: step18_mdrun_md/output_trr_file
out: [output_xvg_file]
step20_rmsexp:
label: Post-processing Resulting 3D Trajectory - part 2
run: biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_rms.cwl
in:
config: step20_rmsexp_config
output_xvg_path: step20_rmsexp_name
input_structure_path: step8_grompp_min/output_tpr_file
input_traj_path: step18_mdrun_md/output_trr_file
out: [output_xvg_file]
step21_rgyr:
label: Post-processing Resulting 3D Trajectory - part 3
run: biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_rgyr.cwl
in:
config: step21_rgyr_config
input_structure_path: step8_grompp_min/output_tpr_file
input_traj_path: step18_mdrun_md/output_trr_file
out: [output_xvg_file]
step22_image:
label: Post-processing Resulting 3D Trajectory - part 4
run: biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_image.cwl
in:
config: step22_image_config
input_top_path: step17_grompp_md/output_tpr_file
input_traj_path: step18_mdrun_md/output_trr_file
out: [output_traj_file]
step23_dry:
label: Post-processing Resulting 3D Trajectory - part 5
run: biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_trjconv_str.cwl
in:
config: step23_dry_config
input_structure_path: step18_mdrun_md/output_gro_file
input_top_path: step17_grompp_md/output_tpr_file
out: [output_str_file]