Workflow: Protein Ligand Complex MD Setup tutorial using BioExcel Building Blocks (biobb)
Fetched 2024-05-20 17:32:41 GMT
Verified with cwltool version 3.1.20221201130942
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).
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| step1_pdb_name | String | ||
| step1_pdb_config | String | ||
| step23_dry_config | String | ||
| step20_rmsexp_name | String | ||
| step21_rgyr_config | String | ||
| step17_gppmd_config | String | ||
| step22_image_config | String | ||
| step6_gppion_config | String | ||
| step7_genion_config | String | ||
| step8_gppmin_config | String | ||
| step11_gppnvt_config | String | ||
| step14_gppnpt_config | String | ||
| step19_rmsfirst_name | String | ||
| step20_rmsexp_config | String | ||
| step4_editconf_config | String | ||
| step10_energy_min_name | String | ||
| step13_energy_nvt_name | String | ||
| step16_energy_npt_name | String | ||
| step19_rmsfirst_config | String | ||
| step10_energy_min_config | String | ||
| step13_energy_nvt_config | String | ||
| step16_energy_npt_config | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| step1_pdb |
biobb/biobb_adapters/cwl/biobb_io/mmb_api/pdb.cwl
(CommandLineTool)
|
||
| step23_dry |
biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_trjconv_str.cwl
(CommandLineTool)
|
||
| step21_rgyr |
biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_rgyr.cwl
(CommandLineTool)
|
||
| step22_image |
biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_image.cwl
(CommandLineTool)
|
||
| step7_genion |
biobb/biobb_adapters/cwl/biobb_md/gromacs/genion.cwl
(CommandLineTool)
|
||
| step20_rmsexp |
biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_rms.cwl
(CommandLineTool)
|
||
| step3_pdb2gmx |
biobb/biobb_adapters/cwl/biobb_md/gromacs/pdb2gmx.cwl
(CommandLineTool)
|
||
| step5_solvate |
biobb/biobb_adapters/cwl/biobb_md/gromacs/solvate.cwl
(CommandLineTool)
|
||
| step4_editconf |
biobb/biobb_adapters/cwl/biobb_md/gromacs/editconf.cwl
(CommandLineTool)
|
||
| step18_mdrun_md |
biobb/biobb_adapters/cwl/biobb_md/gromacs/mdrun.cwl
(CommandLineTool)
|
||
| step19_rmsfirst |
biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_rms.cwl
(CommandLineTool)
|
||
| step9_mdrun_min |
biobb/biobb_adapters/cwl/biobb_md/gromacs/mdrun.cwl
(CommandLineTool)
|
||
| step12_mdrun_nvt |
biobb/biobb_adapters/cwl/biobb_md/gromacs/mdrun.cwl
(CommandLineTool)
|
||
| step15_mdrun_npt |
biobb/biobb_adapters/cwl/biobb_md/gromacs/mdrun.cwl
(CommandLineTool)
|
||
| step17_grompp_md |
biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
(CommandLineTool)
|
||
| step8_grompp_min |
biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
(CommandLineTool)
|
||
| step10_energy_min |
biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_energy.cwl
(CommandLineTool)
|
||
| step11_grompp_nvt |
biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
(CommandLineTool)
|
||
| step13_energy_nvt |
biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_energy.cwl
(CommandLineTool)
|
||
| step14_grompp_npt |
biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
(CommandLineTool)
|
||
| step16_energy_npt |
biobb/biobb_adapters/cwl/biobb_analysis/gromacs/gmx_energy.cwl
(CommandLineTool)
|
||
| step2_fixsidechain |
biobb/biobb_adapters/cwl/biobb_model/model/fix_side_chain.cwl
(CommandLineTool)
|
||
| step6_grompp_genion |
biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| cpt | File | Checkpoint file |
GROMACS portable checkpoint file, allowing to restore (continue) the simulation from the last step of the setup process. |
| gro | File | Structures - Raw structure |
Raw structure from the free simulation step. |
| top | File | GROMACS topology file |
GROMACS topology file, containing the molecular topology in an ASCII readable format. |
| tpr | File | Topologies GROMACS portable binary run |
GROMACS portable binary run input file, containing the starting structure of the simulation, the molecular topology and all the simulation parameters. |
| trr | File | Trajectories - Raw trajectory |
Raw trajectory from the free simulation step |
| gro_dry | File | Resulting protein structure |
Resulting protein structure taken from the post-processed trajectory, to be used as a topology, usually for visualization purposes. |
| xvg_min | File | System Setup Observables - Potential Energy |
Potential energy of the system during the minimization step. |
| xvg_npt | File | System Setup Observables - Pressure and density | |
| xvg_nvt | File | System Setup Observables - Temperature |
Temperature of the system during the NVT equilibration step. |
| xvg_rgyr | File | Simulation Analysis |
Radius of Gyration (RGyr) of the molecule throughout the whole free simulation step |
| xvg_rmsexp | File | Simulation Analysis |
Root Mean Square deviation (RMSd) throughout the whole free simulation step against the experimental structure (minimized system). |
| xvg_rmsfirst | File | Simulation Analysis |
Root Mean Square deviation (RMSd) throughout the whole free simulation step against the first snapshot of the trajectory (equilibrated system). |
| trr_imaged_dry | File | Trajectories - Post-processed trajectory |
Post-processed trajectory, dehydrated, imaged (rotations and translations removed) and centered. |
https://w3id.org/cwl/view/git/c7a9b4180e1e65f2e6d8fdeb7f8dbbf5c2433dfa/protein_md.cwl
