Protein MD Setup tutorial using BioExcel Building Blocks (biobb)

Workflow Type: Common Workflow Language
Stable

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). This workflow returns a resulting protein structure and simulated 3D trajectories.

Inputs

ID Name Description Type
step1_pdb_name n/a n/a n/a
step1_pdb_config n/a n/a n/a
step4_editconf_config n/a n/a n/a
step6_gppion_config n/a n/a n/a
step7_genion_config n/a n/a n/a
step8_gppmin_config n/a n/a n/a
step10_energy_min_config n/a n/a n/a
step10_energy_min_name n/a n/a n/a
step11_gppnvt_config n/a n/a n/a
step13_energy_nvt_config n/a n/a n/a
step13_energy_nvt_name n/a n/a n/a
step14_gppnpt_config n/a n/a n/a
step16_energy_npt_config n/a n/a n/a
step16_energy_npt_name n/a n/a n/a
step17_gppmd_config n/a n/a n/a
step19_rmsfirst_config n/a n/a n/a
step19_rmsfirst_name n/a n/a n/a
step20_rmsexp_config n/a n/a n/a
step20_rmsexp_name n/a n/a n/a
step21_rgyr_config n/a n/a n/a
step22_image_config n/a n/a n/a
step23_dry_config n/a n/a n/a

Steps

ID Name Description
step1_pdb Fetch PDB Structure Download a protein structure from the PDB database
step2_fixsidechain Fix Protein structure Fix the side chains, adding any side chain atoms missing in the original structure.
step3_pdb2gmx Create Protein System Topology
step4_editconf Create Solvent Box
step5_solvate Fill the Box with Water Molecules
step6_grompp_genion Add Ions - part 1
step7_genion Add Ions - part 2
step8_grompp_min Energetically Minimize the System - part 1
step9_mdrun_min Energetically Minimize the System - part 2
step10_energy_min Energetically Minimize the System - part 3
step11_grompp_nvt Equilibrate the System (NVT) - part 1
step12_mdrun_nvt Equilibrate the System (NVT) - part 2
step13_energy_nvt Equilibrate the System (NVT) - part 3
step14_grompp_npt Equilibrate the System (NPT) - part 1
step15_mdrun_npt Equilibrate the System (NPT) - part 2
step16_energy_npt Equilibrate the System (NPT) - part 3
step17_grompp_md Free Molecular Dynamics Simulation - part 1
step18_mdrun_md Free Molecular Dynamics Simulation - part 2
step19_rmsfirst Post-processing Resulting 3D Trajectory - part 1
step20_rmsexp Post-processing Resulting 3D Trajectory - part 2
step21_rgyr Post-processing Resulting 3D Trajectory - part 3
step22_image Post-processing Resulting 3D Trajectory - part 4
step23_dry Post-processing Resulting 3D Trajectory - part 5

Outputs

ID Name Description Type
trr Trajectories - Raw trajectory Raw trajectory from the free simulation step File
trr_imaged_dry Trajectories - Post-processed trajectory Post-processed trajectory, dehydrated, imaged (rotations and translations removed) and centered. File
gro_dry Resulting protein structure Resulting protein structure taken from the post-processed trajectory, to be used as a topology, usually for visualization purposes. File
gro Structures - Raw structure Raw structure from the free simulation step. File
cpt Checkpoint file GROMACS portable checkpoint file, allowing to restore (continue) the simulation from the last step of the setup process. File
tpr 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. File
top GROMACS topology file GROMACS topology file, containing the molecular topology in an ASCII readable format. File
xvg_min System Setup Observables - Potential Energy Potential energy of the system during the minimization step. File
xvg_nvt System Setup Observables - Temperature Temperature of the system during the NVT equilibration step. File
xvg_npt System Setup Observables - Pressure and density n/a File
xvg_rmsfirst Simulation Analysis Root Mean Square deviation (RMSd) throughout the whole free simulation step against the first snapshot of the trajectory (equilibrated system). File
xvg_rmsexp Simulation Analysis Root Mean Square deviation (RMSd) throughout the whole free simulation step against the experimental structure (minimized system). File
xvg_rgyr Simulation Analysis Radius of Gyration (RGyr) of the molecule throughout the whole free simulation step File
help Creators and Submitter
Creator
Submitter
Citation
Long, R., Lowe, D., & Bayarri, G. (2021). Protein MD Setup tutorial using BioExcel Building Blocks (biobb). WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.29.3
Activity

Views: 1212   Downloads: 52

Created: 16th Jun 2020 at 09:50

Last updated: 26th Sep 2021 at 20:44

Last used: 15th Oct 2021 at 16:57

Version History

Version 3 (latest) Created 10th May 2021 at 10:00 by Robin Long

Changing CWL label to test if this corrects the workflow title.

Version 2 Created 7th May 2021 at 16:27 by Douglas Lowe

Update to paths for BioBB tools. Taken from Git commit 46f24f0

Version 1 (earliest) Created 16th Jun 2020 at 09:50 by Robin Long

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