Protein MD Setup tutorial using BioExcel Building Blocks (biobb)
Version 1

Workflow Type: Galaxy
Work-in-progress

Galaxy workflow 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.

Designed for running on the https://dev.usegalaxy.es Galaxy instance.

Inputs

ID Name Description Type
input_solvent_gro_path input_solvent_gro_path runtime parameter for tool Solvate n/a
input_cpt_path input_cpt_path runtime parameter for tool Grompp n/a
input_mdp_path input_mdp_path runtime parameter for tool Grompp n/a
input_ndx_path input_ndx_path runtime parameter for tool Grompp n/a
input_ndx_path input_ndx_path runtime parameter for tool Genion n/a
input_cpt_path input_cpt_path runtime parameter for tool Grompp n/a
input_gro_path input_gro_path runtime parameter for tool Grompp n/a
input_mdp_path input_mdp_path runtime parameter for tool Grompp n/a
input_ndx_path input_ndx_path runtime parameter for tool Grompp n/a
input_top_zip_path input_top_zip_path runtime parameter for tool Grompp n/a
input_cpt_path input_cpt_path runtime parameter for tool Mdrun n/a
input_cpt_path input_cpt_path runtime parameter for tool Grompp n/a
input_gro_path input_gro_path runtime parameter for tool Grompp n/a
input_mdp_path input_mdp_path runtime parameter for tool Grompp n/a
input_ndx_path input_ndx_path runtime parameter for tool Grompp n/a
input_top_zip_path input_top_zip_path runtime parameter for tool Grompp n/a
input_cpt_path input_cpt_path runtime parameter for tool Mdrun n/a
input_cpt_path input_cpt_path runtime parameter for tool Grompp n/a
input_gro_path input_gro_path runtime parameter for tool Grompp n/a
input_mdp_path input_mdp_path runtime parameter for tool Grompp n/a
input_ndx_path input_ndx_path runtime parameter for tool Grompp n/a
input_top_zip_path input_top_zip_path runtime parameter for tool Grompp n/a
input_cpt_path input_cpt_path runtime parameter for tool Mdrun n/a
input_cpt_path input_cpt_path runtime parameter for tool Grompp n/a
input_gro_path input_gro_path runtime parameter for tool Grompp n/a
input_mdp_path input_mdp_path runtime parameter for tool Grompp n/a
input_ndx_path input_ndx_path runtime parameter for tool Grompp n/a
input_top_zip_path input_top_zip_path runtime parameter for tool Grompp n/a
input_cpt_path input_cpt_path runtime parameter for tool Mdrun n/a
input_index_path input_index_path runtime parameter for tool GmxRms n/a
input_index_path input_index_path runtime parameter for tool GmxImage n/a
input_index_path input_index_path runtime parameter for tool GmxTrjconvStr n/a
input_index_path input_index_path runtime parameter for tool GmxRms n/a
input_index_path input_index_path runtime parameter for tool GmxRgyr n/a

Steps

ID Name Description
0 step1_pdb Download a protein structure from the PDB database biobb_io_pdb_ext
1 step2_fixsidechain Fix the side chains, adding any side chain atoms missing in the original structure biobb_model_fix_side_chain_ext
2 step3_pdb2gmx Create Protein System Topology biobb_md_pdb2gmx_ext
3 step4_editconf Create Solvent Box biobb_md_editconf_ext
4 step5_solvate Fill the box with water molecules biobb_md_solvate_ext
5 step6_grompp_genion Add Ions - part 1 biobb_md_grompp_ext
6 step7_genion Add Ions - part 2 biobb_md_genion_ext
7 step8_grompp_min Energetically minimize the system - part 1 biobb_md_grompp_ext
8 step9_mdrun_min Energetically minimize the system - part 2 biobb_md_mdrun_ext
9 step11_grompp_nvt Equilibriate the system (NVT) - part 1 biobb_md_grompp_ext
10 step10_energy_min Energetically minimize the system - part 3 biobb_analysis_gmx_energy_ext
11 step12_mdrun_nvt Equilibrate the system (NVT) - part 2 biobb_md_mdrun_ext
12 step14_grompp_npt Equilibrate the system (NPT) - part 1 biobb_md_grompp_ext
13 step13_energy_nvt Equilibrate the system (NVT) - part 3 biobb_analysis_gmx_energy_ext
14 step15_mdrun_npt Equilibrate the system (NPT) - part 2 biobb_md_mdrun_ext
15 step17_grompp_md Free molecular dynamics simulation - part 1 biobb_md_grompp_ext
16 step16_energy_npt Equilibrate the system (NPT) - part 3 biobb_analysis_gmx_energy_ext
17 step18_mdrun_md Free molecular dynamics simulation - part 2 biobb_md_mdrun_ext
18 step19_rmsfirst Post-processing resulting 3D trajectory - part 1 biobb_analysis_gmx_rms_ext
19 step22_image Post-processing resulting 3D trajectory - part 4 biobb_analysis_gmx_image_ext
20 step23_dry Post-processing resulting 3D trajectory - part 5 biobb_analysis_gmx_trjconv_str_ext
21 step20_rmsexp Post-processing resulting 3D trajectory - part 2 biobb_analysis_gmx_rms_ext
22 step21_rgyr Post-processing resulting 3D trajectory - part 3 biobb_analysis_gmx_rgyr_ext

Outputs

ID Name Description Type
output_pdb_path output_pdb_path n/a pdb
output_pdb_path output_pdb_path n/a pdb
output_gro_path output_gro_path n/a gro
output_top_zip_path output_top_zip_path n/a zip
output_gro_path output_gro_path n/a gro
output_gro_path output_gro_path n/a gro
output_top_zip_path output_top_zip_path n/a zip
output_tpr_path output_tpr_path n/a tpr
output_gro_path output_gro_path n/a gro
output_top_zip_path output_top_zip_path n/a zip
output_tpr_path output_tpr_path n/a tpr
output_trr_path output_trr_path n/a trr
output_gro_path output_gro_path n/a gro
output_edr_path output_edr_path n/a edr
output_log_path output_log_path n/a log
output_xtc_path output_xtc_path n/a xtc
output_cpt_path output_cpt_path n/a cpt
output_dhdl_path output_dhdl_path n/a xvg
output_tpr_path output_tpr_path n/a tpr
output_xvg_path output_xvg_path n/a xvg
output_trr_path output_trr_path n/a trr
output_gro_path output_gro_path n/a gro
output_edr_path output_edr_path n/a edr
output_log_path output_log_path n/a log
output_xtc_path output_xtc_path n/a xtc
output_cpt_path output_cpt_path n/a cpt
output_dhdl_path output_dhdl_path n/a xvg
output_tpr_path output_tpr_path n/a tpr
output_xvg_path output_xvg_path n/a xvg
output_trr_path output_trr_path n/a trr
output_gro_path output_gro_path n/a gro
output_edr_path output_edr_path n/a edr
output_log_path output_log_path n/a log
output_xtc_path output_xtc_path n/a xtc
output_cpt_path output_cpt_path n/a cpt
output_dhdl_path output_dhdl_path n/a xvg
output_tpr_path output_tpr_path n/a tpr
output_xvg_path output_xvg_path n/a xvg
output_trr_path output_trr_path n/a trr
output_gro_path output_gro_path n/a gro
output_edr_path output_edr_path n/a edr
output_log_path output_log_path n/a log
output_xtc_path output_xtc_path n/a xtc
output_cpt_path output_cpt_path n/a cpt
output_dhdl_path output_dhdl_path n/a xvg
output_xvg_path output_xvg_path n/a xvg
output_traj_path output_traj_path n/a text
output_str_path output_str_path n/a text
output_xvg_path output_xvg_path n/a xvg
output_xvg_path output_xvg_path n/a xvg
help Creators and Submitter
Creators
Not specified
Submitter
Citation
Lowe, D. (2021). Protein MD Setup tutorial using BioExcel Building Blocks (biobb). WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.194.1
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Views: 63   Downloads: 2

Created: 26th Sep 2021 at 20:50

Last updated: 26th Sep 2021 at 21:07

Last used: 16th Oct 2021 at 22:43

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Version 1 Created 26th Sep 2021 at 20:50 by Douglas Lowe

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