Workflow Type: Galaxy
Stable

Protein MD Setup tutorial using BioExcel Building Blocks (biobb)


This workflow must be run in biobb.usegalaxy.es. Please, click here to access.


Based on the official GROMACS tutorial.


This tutorial aims to 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).


Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728).

Licensed under the Apache License 2.0, see the file LICENSE for details.

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_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_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_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_cpt_path input_cpt_path runtime parameter for tool Mdrun 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_cpt_path input_cpt_path runtime parameter for tool Mdrun 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_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 GmxRms n/a
input_index_path input_index_path runtime parameter for tool GmxRgyr 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

Steps

ID Name Description
0 Pdb biobb_io_pdb_ext
1 FixSideChain biobb_model_fix_side_chain_ext
2 Pdb2gmx biobb_md_pdb2gmx_ext
3 Editconf biobb_md_editconf_ext
4 Solvate biobb_md_solvate_ext
5 Grompp Ion biobb_md_grompp_ext
6 Genion biobb_md_genion_ext
7 Grompp Min biobb_md_grompp_ext
8 Mdrun Min biobb_md_mdrun_ext
9 Grompp NVT biobb_md_grompp_ext
10 GmxEnergy Min biobb_analysis_gmx_energy_ext
11 Mdrun NVT biobb_md_mdrun_ext
12 Grompp NPT biobb_md_grompp_ext
13 GmxEnergy NVT biobb_analysis_gmx_energy_ext
14 Mdrun NPT biobb_md_mdrun_ext
15 Free Grompp biobb_md_grompp_ext
16 GmxEnergy NPT biobb_analysis_gmx_energy_ext
17 Free Mdrun biobb_md_mdrun_ext
18 GmxRms biobb_analysis_gmx_rms_ext
19 GmxRms Exp biobb_analysis_gmx_rms_ext
20 GmxRgyr biobb_analysis_gmx_rgyr_ext
21 GmxImage biobb_analysis_gmx_image_ext
22 GmxTrjconvStr biobb_analysis_gmx_trjconv_str_ext

Outputs

ID Name Description Type
output_pdb_path output_pdb_path n/a
output_pdb_path output_pdb_path n/a
output_gro_path output_gro_path n/a
output_top_zip_path output_top_zip_path n/a
output_gro_path output_gro_path n/a
output_gro_path output_gro_path n/a
output_top_zip_path output_top_zip_path n/a
output_tpr_path output_tpr_path n/a
output_gro_path output_gro_path n/a
output_top_zip_path output_top_zip_path n/a
output_tpr_path output_tpr_path n/a
output_trr_path output_trr_path n/a
output_gro_path output_gro_path n/a
output_edr_path output_edr_path n/a
output_log_path output_log_path n/a
output_xtc_path output_xtc_path n/a
output_cpt_path output_cpt_path n/a
output_dhdl_path output_dhdl_path n/a
output_tpr_path output_tpr_path n/a
output_xvg_path output_xvg_path n/a
output_trr_path output_trr_path n/a
output_gro_path output_gro_path n/a
output_edr_path output_edr_path n/a
output_log_path output_log_path n/a
output_xtc_path output_xtc_path n/a
output_cpt_path output_cpt_path n/a
output_dhdl_path output_dhdl_path n/a
output_tpr_path output_tpr_path n/a
output_xvg_path output_xvg_path n/a
output_trr_path output_trr_path n/a
output_gro_path output_gro_path n/a
output_edr_path output_edr_path n/a
output_log_path output_log_path n/a
output_xtc_path output_xtc_path n/a
output_cpt_path output_cpt_path n/a
output_dhdl_path output_dhdl_path n/a
output_tpr_path output_tpr_path n/a
output_xvg_path output_xvg_path n/a
output_trr_path output_trr_path n/a
output_gro_path output_gro_path n/a
output_edr_path output_edr_path n/a
output_log_path output_log_path n/a
output_xtc_path output_xtc_path n/a
output_cpt_path output_cpt_path n/a
output_dhdl_path output_dhdl_path n/a
output_xvg_path output_xvg_path n/a
output_xvg_path output_xvg_path n/a
output_xvg_path output_xvg_path n/a
output_traj_path output_traj_path n/a
output_str_path output_str_path n/a

Version History

Version 2 (latest) Created 22nd Nov 2022 at 09:46 by Genís Bayarri

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Frozen Version-2 7703166

Version 1 (earliest) Created 14th Mar 2022 at 10:15 by Genís Bayarri

Initial commit


Frozen Version-1 e55fd41
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Citation
Hospital, A., & Bayarri, G. (2022). Galaxy Protein MD Setup tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.277.2
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Views: 651

Created: 14th Mar 2022 at 10:15

Last updated: 23rd Mar 2022 at 14:17

Last used: 8th Dec 2022 at 20:01

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