Jupyter Notebook Protein MD Setup tutorial
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Version 6 (latest)

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Version 1 (earliest)

Workflow Type: Unrecognized workflow type

Stable

Summary

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).

Workflow engine is a jupyter notebook. It can be run in binder, following the link given, or locally. Auxiliar libraries used are: nb_conda_kernels, nglview, ipywidgets, plotly, and simpletraj. Environment can be setup using the included environment.yml file.

Parameters

Inputs

Parameters needed to configure the workflow:

pdbCode: PDB code of the protein-ligand complex structure (e.g. 1AKI)

Outputs

Output files generated (named according to the input parameters given above):

output_md_gro: final structure of the MD setup protocol
output_md_trr: final trajectory of the MD setup protocol
output_md_cpt: final checkpoint file
output_gppmd_tpr: final tpr file
output_genion_top_zip: final topology of the MD system

SEEK ID: https://workflowhub.eu/workflows/120?version=1

DOI: 10.48546/workflowhub.workflow.120.1

Version History

Version 6 (latest) Created 4th Mar 2024 at 14:12 by Genís Bayarri

Update to BioBB 4.1.*

Frozen Version-6 bab3b25

Version 5 Created 26th Jul 2023 at 10:17 by Genís Bayarri

Fixed importlib_metadata bug

Frozen Version-5 f86759d

Version 4 Created 13th Apr 2023 at 16:35 by Genís Bayarri

Update to BioBB 4.0.*

Frozen Version-4 efc1897

Version 3 Created 15th Sep 2022 at 10:24 by Genís Bayarri

Update to BioBB 3.8.*. taken from Git commit 77a78a

Frozen Version-3 471a68f

Version 2 Created 1st Jul 2021 at 15:51 by Douglas Lowe

No revision comments

Frozen Version-2 d4040dc

Version 1 (earliest) Created 7th May 2021 at 14:51 by Douglas Lowe

Uses GROMACS 2020.4 and BioExcel Building Blocks version 3.5. Taken from Git commit a81b483

Frozen master 46c5b2e

Creators and Submitter

Creators

Submitter

Douglas Lowe

Discussion Channels

BioExcel Workflows

Tutorial

Documentation

Launch on MyBinder

Launch on Colab

Citation

Lowe, D., & Bayarri, G. (2021). Protein MD Setup tutorial using BioExcel Building Blocks (biobb) (jupyter notebook). WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.120.1

License

Apache License 2.0

Activity

Views: 6653 Downloads: 1427

Created: 7th May 2021 at 14:51

Last updated: 13th Apr 2023 at 16:40

Jupyter Notebook Protein MD Setup tutorial Version 1 (earliest) Version 6 (latest) Version 5 Version 4 Version 3 Version 2 Version 1 (earliest)