Protein MD Setup tutorial using BioExcel Building Blocks (biobb)
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Overview
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Workflow Type: Jupyter

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=2

DOI: 10.48546/workflowhub.workflow.120.2

Total size: 51.8 KB

Creators and Submitter

Creators

Submitter

Douglas Lowe

Discussion Channels

BioExcel Workflows

Tutorial

Documentation

Launch on MyBinder

Citation

Lowe, D., Bayarri, G., & Hospital, A. (2021). Protein MD Setup tutorial using BioExcel Building Blocks (biobb). WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.120.2