esguerra / mapk11

BioBB workflow for MAPK11

MD Setup for MAPK11 using BioBB

Based on the workflow from BioBB which in turn is based NOT on an official GROMACS tutorial, but justin lemkul's

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This is not a tutorial but a public workflow for testing its utility on MAPK11.

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Settings

Biobb modules used

• biobb_model: Tools to model macromolecular structures.
• biobb_md: Tools to setup and run Molecular Dynamics simulations.
• biobb_analysis: Tools to analyse Molecular Dynamics trajectories.

Auxiliar libraries used

• nb_conda_kernels: Enables a Jupyter Notebook or JupyterLab application in one conda environment to access kernels for Python, R, and other languages found in other environments.
• nglview: Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.
• ipywidgets: Interactive HTML widgets for Jupyter notebooks and the IPython kernel.
• plotly: Python interactive graphing library integrated in Jupyter notebooks.
• simpletraj: Lightweight coordinate-only trajectory reader based on code from GROMACS, MDAnalysis and VMD.

Conda Installation and Launch

git clone https://github.com/esguerra/mapk11
cd mapk11
conda env create -f conda_env/environment.yml python=3.7
conda activate mapk11
jupyter-nbextension enable --py --user widgetsnbextension
jupyter-nbextension enable --py --user nglview
jupyter-notebook mapk11/notebooks/mapk11_wf.ipynb

Version

2021.1 Release

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).

• (c) 2015-2021 Barcelona Supercomputing Center
• (c) 2015-2021 Institute for Research in Biomedicine

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