# Research Object Crate for Python Mutation Free Energy Calculations using BioExcel Building Blocks (biobb)

Original URL: https://workflowhub.eu/workflows/328/ro_crate?version=5

# Mutation Free Energy Calculations using BioExcel Building Blocks (biobb) *** **Based on the official [pmx tutorial](http://pmx.mpibpc.mpg.de/sardinia2018_tutorial1/index.html).** *** This tutorial aims to illustrate how to compute a **fast-growth mutation free energy** calculation, step by step, using the BioExcel **Building Blocks library (biobb)**. The particular example used is the **Staphylococcal nuclease** protein (PDB code 1STN), a small, minimal protein, appropriate for a short tutorial. The **non-equilibrium free energy calculation** protocol performs a **fast alchemical transition** in the direction **WT->Mut** and back **Mut->WT**. The two equilibrium trajectories needed for the tutorial, one for **Wild Type (WT)** and another for the **Mutated (Mut)** protein (Isoleucine 10 to Alanine -I10A-), have already been generated and are included in this example. We will name **WT as stateA** and **Mut as stateB**. ![](https://raw.githubusercontent.com/bioexcel/biobb_wf_pmx_tutorial/master/biobb_wf_pmx_tutorial/notebooks/schema.png) The tutorial calculates the **free energy difference** in the folded state of a protein. Starting from **two 1ns-length independent equilibrium simulations** (WT and mutant), snapshots are selected to start **fast (50ps) transitions** driving the system in the **forward** (WT to mutant) and **reverse** (mutant to WT) directions, and the **work values** required to perform these transitions are collected. With these values, **Crooks Gaussian Intersection** (CGI), **Bennett Acceptance Ratio** (BAR) and **Jarzynski estimator** methods are used to calculate the **free energy difference** between the two states. *Please note that for the sake of disk space this tutorial is using 1ns-length equilibrium trajectories, whereas in the [original example](http://pmx.mpibpc.mpg.de/sardinia2018_tutorial1/eq.mdp) the equilibrium trajectories used were obtained from 10ns-length simulations.* *** ## Copyright & Licensing This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)). * (c) 2015-2025 [Barcelona Supercomputing Center](https://www.bsc.es/) * (c) 2015-2025 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/) Licensed under the [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details. ![](https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png "Bioexcel")

Author
  Adam Hospital, Genís Bayarri
License
  Apache-2.0

## Contents

Main Workflow: Python Mutation Free Energy Calculations using BioExcel Building Blocks (biobb)
Size: 9316 bytes
https://github.com/bioexcel/biobb_workflows/blob/master/biobb_wf_pmx_tutorial/python/stateA.tpr
https://github.com/bioexcel/biobb_workflows/blob/master/biobb_wf_pmx_tutorial/python/stateA_1ns.xtc
https://github.com/bioexcel/biobb_workflows/blob/master/biobb_wf_pmx_tutorial/python/stateB.tpr
https://github.com/bioexcel/biobb_workflows/blob/master/biobb_wf_pmx_tutorial/python/stateB_1ns.xtc
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_pmx_tutorial/python/README.md
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_pmx_tutorial/python/workflow.env.yml
https://github.com/bioexcel/biobb_workflows/blob/main/biobb_wf_pmx_tutorial/python/workflow.yml