# Summary 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. Workflow engine is a jupyter notebook. Auxiliary libraries used are nb\_conda\_kernels, os, and plotly. Environment setup can be carried out using the environment.yml in the code repository. The tutorial uses docker for running pmx - a local setup can be used instead, see notes in the tutorial. # Parameters ## Inputs Workflow Input files needed: * **stateA_traj**: Equilibrium trajectory for the WT protein. * **stateB_traj**: Equilibrium trajectory for the Mutated protein. * **stateA_tpr**: WT protein topology (GROMACS tpr format). * **stateB_tpr**: Mutated protein topology (GROMACS tpr format). Auxiliar force field libraries needed: * **mutff45 (folder)**: pmx mutation force field libraries. ## Outputs * **pmx.outputs**: Final free energy estimation. Summary of information got applying the different methods. * **pmx.plots.png**: Final free energy plot of the Mutation free energy pipeline.