Mutation Free Energy Calculations using BioExcel Building Blocks (biobb)
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.
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.
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.