a step-by-step guide to perform Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) calculations on a GROMACS input file.
This Jupyter notebook provides a step-by-step guide to perform Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) calculations on a GROMACS input file (based on gmx_MMPBSA project). The notebook utilizes the Python scripts provided with AmberTools to carry out the necessary steps for MMPBSA analysis for a protein-ligand simulation.
To run this Jupyter notebook and perform the MMPBSA calculation, the following files are required:
GROMACS input file (.gro)
mmpbsa.in setting using gmx_MMPSA
GROMACS topology file (.top)
Trajectory file (.xtc)
index file(.ndx)
portable binary run input file (.tpr)
AmberTools20 or higher
To run the notebook, simply open it in Jupyter and execute each cell in order. The notebook contains detailed explanations and instructions for each step of the MMPBSA calculation process.
Note: It is recommended to run this notebook on a machine with sufficient computational resources as MMPBSA calculations can be computationally intensive.
