Examples

Here you can find a representation of almost all the types of calculations and analyses that you can perform with gmx_MMPBSA. Although each example focuses on specific cases, you can use gmx_MMPBSA on systems that combine a number of different components (i.e. metalloprotein-ligand complex, Protein-DNA-ligand, etc.). In addition, several types of calculations (e.g. GB, Alanine scanning and Per-residue decomposition; PB, Interaction Entropy, and Per-wise decomposition) can be also performed in the same run for a specific system.

Jupyter notebooks¶

Two Jupyter notebooks are available for interactive use:

• Google Colab notebook: installs a conda-based CPU environment, runs bundled examples, supports uploaded user files, and displays results through the Python API.
• Local notebook: runs or loads local results, extracts data with the Python API, and plots energy terms with seaborn.

Systems¶

This is a representation of the systems that can be processed and analyzed with gmx_MMPBSA. Our program has a robust method to process input structures. Even if your system is not represented here, still have a go, you won't be disappointed! 😀

• Protein-protein¹²³
• Protein-ligand¹²
• Protein-DNA¹²³
• Protein-glycan¹²³
• MMPBSA with membrane proteins¹²
• Metalloprotein-ligand¹²
• Multicomponent system (Protein-DNA-RNA-Ions-Ligand)¹²³
• COVID-19 related proteins
  • Info
  • Main protease
  • Papain-like protease
  • S1-ACE2 complex
  • S1 RBD with antibody

Analyses¶

This section focuses on the analysis that can be performed with gmx_MMPBSA. Although each example focuses on specific cases, you can use gmx_MMPBSA to perform several types of calculations (e.g. GB, Alanine scanning and Per-residue decomposition; PB, Interaction Entropy, and Per-residue decomposition) in the same run for a specific system.

• Single Trajectory Protocol¹²³
• Multiple Trajectory Protocol¹
• Binding free energy calculations
  • Binding free energy calculation with GB
  • Binding free energy calculation with GBNSR6
  • Binding free energy calculation with linear PB (LPBE)
  • Binding free energy calculation with NonLinear PB (non-LPBE)
  • Binding free energy calculation with 3D-RISM model¹
• Alanine scanning¹²³
• Decomposition analysis¹²³
• Entropy
  • Interaction Entropy calculations¹²³
  • NMODE Entropy calculations¹
  • C2 Entropy calculations
• Stability calculations¹²³
• QM/MMGBSA calculations
• Correlation
• Python API extraction
• Local API/seaborn notebook

AMBER support¶

This section focuses more on how to work with systems prepared with AMBER. We only show few examples for better clarity.

• Protein-protein

CHARMMff support¶

This section focuses more on how to work with systems prepared with CHARMM force fields. We only show few examples for better clarity.

• Protein-ligand¹²
• Protein-ligand complex embedded in membrane¹
• Protein-ligand with LPH atoms

OPLSff support¶

This section focuses more on how to work with systems prepared with OPLS force fields. We only show few examples for better clarity.

• Protein-protein

Support for psf_dcd files¶

This section focuses on how to work with psf-dcd files. These files are used for several MD simulation programs such as NAMD, OpenMM or GENESIS. We plan to add more examples in the near future.

• Protein-protein binding free energy calculations
• Protein-ligand binding free energy calculations
• Binding free energy calculations in multicomponent systems