How gmx_MMPBSA works¶

gmx_MMPBSA is a tool based on AMBER's MMPBSA.py that performs end-state free energy calculations using GROMACS files.

But, what does that mean?

Basically, gmx_MMPBSA provides many supported MMPBSA.py workflows and additional GROMACS-oriented tooling. The supported subset depends on the input format, force field, solvent model, entropy method, and trajectory protocol; see compatibility and upgrades and the native-AMBER guide for explicit limits.

MMPBSA.py is a well-established tool for performing end-state binding free energy calculations in AMBER. Tools such as g_mmpbsa are also well known within the GROMACS community. However, using MMPBSA.py with GROMACS inputs traditionally requires substantial file conversion and workflow setup.

We created gmx_MMPBSA to make this workflow accessible to the GROMACS community. It automates the required preparation, supports additional calculation options, and includes the gmx_MMPBSA_ana graphical application for analyzing the results. It also makes several advanced MMPBSA.py capabilities easier for new Amber users to access.

gmx_MMPBSA general workflow¶

The gmx_MMPBSA workflow has three stages, as shown in Figure 1. During Preparation, the program generates the topologies and trajectories, together with calculation-specific inputs such as mutant structures for alanine/glycine scanning or lists of interacting residues for decomposition analysis. During Calculation, it estimates the binding free energies and/or entropies using the selected models. During Analysis, the results can be examined with the gmx_MMPBSA_ana graphical interface.

Topology preparation¶

gmx_MMPBSA requires several input files to prepare the topologies for the calculations.

MD Structure+mass(db) (*.tpr, *.pdb)

This file is used with editconf or trjconv to generate the complex structure in PDB format. We recommend using the *.tpr (production *.tpr) format. Coordinates and atom order must match the GROMACS topology.

Index (*.ndx)

This file organizes atoms from the *.tpr file into index groups. It is required to identify the groups corresponding to the receptor and ligand.

Trajectory (*.xtc, *.trr, *.pdb)

Trajectory files.

Topology (*.top) required

GROMACS topology containing the force-field parameters used in the MD. gmx_MMPBSA converts this topology with ParmEd (-cp; and -rp/-lp for unbound MT tops). Structure-only rebuilds through tleap from extracted PDBs are not supported. Small-molecule ligands must already be present in the topology tree.

Reference Structure

This optional PDB file must contain the complete complex, with the same atoms and residues as the structure supplied for the calculation. It should also contain the intended residue numbering and chain IDs. We recommend providing a reference structure because gmx_MMPBSA uses this information when it extracts the receptor and ligand, prepares alanine-scanning mutations, and performs other structure-sensitive operations.