Galaxy | Tool Preview

MMPBSA/MMGBSA (version 21.10+galaxy0)
Input 0
General parameters
General parameters 0
Details of calculation and parameters
Details of calculation and parameters 0

What it does

This tool calculates the Molecular Mechanics Poisson-Boltzman Surface Area (MMPBSA), which is an estimate of the binding free energy between a ligand and a receptor. It also can calculate the MMGBSA, which is a common alternative, replacing the Poisson-Boltzmann term with the General Born approximation.

How it works

Prior to using this tool, simulations of the ligand complexed with the receptor must be run. This tool, which wraps AmberTools, requires a prmtop (Amber parameter topology) file for the receptor, ligand and the complex and the trajectory in netCDF format.

If simulations were performed using the Galaxy GROMACS tools, the topology (in top format) and trajectories (in xtc format) can be converted to Amber prmtop and netcdf formats using the Convert Parameters and MDTraj file converter tools respectively.

Outputs created

User guide and documentation