g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations.

TLDR: A new tool, g_mmpbsa, which implements the MM-PBSA approach using subroutines written in-house or sourced from the GROMACS and APBS packages is described, and the calculated interaction energy of 37 structurally diverse HIV-1 protease inhibitor complexes is compared.

Abstract: Molecular mechanics Poisson–Boltzmann surface area (MM-PBSA), a method to estimate interaction free energies, has been increasingly used in the study of biomolecular interactions. Recently, this method has also been applied as a scoring function in computational drug design. Here a new tool g_mmpbsa, which implements the MM-PBSA approach using subroutines written in-house or sourced from the GROMACS and APBS packages is described. g_mmpbsa was developed as part of the Open Source Drug Discovery (OSDD) consortium. Its aim is to integrate high-throughput molecular dynamics (MD) simulations with binding energy calculations. The tool provides options to select alternative atomic radii and different nonpolar solvation models including models based on the solvent accessible surface area (SASA), solvent accessible volume (SAV), and a model which contains both repulsive (SASA-SAV) and attractive components (described using a Weeks–Chandler–Andersen like integral method). We showcase the effectiveness of the tool ...