Gmx_qk

Gmx_qk automates protein and protein–ligand complex molecular dynamics simulations in Gromacs and performs MM/PBSA calculations to estimate binding affinities.

Key Features:

• Automated MD workflow: Executes energy minimization, NVT and NPT equilibration, and production MD simulations in an automated bash workflow.
• Gromacs integration: Uses Gromacs for all MD simulation steps and trajectory generation.
• MM/PBSA bridging: Performs MM/PBSA calculations on simulation outputs to derive binding affinity estimates.
• Parameter-driven execution: Accepts inputs including energy minimization parameters, simulation duration, and output file naming to control the automated run.
• Reproducibility and standardization: Standardizes the simulation protocol to improve reproducibility and reduce user-induced variability.

Scientific Applications:

• Drug discovery: Estimation of binding affinities for protein–ligand complexes to support compound prioritization.
• Protein–protein and protein–ligand interaction analysis: Simulation of protein/protein-ligand complexes to study molecular interactions and complex stability.
• Binding energy evaluation: MM/PBSA-based binding affinity evaluation from MD trajectories.

Methodology:

A bash workflow invokes Gromacs to perform energy minimization, NVT and NPT equilibration, and MD production runs, then applies MM/PBSA calculations to the simulation outputs using provided protein or protein–ligand complex files and specified parameters.