AmberEnergy is fairly simple C++ program dedicated to:

  • read a file containing the topologies/parameters of a system (prmtop);
  • read a MM simulation trajectory file in amber format;
  • compute interaction energies in the trajectory.

It was originally developed to compute interaction energies between a ligand and a given residue in the active site, for example. However, but might be useful to evaluate interaction energies between two residues in a protein or even between one residue/ligand and the whole environment (i.e., all other atoms in the system).


The current program version supports:

  • Amber PRMTOP file format for system parameters;
  • AMBER coordinates in text or gzipped format;
  • AMBER NetCDF trajectory format;
  • XPLOR/CHARMM/NAMD DCD file format for trajectories;


In order to compile the provided source code, the user will need:

A tutorial on how to compile and use the program will soon be available.