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 c++ compiler (works fine with gnu g++, including MinGW);
- the the gzstream library (which requires the zlib library). This libray adds the support to read the gzipped trajectory files. This library can be obtained from http://www.cs.unc.edu/Research/compgeom/gzstream
- NETCDF library (version 3), available in http://www.unidata.ucar.edu/downloads/netcdf/index.jsp