Editing AMBER (section)

=== Programs ===
* ''LEaP'' prepares input files for the simulation programs.
* ''Antechamber'' automates the process of parameterizing small organic molecules using GAFF.
* ''Simulated Annealing with NMR-Derived Energy Restraints'' (SANDER) is the central simulation program and provides facilities for energy minimizing and molecular dynamics with a wide variety of options.
* ''pmemd'' is a somewhat more feature-limited reimplementation of SANDER by Bob Duke. It was designed for [[parallel computing]], and performs significantly better than SANDER when running on more than 8–16 processors.
** ''pmemd.cuda'' runs simulations on machines with [[graphics processing unit]]s (GPUs).
** ''pmemd.amoeba'' handles the extra parameters in the polarizable AMOEBA force field.
* ''nmode'' calculates normal modes.
* ''ptraj'' numerically analyzes simulation results. AMBER includes no visualizing abilities, which is commonly performed with [[Visual Molecular Dynamics]] (VMD). Ptraj is now unsupported as of AmberTools 13. 
* ''cpptraj'' is a rewritten version of ptraj made in [[C++]] to give faster analysis of simulation results. Several actions have been made parallelizable with OpenMP and MPI.
* ''MM-PBSA'' allows implicit solvent calculations on snap shots from molecular dynamics simulations.
* ''NAB'' is a built-in nucleic acid building environment made to aid in the process of manipulating proteins and nucleic acids where an atomic level of description will aid computing.