Information that all the simulation programs need:
1. Cartesian coordinates for each atom in the system.
2. "Topology": connectivity, atom names, atom types, residue names, and charges.This information
comes from the database, which is found in the amber10/dat/leap/prep directory.
3. Force field: Parameters for all of the bonds, angles, dihedrals, and atom types in the system.
The standard parameters for several force fields are found in the amber10/dat/leap/parm
Preparatory programs
LEaP
ANTECHAMBER
Simulation programs
SANDER (Simulated Annealing with NMRDerived Energy Restraints)
PMEMD
Analysis programs
PTRAJ
MM-PBSA