I am actually performing an Md Simulation study of the protein+DNA complex and using Amber99 ff. but I am confused about what concentration of salt to take for the simulation.
Rajdeep--the salts concentration varies depending on the type of cell (e.g. bacterial, yeast, mammalian); I vaguely recall that for mammalian cells, the overall salt concentration is somewhat close to that of ocean water.
For conformation of protein/DNA complexes, not only the overall salt concentration, but also the amounts of specific types of salts (e.g. monovalent cations and bivalent cations) can have a large influence on the folding conformation.