AMBER potential energy functions

Of the biomolecular force fields, AMBER [21] is considered to be transferable, whereas academic CHARMM [20] is not transferable. Considering the simplistic form of the potential energy functions used in these force fields, the extent of transferability should be considered to be minimal, as has been shown recently [52]. As stated above, the user should perform suitable tests on any novel compounds to ensure that the force field is treating the systems of interest with sufficient accuracy. 

The free energy calculations with complexes of oligomeric DNA with distamycin and netropsin presented in this chapter were carried out using the AMBER force field2 and the AMBER software.21 The associated potential energy function is ... 

Our initial, small models of an isolated cellulose chain ranged from the dimer (cellobiose) to the octamer. The dynamics of these fragments have thus far been simulated only in vacuum, using different potential energy functions such as those of MM2(85) (9) and AMBER (10), with and without contributions from electrostatic terms and hydrogen bonds, etc. (The program DISCOVER, customized for carbohydrates and for operation on the Alliant FX/80 computer, has been used (12).) Generally, the time span for the simulations has been of the order of several hundred picoseconds to 1 nanosecond. 

Most force fields used in coordination chemistry, in respect of the organic part of the molecules, are based on or are at least similar to the MM2 11 or AMBER 11 parameterization schemes, or mixtures thereof. However, it is of importance to stress again that transferring parameters from one force field to another without appropriate checks is not valid. This is not only a question of the different potential energy functions that may be used, but it is also a consequence of the interrelatedness of the entire set of parameters. Force field parameters imported from any source, whether a well-established force field or experimental data, should only be used as a starting point for further parameter refinement. 

Some formulations of the potential energy function (e.g., References 27 and 79, and AMBER, CHARMM, and DISCOVER, as well as most force fields used in small-molecule studies) include terms that allow for bond stretching and bond angle bending, that is, for flexible geometry. Hence, the terms in Eq. [1] are augmented by the expression27... 

The success of any molecular simulation method relies on the potential energy function for the system of interest, also known as force fields [27]. In case of proteins, several (semi)empirical atomistic force fields have been developed over the years, of which ENCAD [28,29], AMBER [30], CHARMM [31], GRO-MOS [32], and OPLSAA [33] are the most well known. In principle, the force field should include the electronic structure, but for most except the smallest systems the calculation of the electronic structure is prohibitively expensive, even when using approximations such as density functional theory. Instead, most potential energy functions are (semi)empirical classical approximations of the Born-Oppenheimer energy surface. 

Molecular modeling and computer simulation with empirical potential energy function (force field) are now routinely carried out to help understand and predict structures and dynamics of proteins and other macromolecules of biological relevance in water and membrane environments. After over 40 years of development, popular force fields such as AMBER, CHARMM, OPLS and GROMOS have been widely employed in biomolecular simulations. These force fields are used dominantly in highly optimized molecular dynamics... 

Among the most used force fields of this kind we cite AMBER-GAFF [9, 10], OPLS [11], and CHARMM [12], all relying on intramolecular potential energy functions like the following ... 

Suppose, rather than one diatomic molecule, we have one or more solute molecules surrounded by a large number of solvent molecules in a condensed state. We have several additional issues to deal with. We need to describe the interaction of the solute molecules with one another and with the solvent molecules and we need to describe the interaction of the solvent molecules with one another. The standard approach is to define a potential energy function (or force field). One such function is the AMBER force field d... 

We aim at deriving parameters for ethers that are compatible with the AMBER force field. The potential energy function used in AMBER is ... 

The energy functions for folding simulations include atom-based potentials from molecular mechanics packages [164] such as CHARMM [81], AMBER [165], and ECEPP... 

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