AMBER energy functions

Figure 4 The frequency of predicting the crystal structure of the SB203386-HIV-1 protease complex in docking simulations with the ensemble of 6 protein conformations (a). The RMSD of the docked inhibitor conformations from the crystal structure ranked by energy in simulations with the ensemble of 6 protein conformations (b) The energy distribution histogram of the docked conformations (c). The filled histogram (d) reflects the energies of the minimized crystal structures for 1) Isbg, 2) Ibdl, 3) Ibdq), 4) Ibdr, 5) Itcx, 6) Itcw protein structures. The standard AMBER energy function is used.

FF scoring most often relies on the nonbonded interaction energy terms of standard force fields, e.g., in vacuo electrostatic terms (sometimes modified by scaling constants that assume the protein to be an electrostatic continuum) and vdW terms [22,105,128,129]. As an example, DOCK and GREEN [130] have implemented the intermolecular terms of the AMBER energy function [103,104] with the exception of an explicit hydrogen-bonding term [42] ... 

The simulation methodologies applied to proteins and nucleic acids are applicable to the biomembrane modeling at the atomic level. The jvidely distributed programs, CHARMM, AMBER, and GROMOS, have been applied for biomembrane studies. The common energy parameters of proteins, nucleic acids, and water are used with minor modifications for lipids. For instance, the AMBER energy function is written as follows ... 

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

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... 

We have pursued a plug-and-play strategy with two different energy functions, a molecular mechanics AMBER force field [131,132] and a simplified energy function, along with two different sampling techniques, evolutionary programming [91] and Monte Carlo simulations [118,119,127,128]. 

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. 

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