AMBER force field, molecular modelling

AMBER force field, molecular modelling 77 anchoring 12... 

Molecular modeling of the noncovalent interaction between trisphenanthroline metal complexes and DNA has been used to aid in the interpretation of the NMR spectra of these systems12161. The AMBER force field was used to model the DNA, and the metal complex/DNA systems were energy-minimized. Distances from the energy-minimized models were used to calculate relaxation rates and compared with the experimentally determined data12161. 

Specific solute-solvent interactions, which are not explicitly taken into account in continuum models, can play a significant role especially for charged species. A typical cluster formed by the glycine anion radical with four water molecules is shown in figure 16. The analogous supermolecule obtained for the neutral form is quite similar, except for the much weaker interaction energies involved in the neutral species. The number and the position of the solvent molecules are determined by molecular dynamics simulations performed by the AMBER force field [141]. 

Arad et al. (1990) simulated the reaction sequence of papain by constructing several enzyme-substrate models with molecular mechanics and following reaction paths with semiempirical quantum mechanics. AMBER force field (Weiner et al., 1986a) was employed for the construction. AMI (Dewar et al, 1985) results for proton affinities of the modeled molecules were compared to 4-31G and to experiments. AMI underestimates the proton affinities of methanethiol and of imidazole but overestimates the proton affinity of methanol. However, the proton transfer reactions from methanol to imidazole and from methanethiol to imidazole are overestimated by only 6 and 11 kcal/mol, respectively, and PT from imidazolium to formamide is underestimated by 6 kcal/mol. 

Kollman and coworkers apphed a variety of computational methods to this mechanistic problem—including quantum mechanics on small model systems, molecular dynamics simulations with the AMBER force field on the whole ODCase-substrate system, and MM-PBSA free energy calculations on ODCase with bound OMP [38]. Based on their results, they proposed a decarboxylation mechanism for ODCase that involves C5 protonation. Their calculations at the MP2/6-31+G //HF/6-31+G level showed that C5 has a greater intrinsic proton affinity than C6, 02, and even 04. This, coupled with the fact that Lys72 (M. thermoautotrophicum numbering see Table 2) is near C5 and C6 in the inhibitor-bound crystal structures, prompted the authors to embrace a C5 protonation mechanism. However, the authors themselves acknowledged the uncertainties of their calculations because of approximations employed in representing the enzyme active site. 

The AMBERS force field (all-atom, version 3.0) i° was employed, as implemented in the molecular modeling program HyperChem. n... 

Modifications have been made to the AMBER force field to improve the correlations between calculated and observed molecular properties of a-linked saccharides these led to refinements in solvation studies on maltose, a-, p- and Y-cyclodextrin and two larger cyclodextrins (DP 10 and 21). A molecular dynamics simulation investigation of the solvation patterns of the model disaccharide 4 in aqueous DMSO defined regions in which competition exists... 

In molecular dynamics simulations, it is useful to include specific parameters describing the influence of intra- and intermolecular interactions of water molecules. These parameter sets represent water models such as SPC, SPC/E, ST2, TIP3P and TIP4P. Such models were successfully used for the prediction of thermodynamic data of liquid water. If a special water model is chosen in combination with the AMBER force field for calculation of the potential energy according to equation (23.1), term (6) is omitted. 

AMBER A Program for Simulation of Biological and Organic Molecules Biomembranes Modeling CHARMM The Energy Function and Its Parameterization Environment of a Membrane Protein Force Fields A General Discussion GROMOS Force Field Molecular Dynamics Techniques and Applications to Proteins OPLS Force Fields Permeation of Lipid Membranes Molecular Dynamics Simulations Time Correlation Functions. 

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