AMBER modeling

Figure 2-13. RMS deviations between X-ray structure and optimized geometries for active-site and ONIOM (B3LYP Amber) models...

From a structural point of view the OPLS results for liquids have also shown to be in accord with available experimental data, including vibrational spectroscopy and diffraction data on, for Instance, formamide, dimethylformamide, methanol, ethanol, 1-propanol, 2-methyl-2-propanol, methane, ethane and neopentane. The hydrogen bonding in alcohols, thiols and amides is well represented by the OPLS potential functions. The average root-mean-square deviation from the X-ray structures of the crystals for four cyclic hexapeptides and a cyclic pentapeptide optimized with the OPLS/AMBER model, was only 0.17 A for the atomic positions and 3% for the unit cell volumes. 

Top Observed A° values and excited state lifetimes associated with the initial steps of the photoisomerization of Rh. Bottom Schematic representation of the excited state isomerization motion of PSB11 dominated by an asynchronous crankshaft structure deformation (Frutos et al. 2007) and documented for a CASSCF/AMBER model of Rh... 

Fig. 1. The time evolution (top) and average cumulative difference (bottom) associated with the central dihedral angle of butane r (defined by the four carbon atoms), for trajectories differing initially in 10 , 10 , and 10 Angstoms of the Cartesian coordinates from a reference trajectory. The leap-frog/Verlet scheme at the timestep At = 1 fs is used in all cases, with an all-atom model comprised of bond-stretch, bond-angle, dihedral-angle, van der Waals, and electrostatic components, a.s specified by the AMBER force field within the INSIGHT/Discover program.

The AMBER (Assisted Model Building and Energy Refin emeni) is based on a force field developed for protein and nucleic acid computations by members of the Peter Kollman research group at the... 

Many of the torsional terms in the AMBER force field contain just one term from the cosine series expansion, but for some bonds it was found necessary to include more than one term. For example, to correctly model the tendency of O-C—C-O bonds to adopt a gauche conformation, a torsional potential with two terms was used for the O—C—C—O contribution ... 

Assisted model building with energy refinement (AMBER) is the name of both a force field and a molecular mechanics program. It was parameterized specifically for proteins and nucleic acids. AMBER uses only five bonding and nonbonding terms along with a sophisticated electrostatic treatment. No cross terms are included. Results are very good for proteins and nucleic acids, but can be somewhat erratic for other systems. 

YETI is a force held designed for the accurate representation of nonbonded interactions. It is most often used for modeling interactions between biomolecules and small substrate molecules. It is not designed for molecular geometry optimization so researchers often optimize the molecular geometry with some other force held, such as AMBER, then use YETI to model the docking process. Recent additions to YETI are support for metals and solvent effects. 

AMBER (assisted model building with energy refinement) a molecular mechanics force field... 

Another difference between the force fields is the calculation of electrostatic interactions. AMBER, BIO+, and OPLS use point charges to model electrostatic interactions. MM+ calculates electrostatic interactions using bond dipoles. The bond dipole method may not adequately simulate very polar or charged systems. 

P. A. KoUman and co-workers, AMBER Assisted Model Building and Energy Refinement, Urdversity of CaUforrda, San Erancisco, 1980—present ... 

AMBER (Assisted Model Building and Energy Refinement)... 

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