Optimized AMBER model

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. 

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. 

Calculated for a simplified model system [100] at the MP2/6-31+G(d)//HF/3-21G level. The value in parenthesis was calculated at the MP2/6-31+G(d)//B3LYP/6-31G(d) level Calculated for the real enzymatic reaction system by using the QM/MM method at the MP2/6-31+G(d) Amber level with the geometries optimized at the HF/3-21G Amber level... 

The shared-memory programming model on the KSR allows a straightforward port of large applications to at least a single processor. KSR claims that an optimized port of AMBER took only three days. KSR has two full-time computational chemists in-house with other systems development staff who were trained as computational chemists. 

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