Pseudoenergy function

These conformations were subjected to a combined MD/EM refinement using the NOESY derived constraints as pseudoenergy functions. Families of conformations for the whole molecule were then constructed from the structures derived for each linkage. This procedure was demonstrated on a fragment from the carbohydrate-protein linkage region of connective tissue proteoglycans. 

In order to incorporate distance constraints derived from two-dimensional crossrelaxation data in a molecular mechanics program, we have chosen to treat the constraints as a pseudoenergy function. This function should ideally reflect the distance dependence of cross relaxation rates. Previously, we had proposed a function of the form (40) ... 

Functions such as 1 and 2 permit the inclusion of a pseudoenergy term for all pairs of protons in a molecule, whether or not cross relaxation rates are sufficiently large to be observed. This is made possible by the fact that for sufficiently long distances, the energy contributions from these functions are negligible. For cases where no connectivity is observed between a pair of protons roa6 is set equal to some distance, in our case 4.0A, beyond which a connectivity between protons would be lost in the noise. Inclusion of a pseudoenergy term in the absence of an observed connectivity is important since it serves to exclude conformers with interproton distances short enou to produce a connectivity when none is observed. We shall make limited use of this fact in our structural determinations. 

Figure 5. The deviation of the designed sites fiom the ideal pentagonal bipyramidal geometry (pseudoenergy U(p)) as a function the designed calcium binding sites. The natural calcium binding sites I-IV of calmodulin are shown as black dots.

With ab initio methods there are two distinct approaches to calculating time dependent properties. One is the analytic derivative approach, where explicit expressions are obtained for the derivatives of the dipole moment or of the pseudoenergy. The other approach, known as response theory calculates the response function directly by time dependent perturbation theory. In general finite field methods are not applicable for dynamit properties except that, e.g., j8(ru 0, ru) could be calculated by the finite difference of a ay,a)) calculated at two different field strengths. Consider first methods based on Hartree-Fock theory, known collectively as TDHF. 

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