Jan Jensen edited In_the_case_of_CA__.tex  almost 9 years ago

Commit id: cbd3d854a0dec6255115b6a8011f554d3929a722

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In the case of CA removing $\Delta \sigma_{1^\circ HB}^i$, $\Delta \sigma_{2^\circ HB}^i$, and $\Delta \sigma_{1^\circ H\salpha H\alpha  B}^i$ lowers the RMSD value by 0.0 - 0.2 ppm and removing all three lowers the RMSD by 0.2 - 0.3 ppm while increasing $r$ by 0.03 - 0.06. In the case of $\Delta \sigma_{1^\circ HB}^i$ and $\Delta \sigma_{2^\circ HB}^i$ this is not particularly surprising as CA is approximated as a methyl group in the structural model. Accordingly these three terms are removed from ProCS15, while all other terms are kept (note the ring current is only included for hydrogen atoms). Similarly for CB, For CB  removing $\Delta \sigma_{1^\circ H\salpha H\alpha  B}^i$ decreases the RMSD by 0.2 - 0.5 ppm, while $\Delta \sigma_{BB}^{i-1}$ and $\Delta \sigma_{BB}^{i+1}$ increases and decreases the RMSD value depending on the protein. Accordingly only $\Delta \sigma_{1^\circ H\salpha H\alpha  B}^i$ is removed. Note that the structural models used for $\Delta \sigma_{1^\circ HB}^i$ and $\Delta \sigma_{2^\circ HB}^i$ do not contain a CB so there is no such contribution for this nucleus.