Abstract
As had been previously reported standard AMBER parameters do not reproduce adequately ab initio calculations performed on the pentacycloundecane cage residue. The analysis of the geometries of the minimum energy structures compared with other residues allowed us to suspect the importance of bond stretching parameters in this case. Accordingly, we proceeded to compute new stretching and bending parameters from density functional theory calculations. Accordingly, the reliability of these parameters have been validated by predicting the correct conformational Ramachandran map. This is an example where the geometry of the side chain constrains the geometry of the residue backbone in such a way that you can get the right conformational profile by simple modification of some stretching and bending parameters.
Published Version
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