Polymer conformations in internal (polyspherical) coordinates

摘要: The small-amplitude conformational changes in macromolecules can be described by the bond lengths and angles. descriptors of large scale are torsions. We present a recursive algorithm, which vector is explicitly written terms these internal, or polyspherical coordinates, local frame defined two other vectors their cross product. Conformations linear branched molecules, as well molecules containing rings this way. orientation molecule body frame. It parametrized instantaneous rotation angle, angles that parametrize axis. reason not to use more conventional Euler due fact well-defined gimbal lock (i.e., when axis becomes aligned with its space fixed counter part). position center mass. Original calculated positions compared for several proteins, up about 100,000 atoms. © 2010 Wiley Periodicals, Inc. J Comput Chem,