Formulation of Static and Dynamic Conformational Energy Analysis of Biopolymer Systems Consisting of Two or More Molecules

Abstract

Two computational problems arise from inclusion of six external variables between two molecules in a biopolymer system in the conformational energy analysis in which bond lengths and bond angles are kept fixed and only dihedral angles are treated as independent variables. They are the calculation of the first and second derivatives of the conformational energy function and the calculation of the coefficient matrix in the kinetic energy Lagrangian. These two problems are studied and formulae are given, which turn out to be minor modifications of those already derived for cases of one polymer molecule.