Definition of Systematic, Approximately Separable and Modular Internal Coordinates (SASMIC) for macromolecular simulation

Abstract

A set of rules is defined to systematically number the groups and the atoms of organic molecules and, particularly, of polypeptides in a modular manner. Supported by this numeration, a set of internal coordinates is defined. These coordinates (termed Systematic, Approximately Separable and Modular Internal Coordinates, SASMIC) are straightforwardly written in Z-matrix form and may be directly implemented in typical Quantum Chemistry packages. A number of Perl scripts that automatically generate the Z-matrix files for polypeptides are provided as supplementary material. The main difference with other Z-matrix-like coordinates normally used in the literature is that normal dihedral angles (``principal dihedrals'' in this work) are only used to fix the orientation of whole groups and a somewhat non-standard type of dihedrals, termed ``phase dihedrals'', are used to describe the covalent structure inside the groups. This physical approach allows to approximately separate soft and hard movements of the molecule using only topological information and to directly implement constraints. As an application, we use the coordinates defined and ab initio quantum mechanical calculations to assess the commonly assumed approximation of the free energy, obtained from ``integrating out'' the side chain degree of freedom chi, by the Potential Energy Surface (PES) in the protected dipeptide HCO-L-Ala-NH2. We also present a sub-box of the Hessian matrix in two different sets of coordinates to illustrate the approximate separation of soft and hard movements when the coordinates defined in this work are used.