Premium
Definition of Systematic, Approximately Separable, and Modular Internal Coordinates (SASMIC) for macromolecular simulation
Author(s) -
Echenique Pablo,
Alonso J. L.
Publication year - 2006
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20424
Subject(s) - action angle coordinates , generalized coordinates , dihedral angle , log polar coordinates , degrees of freedom (physics and chemistry) , orthogonal coordinates , orientation (vector space) , matrix (chemical analysis) , separable space , physics , computational chemistry , mathematics , chemistry , geometry , molecule , quantum mechanics , mathematical analysis , hydrogen bond , chromatography
Abstract A set of rules is defined to systematically number the groups and the atoms 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 are provided as supplementary material. The main difference with most 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 different 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 χ, by the Potential Energy Surface (PES) in the protected dipeptide HCO‐ L ‐Ala‐NH 2 . We also present a subbox 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. ( PACS: 87.14.Ee, 87.15.‐v, 87.15.Aa, 87.15.Cc) © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 1076–1087, 2006