ISSN:
0192-8651
Schlagwort(e):
Chemistry
;
Theoretical, Physical and Computational Chemistry
Quelle:
Wiley InterScience Backfile Collection 1832-2000
Thema:
Chemie und Pharmazie
,
Informatik
Notizen:
The rotational symmetry boundary condition proposed by Cagin et al. [J. Comp. Chem., 12, 627 (1991)] is implemented in the molecular dynamics simulation program, APRICOT, to make simulations of icosahedrally symmetrical capsids practical. The principle of the rotational symmetry boundary condition is strictly formulated with a new algorithm to track each atom by protomer and cell number. Further, the 60 cells and the 60 protomers of a capsid are treated as elements of the point group I. This treatment is necessary to determine the protomer numbers of atoms and to define indicators of atom pairs named relative protomer numbers. A method designated border residue flags is also introduced to further accelerate neighbor atom pair list generation. The method as we have implemented it is so fast that it was possible, using inexpensive workstations, to perform a 60-ps molecular dynamics simulation on an entire structure of a rhinoviral capsid including a 71-Å-thick shell of water molecules. This work is the first molecular dynamics simulation of an entire capsid under rotational symmetry boundary conditions. The structure of the capsid is well conserved during the simulation. Because conventional periodic boundary conditions are not applicable to rotational symmetries, it has been difficult, until this study, to perform calculations on macromolecules in crystallographic or noncrystallographic symmetries that are composed of rotational symmetries and linear translation. Therefore, our development is expected to provide a powerful tool for studies of macromolecules in such symmetries. The merits, limitations, and possibilities for further elaboration of this development are discussed. © 1996 by John Wiley & Sons, Inc.
Zusätzliches Material:
7 Ill.
Materialart:
Digitale Medien
