|
599. ANNEAL: A Simulated Annealing Program to Study
Polypeptide Conformations
by Brian T. Luke, IBM Corporation, 41UD/276, Neighborhood Road, Kingston, New York 12401 ANNEAL is a simulated annealing program which searches the conformational space of a polypeptide. In this search, only the dihedral angles are varied (i.e., the bond lengths and bond angles remain constant). In particular, ANNEAL can be used to: 1. Search the torsional conformation space of a single polypeptide a. With or without distance constraints b. With or without water 2. Study the interaction of two or more rigid polypeptides a. With or without water 3. Examine the orientation of water around one or more rigid polypeptides ANNEAL is distributed in two different forms -- a batch version for large simulations and an interactive version for small simulations. A random number generator is used to vary the dihedral angles, and the ECEPP/2 empirical energy program1 calculates the energy of the configuration. The Metropolis Monte Carlo method2 is used to accept or reject a particular conformation, as the value of the temperature is constantly decreased in the Boltzmann distribution of occurrence3. Four different versions of ANNEAL are present on the distribution tape. There are batch and interactive versions for an IBM mainframe, which works under both the MVS and VM operating systems, and batch and interactive versions for RT/PC or RS/6000 under the AIX operating system. The only software requirement is with the interactive versions of ANNEAL, since it is graphically oriented. All of the graphics are written in the IBM Programmers's Hierarchical Interactive Graphics System, also called the IBM graPHIGS* Programming Interface. On a workstation, IBM Personal graPHIGS* must be installed, and the workstation must have a graphics terminal. On a mainframe, graPHIGS must be present. If the graphics is done on an IBM 5080 Graphics System, this is all that is needed. If the terminal is a Graphical Data Display Manager (GDDM*) graphical device, GDDM/Base must also be installed. The user should be aware that the current version of ANNEAL contains a very simplified treatment of water. In particular, the parameters for the oxygen atom in each water molecule are set to the same values as for hydroxyl oxygen in tyrosine. The hydrogens in each water are given the same parameters
_____ * Denotes registered trademarks of the IBM Corporation as tyrosine's hydroxyl hydrogen, except that the partial charge is slightly modified to make each water neutral. _________ References: 1. R. A. Momany, R. F. McGuire, A. W. Burgess and H. A. Scheraga, J. Phys. Chem., 79, 2361 (1975); H. A. Scheraga et al., QCPE Bull., 8, 139 (1988). 2. N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller and E. Teller, J. Chem. Phys., 21, 1087 (1953). 3. S. Kirkpatrick, C. D. Gelatt and M. P. Vecchi, Science, 220, 671 (1983). _________ NOTE:This program is distributed as 26 sequential files with a record length of 80 and BLKSIZE = 800. FORTRAN Lines of Code: 24,685 |