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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
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* 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.
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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).
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NOTE:This program is distributed as 26 sequential
files with a record length of 80 and BLKSIZE =
800.
FORTRAN
Lines of Code: 24,685
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