Chem3D Users Manual - CambridgeSoft

Administrator
Editing Parameters
You can edit the parameters that come with
Chem3D. Parameters that you add or change can
be guesses or approximations that you make, or
values obtained from current literature.
In addition, there are several adjustable parameters
available in the MM2 Constants table. For
information on parameters and MM2 constants, see
“The Force-Field” on page 136.
NOTE: Before performing any editing we strongly
recommend that you create back-up copies of all the
parameter files located in the C3DTable directory.
To add a new parameter to the Torsional
parameters table:
1. From the View menu, point to Parameter
Tables and choose Torsional Parameters.
The Torsional Parameters table opens in a
window.
2. Enter the appropriate data in each field of the
parameter table. Be sure that the name for the
parameter is not duplicated elsewhere in the
table.
3. Close and Save the table.
The MM2 Force Field
in Chem3D
Chem3D includes a new implementation of
Norman L. Allinger’s MM2 force field based in
large measure on work done by Jay W. Ponder of
Washington University. This appendix does not
attempt to completely describe the MM2 force
field, but discusses the way in which the MM2 force
field is implemented and used in Chem3D and the
differences between this implementation, Allinger’s
MM2 program (QCPE 395), and Ponder’s
TINKER system (M.J. Dudek and J.W. Ponder, J.
Comput. Chem., 16, 791-816 (1995)).
For a review of MM2 and applications of molecular
mechanics methods in general, see Molecular
Mechanics, by U. Burkert and N. L. Allinger, ACS,
Washington, D.C., USA, 1982. Computational
Chemistry, by T. Clark, Wiley, N.Y., USA, 1985, also
contains an excellent description of molecular
mechanics.
For a description of the TINKER system and the
detailed rationale for Ponder’s additions to the
MM2 force field, visit the TINKER home page at
http://dasher.wustl.edu/tinker.
For a description and review of molecular
dynamics, see Dynamics of Proteins and Nucleic Acids, J.
Andrew McCammon and Stephen Harvey,
Cambridge University Press, Cambridge, UK, 1987.
Despite its focus on biopolymers, this book
contains a cogent description of molecular
dynamics and related methods, as well as
information applicable to other molecules.
Chem3D Changes to
Allinger’s Force Field
The Chem3D implementation of the Allinger Force
Field differs in these areas:
1. A charge-dipole interaction term
2. A quartic stretching term
3. Cutoffs for electrostatic and van der Waals
terms with a fifth-order polynomial switching
function
4. Automatic pi system calculation when
necessary
290• MM2 CambridgeSoft
Editing Parameters