Chem3D Users Manual - CambridgeSoft

Chapter 9: MM2 and MM3
Computations
CS Mechanics
Overview
The CS Mechanics add-in module for Chem3D
provides three force-fields—MM2, MM3, and
MM3 (Proteins)—and several optimizers that allow
for more controlled molecular mechanics
calculations. The default optimizer used is the
Truncated-Newton-Raphson method, which
provides a balance between speed and accuracy.
Other methods are provided that are either fast and
less accurate, or slow but more accurate.
The Chem3D atom types are translated to the atom
types required for the calculations implemented in
CS Mechanics. In some cases the translation is not
quite correct since Chem3D has many more atom
types than the standard MM2 and MM3 parameters,
and also has the ability to guess missing types. In
other cases the atom types are correctly defined,
however the force field parameters may not be
defined. This will result in calculations failing due
to missing atom types or parameters. This problem
can be resolved either by adding the missing
parameters using the Additional Keywords section
of the CS Mechanics interface, or by creating an
input file which can be corrected with a text editor.
The calculation can then be run by using the Run
Input command in the Mechanics submenu of the
Calculations menu. Further details on how to
define missing parameters can be found in the
Tinker manual (Tinker.pdf) on the ChemOffice
CDROM.
The behavior of the user interface closely matches
that of the other add-in modules such as MOPAC
and Gaussian. The calculations can be set-up by
making selections of force-field, termination
criteria etc. Various properties can be computed as
part of the single point or geometry optimization
calculations. These can be selected from the
Properties panel.
The Chem3D MM2 submenu of the Calculations
menu provides computations using the MM2 force
field.
The MM2 procedures described assume that you
understand how the potential energy surface relates
to conformations of your model. If you are not
familiar with these concepts, see ‘Computation
Concepts”
As discussed in , the energy minimization routine
performs a local minimization only. Therefore, the
results of minimization may vary depending on the
starting conformation in a model.
Minimize Energy
To minimize the energy of the molecule based on
MM2 Force Field:
NOTE: You cannot minimize models containing phosphate
groups drawn with double bonds. For information on how to
create a model with phosphate groups you can minimize, see
the Chem3D Drawing FAQ at:
http://www.cambridgesoft.com/services/faqs.cfm
1. Build the model for which you want to
minimize the energy.
2. To impose constraints on model
measurements, set Optimal column
measurements in the Measurements table.
ChemOffice 2005/Chem3D MM2 and MM3 Computations • 151
Minimize Energy