Gaussian 03 Online ManualLast update: 2 October 2006 | |

## Molecular Mechanics MethodsThere are three
molecular mechanics methods available in The following force fields are available:
## CHARGE ASSIGNMENT-RELATED OPTIONSUnless set in the molecule specification input, no charges are assigned to atoms by default when using any molecular mechanics force field. Options are available to estimate charges at the initial point using the QEq algorithm under control of the following options for any of the mechanics keywords:
## PARAMETER PRECEDENCE OPTIONS
## HANDLING MULTIPLE PARAMETER SPECIFICATION MATCHESSince parameters can be specified using wildcards, it is possible for more than one parameter specification to match a given structure. The default is to abort if there are any ambiguities in the force field. The following options specify other ways of dealing with multiple matches.
## INPUT CONVENTIONSAMBER calculations require that all atom types be explicitly specified using the usual notation within the normal molecule specification section: C-CT Consult the AMBER paper [37] for definitions of atom types and their associated keywords. Atom types and charges may also be provided for UFF and DREIDING calculations, but they are not required. For these methods, the program will attempt to determine atom types automatically. Analytic energies, gradients, and frequencies. ## GENERAL MOLECULAR MECHANICS FORCE FIELD SPECIFICATIONSUnless otherwise indicated, distances are in Angstroms, angles are in degrees, energies are in Kcal/mol and charges are in atomic units. Function equivalencies to those found in standard force fields are indicated in parentheses. In equations, R refers to distances and θ refers to angles. Wildcards may be used in any function definition. They are indicated by a 0 or an asterisk. In MM force fields, the non-bonded (Vanderwaals and electrostatic) interactions are evaluated for every possible pair of atoms. However, interactions between pairs of atoms that are separated by three bonds or less are usually scaled down (in most force fields, using a factor 0.0 for pairs separated by one or two bonds, and some value between 0.0 and 1.0 for pairs that are separated by three bonds). There are a number of ways to implement the calculation of non-bonded interactions. We follow a two-step procedure. First, we calculate the interactions between all pairs, without taking the scaling into account. In this step, we can use computationally efficient (linear scaling) algorithms. In the second step, we subtract out the contributions that should have been scaled, but were included in the first step. Since this involves only pairs that are close to each other based on the connectivity, the computer time for this step scales again linearly with the size of the system. Although at first sight it seems that too much work is done, the overall algorithm is the more efficient than the alternatives. In the soft force field input, the Vanderwaals parameters, used for
MMFF94 type Vanderwaals parameters (used
for
MMFF94 electrostatic buffering
Non-bonded interaction master function. This function will be expanded
into pairs and a direct function (
Coulomb and Vanderwaals direct (evaluated for all atom pairs).
Coulomb and Vanderwaals single term cutoffs
Atomic single bond radius
Effective charge (UFF)
GMP Electronegativity (UFF)
Step down table
Harmonic stretch
I (Amber [1]):
Harmonic stretch II (Dreiding [4a]):
Harmonic stretch III (UFF [1a]): Equilibrium
bond length R
Morse stretch
I (Amber):
Morse stretch II (Dreiding [5a]):
Morse stretch
III (UFF [1b]): Equilibrium bond length
R
Quartic stretch I (MMFF94 [2]): (
Atomic torsional barrier for the oxygen column (UFF [16])
Atomic sp3 torsional barrier (UFF [16])
Atomic sp2 torsional barrier (UFF [17])
Harmonic bend (Amber [1]):
Harmonic Bend (Dreiding [10a]): [
Dreiding Linear Bend (Dreiding [10c]):
UFF 3-term bend (UFF [11]): k*(C0 + C1*cos(θ))+C2*cos(2θ)
where C2=1/(4 * sin(θ
θ
UFF 2-term bend (UFF [10]): [k/( Force
constant: k = 664.12*Z
Zero bend term: used in rare cases where a bend is zero. This term is needed for the program not to protest about undefined angles.
Cubic bend I (MMFF94 [3]):
(
MMFF94 Linear Bend (MMFF94 [4]):
Amber torsion (Amber [1]): Σ
Dreiding torsion (Dreiding [13]):
UFF torsion with constant barrier height (UFF [15]):
[
UFF torsion with bond order
based barrier height (UFF [17]):
UFF torsion with atom type-based barrier height (UFF [16]):
UFF torsion with atom type based barrier height (UFF [16]) (differs
from
Dreiding special torsion for compatibility with If there are three atoms bonded to the third center and the fourth center is H, it is removed. If there are three atoms bonded to the third center, and at least one of them is H, but the fourth center is not H, then these values are used: *V*=4.0,*PO*=0.0,*Period*=3.0, and*NPaths*=-1.0.Otherwise, these values are used: *V*=1.0,*PO*=0.0,*Period*=6.0, and*NPaths*=-1.0.
Improper torsion (Amber
[1]):
Three term Wilson angle (Dreiding [28c], UFF [19]):
Harmonic Wilson angle (MMFF94 [6]): (
Stretch-bend I (MMFF94 [5]): (
## USING SUBSTRUCTURESSubstructures may be used to define
different parameter values for a function for distinct ranges of some geometrical
characteristic. Substructure numbers are appended to the function name, separated
by a hyphen (e.g., The following substructures apply to functions related to bond stretches: -1 Single bond: 0.00 ≤ *bond order*< 1.50-2 Double bond: 1.50 ≤ *bond order*< 2.50-3 Triple bond: *bond order*≥ 2.50
The following substructures apply to functions for bond angles (values in degrees):
-1 0 ≤ θ ≤ 45 -2 45 < θ ≤ 135 -3 135 < θ ≤ 180
- *i-n*Number of atoms bonded to the central one.
For dihedral angles, one or
two substructures may be used (e.g.,
-0 Skip this substructure (substructure "wildcard") -1 Single central bond: 0.00 ≤ *bond order*< 1.50-2 Double central bond: 1.50 ≤ *bond order*< 2.50-3 Triple central bond: *bond order*≥ 2.50
- *i*-1 Resonance central bond (1.30 ≤*bond order*≤ 1.70)- *i*-2 Amide central bond (priority over resonance)- *i*-3 None of the above
Here is some simple MM force field definition input: HrmStr1 H_ C_2 360.0 1.08 HrmStr1-1 C_2 C_2 350.0 1.50 HrmStr1-2 C_2 C_2 500.0 1.40 HrmBnd2 * C_2 * 50.0 120.0 DreiTrs-1 * C_2 C_2 * 5.0 180.0 2.0 -1.0 DreiTrs-2 * C_2 C_2 * 45.0 180.0 2.0 -1.0 |