Molecular Mechanics FAQs
Author: Phil Klunzinger
- What does the energy mean in
molecular mechanics and
can I compare it to other methods?
The energy reported in mechanics is a "strain energy". The
functional form can be found in
J. Comp. Chem., (17) 1996, 490-641,
but can be summarized as the strain in each bond, angle, and
torsion, as well as the energy of non-bonded terms. It is
important to note that this energy is relative to an
unstrained version of the molecule being examined.
Thus this energy cannot be compared with energy of other
molecules. Even comparing energies of structural molecules
is not appropriate with molecular mechanics. What molecular
mechanics is good at
is getting structures and conformational energy. More
discussion on the appropriate use of Energies can be found
A Guide to Molecular
Mechanics and Quantum Chemical Calculations.
A quick summary of this guide can be found in
Selecting a Theoretical
model & Calculation Times, as well as the
Quantum Mechanics Energy
Questions FAQ document.
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- How can I specify charge in molecular mechanics?
At times the MMFF atom-typing algorithms cannot
correctly type an atom. For example, an Iron ion
with no bonds can be either Fe+2 or Fe+3.
The FFHINT keyword is a way to bypass the
atom-typing. The general format is:
for example: FFHINT=FE1~~+3
| 'name'|| is the label of the atom to change,
for example 'Fe1' or 'Fe2'.|
Characters are case insensitive, and if the last
character of name is an asterisk (*) then name is
treated as a wildcard. i.e. 'Fe*' matches 'Fe1', 'FE3',
'fe', and 'fe123'.
|'~~' || are two tildes in a row|
| 'hint'|| can be: |
- a type name, for example Fe+3
- a type number, for example 88 for Fe+3.
- a charge, for example +2, -1, +,-
(the charge must be in the type name).
This charge will attempt to be enforced either via
the type name or by setting the partial charge.
- a fractional charge, for example -2/3, +1/5.
The denominator must be commensurate with 360.
(i.e. 360/n is an integer given a fraction m/n.)
Using the fractional hints can lead to very bad
force-fields if not used correctly so user beware.
- The special "positive zero" charge +0 is used to
indicate a radical.
- An "X" atom type hint can be given.
- x2 : linear
- x3 : planar
- x4 : tetrahedral
- x5 : trigonal pyramidal (or subset)
- x6 : octahedral (or subset)
- x50 : D0
Use PRINTLEV=4 or greater for more information on
how specific hints are used internally.
Note that these are "hints" and may be ignored.
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- How are the ligand points used in mechanics?
In Spartan, ligand points are used in the graphical user
interface to represent multi-center ligand bonds. For example
the "eta-5" of the cyclopentadiene anion metal bond found in
metallocenes. It is
important to note that while the "Ligand Point" is important
in mechanics, it is not used in any of the ab initio
- Ligand points:
- The default ligand pt. is type -1 (for use in params.MERCK)
and is defined as the center of ligand atoms
- If the ligand point is not used in any constraint it is,
by definition, the center of its defining points.
- If the ligand point is used in a torsion or length constraint
the ligand is constrained to the center using a quadratic
- eta bonds connecting the defining ligand atoms (ie:
Ti--C in TiCp2) have not stretch-bend component.
- torsion angle force constant cannot use a ligand point
- Angle terms of the form a-M-Lig or Lig-M-Lig may be used
- eta bonds have a bond type (see params.MERCK) of
'-n' where is the order of the bond. A default/fallback
of -1 is used in bond lookup.
- no bond angle or bond torsion force constants use the eta bond.
- Note: Ligand points are an extension to the Merck Force-field.
- Central atoms of high coordinate metals can be a D0 type.
- no torsion contain type 50 in internal (j,k),
- no a-D0-b bond angle, instead 1-4 VdW interactions are
applied to a-b.
- Note: Metals are an extension to the MMFF94 Force field.
- summary example: Cp-M-Cl
- The Cp-M-Cl bond angle can be set (default for type 50: not set).
- The Cp-M distance is controlled by Carbon-M,eta-5 bonds.
A Cp-M bond can be set in the param file
- The ligand is placed in the center of the Cp by a hookian spring.
- All other bond angles which include the ligand point or the new
Carbon-M eta bonds are turned off.
- All torsions contain the Carbon-M bond are turned off.
- All torsions (i,j,k,l) with the ligand point at j or k are turned
- The special case the torsion of eta-2 bonds is not yet
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- What is the minimization algorithm used in mechanics?
The minimization method in mechanics is a "Truncated Newton
Method" using a preconditioned conjugated Gradient (PCG)
algorithm with an exact, sparse, hessian. In the general spirit
of TNPACK Tamar Schlick & Aaron Fogelson in "ACM Transactions on
Mathematical Software, Vol. 18, No. 1 March 1992."
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Last modified: Wed Mar 15 16:04:46 GMT 2017