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Mechanics FAQs

  • What does the energy mean in 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 which is being examined. Thus this energy cannot be compared with energy of other molecules. Even comparing energies of structural molecules is not appropriate with mechanics. What mechanics is good at is getting structures and conformational energy. More discussion on the appropriate use of Energies can be found in the 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 list.

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  • How can I specify charge in 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 asterick (*) 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:
    1. a type name, for example Fe+3
    2. a type number, for example 88 for Fe+3.
    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.
    4. 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.
    5. The special "positive zero" charge +0 is used to indicate a radical.
    6. 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 methods.

    • 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 force.
      • 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 Forcefield.
    • 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 off.
      • The special case the torsion of eta-2 bonds is not yet implemented.

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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 & Aarom Foglson in "ACM Transactions on Mathematical Software, Vol. 18, No. 1 March 1992."

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Last modified: Thu Jun 20 10:47:57 PDT 2013