General parameters file

The general_db file ($ADFHOME/atomicdata/UFF/general_db) contains all the parameters used to calculate the forces and energies. The format is:

MMAtomType, ri, phi, xi, di, psi, zmm, vsp3, vsp2, chi, nc.

The items in the list are:

  • MMAtomType: name, max 5 characters
  • ri: Valence Bond [Å]
  • phi: Valence Angle [Degree]
  • xi: Nonbond Distance [Å]
  • di: Nonbond Energy [kcal/mol]
  • psi: Nonbond scale [Number]
  • zmm: Effective Charge [Charge]
  • vsp3: sp3 Torsional Barrier [kcal/mol]
  • vsp2: sp2 Torsional Barrier [kcal/mol]
  • chi: Electronegativity
  • nc: Number of directly attached atoms, aka coordination number. This is required for counting the number of possible dihedrals, and is defined only for the sp2 and sp3 centers (types 2, R, and 3)

The current set of parameters comes from the deMonNano program, and is a combination of published parameters and fitted data to fill in the gaps. The deMonNano documentation says the following about the parameters:

Implementation of the Universal Force Field (UFF) in deMonNano

As far as possible, UFF molecular mechanics forcefield in deMon
follows the published forcefield definition in [1]. In several
cases, the definitions and expressions in [1] are not consistent
with the published applications of the forcefield [1,5,6].
In those cases, an attept was made to correct the errors and omissions,
using information from [2].

The following changed were made, compared to the published UFF
forcefield description (all equation and page numbers refer to [1]).

1. Sign error in Eq. 2 (equilibrium bond length) was corrected
   - electronegativity correction must be negative!

2. Equilibrium valence angle for O_3_z was corrected from 146.0
   degree to 145.45 degree.

3. Bending periodicity (Eq. 10) for linear coordination was
   corrected from 1 to 2.

4. Sign errors were corrected in eqs. 13 and and unnumbered equation
   for the beta parameter (between eqs. 13 and 14).

5. The reference value of the UFF amide force constant, of 105.5
   kcal/mol/rad**2 (p. 10028) is wrong. The results are consistent
   with the force constant of 211.0 kcal/mol/rad**2.

6. Equilibrium torsional angle for a bond between a group-6A atom
   (oxygen ...) and an sp2 atom (90 degree) is wrong (p. 10028).
   It should be 0 degree.

7. The conditional for the special-case sp2-sp3 torsion (p. 10029)
   is wrong, and should be inverted - see [4].

8. The overall shape of the UFF torsional potential degenerates to
   a Heavyside function when one of the bond angles becomes linear,
   leading to failures in geometry optimization and force constant
   evaluation. The UFF torsional term was augmented with a smooth
   masking function, to avoid this. See "uff_4centre.f90" for

9. UFF inversion potential is not defined in [1] for group 5A
   elements (from phosphorus down). Taking the equilibrium inversion
   coordinate of 87 degree, and the suitable expressions for the
   cosine weights (see uff_get_inversion_shape in "uff_database.f90")
   appears to reproduce published UFF structures and energetics.

The following atom types have been fully tested, and are believed
to reproduce published UFF forcefield results exactly. The examples
refer to the $deMon/examples/ directory.

  Atom type  Example     Description
  ---------  -------     -----------

    Al3      alme3tma    Trivalent aluminum
    As3+3    asf3        Trivalent arsenic
    B_2      bcl3        Planar (sp2) boron
    B_3      b2h5nme2    Tetrahedral (sp2) boron, including
                         charge transfer adducts and borohydrates
    Br       bbr3        Univalent bromine
    C_1      c2h2, co    Linear (sp) carbon
    C_2      acetone     Planar tricoordinated (sp2) carbon
    C_3      c2h6        Tetrahedral (sp3) carbon
    C_R      c4h6        Resonant, variable bond order (sp2) carbon.
    Cl       socl2       Univalent chlorine
    F_       sof2ncl     Univalent fluorine
    Ge3      geh3ogeh3   Tetrahedral (sp3) germanium
    H_       h2o         Normal, non-bridging hydrogen
    H_b      b2h5nme2    Bridging hydrogen, for use in boranes
                         (NOT SUITABLE FOR H-BONDS!)
    I_       bi3         Univalent iodine
    N_1      ch3cn       Monocoordinated (sp) nitrogen, triple bond
    N_2      ch3n2ch3    Dicoordinated (sp2) nitrogen, single-double bond
    N_3      ch3nh2      Amine (sp3) nitrogen, three single bonds
    N_3+4    b2h5nme2    Charged amine (sp3) nitrogen, four single bonds
                         (THIS IS NOT A STANDARD UFF TYPE!)
    N_R      c5h5n       Resonant planar (sp2) nitrogen, for use in
                         aromatics and amides. For amides, use 1.41 bond
    O_1      co          Special "co" type, one triple bond.
    O_2      acetone     One-coordinated (sp2) oxygen, one double bond.
    O_3      h2o         Two-coordinated (sp3) oxygen, two single bonds
    O_3_z    sih3osih3   Special two-coordinated oxygen, for use in
                         Si-O bonds
    O_R      c4h4o       Resonant planar (sp2) oxygen, also for use in
                         nitro groups and such.
    P_3+3    ph3         Pyramidal (sp3) phosphorus, three single bonds
    P_3+5    p4o7        Tetrahedral hypervalent phosphorus
    P_3+q    bh3ph3      Dative tetrahedral (sp3) phosphorus, watch for
                         the bond order!
    S_3+2    ch3sch3     Bent two-coordinated sulfur (sp3), two single bonds
    S_3+4    socl2       Pyramidal three-coordinated hypervalent sulfur
    S_3+6    so2cl2      Tetrahedral four-coordinated hypervalent sulfur
    Se3+2    h2se        Bent two-coordinated (sp3) selenium
    Si3      si4o4h8     Tetrahedral silicon

Additionally, parameter sets for the following atom types are believed
be complete, and may be expected produce results identical to the published
UFF data: Li, Na, K_, Rb, Cs (Note that UFF does not specify atomic charges
- it is your responsibility to assign those, if charges are needed!)

For the remaining atom types, UFF definition [1] relies on an unpublished
set of electronegativities [2]. In deMon, these values were replaced by
Pauling electronegativities, scaled to fit published UFF electronegativities.
This can be expected to produce small deviations in bond lengths and bond
angles, compared to published UFF results.

If you wish to use other parameters, you should copy the general_db file, and rename it. This new file can also be placed outside of $ADFHOME/atomicdata/UFF. To use this new parameter file in UFF, specify the following keyword in your input:

    database /path/to/the/new/file/mygeneral_db