一般参数文件

General_db文件($ adfhome / atomicdata / uff / general_db)包含用于计算力量和能量的所有参数。格式是:

MMatomType,RI,PHI,XI,DI,PSI,ZMM,VSP3,VSP2,CHI,NC。

列表中的项目是:

  • mmatomtype:名称,最多5个字符
  • RI:价键[Å]
  • PHI:价角度[度]
  • xi:非距离[Å]
  • DI:非键能[kcal / mol]
  • PSI:非否定规模[号码]
  • ZMM:有效充电[收费]
  • VSP3:SP3扭转屏障[kcal / mol]
  • VSP2:SP2扭转屏障[kcal / mol]
  • Chi:电信
  • NC:直接附加原子的数量,AKA协调号。计算可能的Dihedrals的数量是必需的,并且仅针对SP2和SP3中心(类型2,R和3)定义

目前的一组参数来自恶魔程序,是发布参数的组合和填充空隙的拟合数据。 Demonnano文档说明了关于参数的以下参数:

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
   details.

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/test.mm 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
                         order!
    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.

如果您希望使用其他参数,则应复制常规_db文件,并重命名。此新文件也可以放在$ ADFHOME / ATOMICDATA / UFF之外。要在UFF中使用此新参数文件,请在输入中指定以下关键字:

uff. 
    database /path/to/the/new/file/mygeneral_db
End