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The file ufftopology

The topology file ufftopology contains the blocks nxtnei12, nxtenei13, nxtnei14, connectivity, angle, torsion, inversion, nonbond and qpartial. It starts with $ufftopology and ends with $end. The first three blocks (nxtnei12, nxtnei13, nxtnei14) have the same form: they start with the atom number and the number of its neighbours, in the next line are the numbers of the neighbour atoms. Then the connectivity-block follows starting with the number of bond terms. Each line contains one bond term:

I        J        d        BO.    

Here are I and J the number of the atoms, d the distance in a.u. and BO is the bond order.

The angle terms follow, starting with the number of the angle terms. In each line is one angle term:

J        I        K        wtyp        θ        nrJI        nrIK.    

Here are J, I and K the atoms number, where atom I is in the apex. ``wtyp'' is the angle type and has the following values:
wtyp = 1
linear case
wtyp = 2
trigonal planar case
wtyp = 3
quadratic planar case
wtyp = 6
octahedral case
wtyp = 9
all other cases.
θ is the angle value in degree. nrJI and nrIK are the number of the bonds between J and I and the bond between I and K . The hybridization of atom I determines ``wtyp''.

Then the torsion terms follow, starting with the number of the torsion terms. Each line contains one torsion term:

I        J        K        L        nrJK        ttyp        φ        θIJK        θJKL.    

Here are I, J, K and L the atom numbers. nrJK is the number of the bond between J and K . ``ttyp'' is the torsion type:
ttyp = 1
J (sp3 )-K (sp3 )
ttyp = 11
like ttyp=1, but one or both atoms are in Group 16
ttyp = 2
J (sp2 )-K (sp3 ) or vice versa
ttyp = 21
like ttyp=2, but one or both atoms are in Group 16
ttyp = 22
like ttyp=2, but J or K is next a sp2 atom
ttyp = 3
J (sp2 )-K (sp2 )
ttyp = 9
all other cases.
φ is the value of the torsion angle in degree. θIJK is the angle value of (I - J - K ) and θJKL is the one for J - K - L . The hybridizations of J and K determine ``ttyp''.

The inversion terms follow starting with the number of inversion terms (e.g. the pyramidalisation of NH3 ). In each line is one inversion term:

I        J        K        L        ityp1        ityp2        ityp3        ω1        ω2        ω3.    

I, J, K and L are the atom numbers. Atom I is the central one. ityp1, ityp2, ityp3 are the types of the inversions:
ityp = 10
atom I is C and atom L is O
ityp = 11
like ityp=10, but L is any atom
ityp = 2
I is P
ityp = 3
I is As
ityp = 4
I is Sb
ityp = 5
I is Bi
ityp = 9
all other cases.
ω1, ω2 and ω3 are the values of the inversion angles in degree.

The nonbond terms follow starting with the number of the non-bonded terms. In each line is one nonbond term:

I        J        d .    

Here I and J are the atom numbers, d the distance in a.u. Then the partial charges follow.

If the determination of the molecule connectivity failed, you can specify the block nxtnei12 in the file ufftopology. Then the program calculates the other blocks.

Based on the numbers of the next neighbours (block nxtnei12 in the file ufftopology) the program tries to determine the UFF type of an atom. The following rules are implemented: If the atom has three next neighbours and it is in the nitrogen group, then it has a hybridization three. If it is not in the nitrogen group, it has hybridization two. If the atom has four next neighbours and it is in the carbon group, it has hybridization three. If it is not in the carbon group, it becomes hybridization four. If the number of next neighbours is six, then it gets the hybridization six.

Since the smallest eigenvalues λi of the Hessian has the greatest influence on the convergence of the geometry optimization, one can shift these values with

$\displaystyle \tilde{{\lambda}}_{i}^{}$ = λi$\displaystyle \left(\vphantom{ \alpha + \beta \cdot e^{-\gamma x} }\right.$α + βe-γx$\displaystyle \left.\vphantom{ \alpha + \beta \cdot e^{-\gamma x} }\right)$    

and calculates a new Hessian with these modified eigenvalues.


next up previous contents index
Next: Keywords for Modules Dscf Up: Keywords for Module Uff Previous: UFF Output Data Blocks   Contents   Index
TURBOMOLE M