|
The Hand
energy is a component of an elastic network and each term consists of
the torsion angle formed by the atoms i, j, k and l,
Et-ijkl is:
Et-ijkl
= Kt-ijkl[ Tijkl
- To-ijkl ]2
where T
is the torsion angle formed by the ordered atoms i, j, k
and l, Kt is the force constant and T0
is the equilibrium angle. The last is specified individually for each
term.
The Hand record must appear only after
the Atom Inclusion Types have been defined. This record must
also appear after the Atom Inclusion Group record if Groups
are used in this record. The Hand
record has the following format:
|
:HAND
|
|
:Typei:Typej:Typek:Typel:
|
Kt-ijkl
|
|
:Typei:Typej:Typek:Typel:
|
Kt-ijkl
|
|
...
|
...
|
|
:END
|
The
opening and closing keywords, like all keywords, begin with a colon and
start on column one of their respective lines. The body of the data
section may contain any number of lines. A line may be empty or may
contain a list of four Atom Inclusion Type or Group
names followed by one number. The names are written amongst five
colons; the colons are not part of the names. The first number is the
force constant in units of kcal/mol/radian2. (Equilibrium
torsion angles are not specified here; each Hand interaction is assigned an
individual angle.) Following the number may be text to serve as
comment. The comment must be separated, by white space, from the number.
An Hand
type defined for Inclusion Atom Types :A:B:C:D: will serve
equally well for an Hand of Types :D:C:B:A:. Only the first
instance of a definition of an Hand type will be saved. Subsequent
definitions for the same Hand torsion type will be silently ignored.
Therefore, definitions using Groups should be placed at the end
of the list so that the generic definitions do not override the
specific definitions.
The
program Yup.fpf will expand Groups
into their component Types, hash each quartet of Types
into a numerical code, and sort the codes. This forms the index table.
The force constants are converted to internal units used by YUP and with the equilibrium
torsion angle these numbers form the data table. The index and data
tables are written to the unformatted file: "Hand
Constants".
|