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The
energy of the bond between atoms i and
j, Eb-ij is given
by:
Eb-ij
= Kb-ij[
bij -
bo-ij
]2
where
b is the distance between atoms i and
j, Kb is the force
constant and b0 is the
equilibrium length of the bond.
The
Bond 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 Bond record has the following
format:
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:BOND
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|
|
:Typei:Typej:
|
Kb-ij
|
b0-ij
|
|
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:Typei:Typej:
|
Kb-ij
|
b0-ij
|
|
|
...
|
...
|
...
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:END
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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 two Atom Inclusion
Type or Group names followed by two
numbers. The names are written between pairs of
colons; the colons are not part of the names. The
first number is the force constant in units of
kcal/mol/Å2. The second number is
the equilibrium bond length in Å. Following
the second number may be text to serve as comment.
The comment must be separated, by white space, from
the second number.
A
bond type defined for Inclusion Atom Types
:A:B: will serve equally well for a bond of
Types :B:A:. Only the first instance of a
definition of a bond type will be saved. Subsequent
definitions for the same bond type will be silently
ignored. Therefore, definitions using Groups
should be placed at the end of the list so that the
generic defintions do not override the specific
definitions.
The
program Yup.fpf
will expand Groups into their component
Types, hash each pair 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 length these numbers form
the data table. The index and data tables are
written to the unformatted file:
"Bond
Constants".
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