|
The
energy of the distance NOE term between atoms
i and j, Enoe-ij is
given by:
|
Enoe-ij
=
|
KL[
dL -
rij
]m
|
if
rij <
dL
|
|
0
|
if
dL <=
rij <=
dH
|
|
KH[
rij -
dH
]n
|
if
rij >
rij
|
where
rij is the distance between atoms
i and j, KL and
KH are force constants,
dL and dH are
contact distances and m and n are exponents. This
function is that of a flat-bottomed well, and the
floor is between dL and
dH. Below the inner contact
distance, the function rises with a power of m.
Above the outer contact distance, the function
rises with the power of n.
The
Noen 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 Noen record has the following
format:
|
:NOEN
|
|
|
:Typei:Typej:
|
KL
|
dL
|
KH
|
dH
|
|
|
:Typei:Typej:
|
KL
|
dL
|
KH
|
dH
|
|
|
...
|
...
|
...
|
...
|
...
|
|
: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 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 and third numbers are the force constants in
units of kcal/mol/Å2. The second
and last numbers are the contact distances in
Å. Following the fourth number may be text to
serve as comment. The comment must be separated, by
white space, from the last number.
A
distance NOE type defined for Inclusion Atom
Types :A:B: will serve equally well for a NOE
of Types :B:A:. Only the first instance of a
definition of a NOE type will be saved. Subsequent
definitions for the same NOE 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:
"Noen
Constants".
Note
that m and n are set with the Noens Energy
object.
There
are virtually no restrictions on the data. The only
requirement is that dL is not
equal to or larger than dH.
Otherwise, if a contact distance is negative, then
that barrier will never come into play.
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