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Each
atom of a molecular model is assigned two mutually
exclusive Atom Types: Inclusion and
Exclusion. The Inclusion Atom Type is
used to index energy terms where interactions are
never implied. Only those that are named in an
Inclusion list are calculated and the
parameters that are to be used are based on the
Atom Inclusion Types of the participating
atoms. The data are listed in the appropriate
sections. Typically, data is available and provided
for only a small fraction of all combinations
because not all combinations of Atom Inclusion
Types will ever occur and some combinations do
not make chemical sense.
The
format of the Atom Inclusion Type record
is:
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:ATOM-INCLUSION-TYPE
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:Name1:
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:Name2:
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...
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:NameN-1:
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:NameN:
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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 name. The name is written between a
pair of colons; the colons are not part of the
name. Following the closing colon may be text to
serve as comment. The comment must be separated
from the name by white space, and may not contain
colons.
The
body of the section is usually indented. Not only
does it make the data stand out but the indentation
make it impossible to mistake a name for a
keyword.
An
Atom Inclusion Type name may be as short as
one character and as long as 127 characters. The
name may not include the following three
characters: ":",
"/",
"\".
A name may not be exactly
"^",
"+"
or "-"
but may contain these characters. Names are
case-sensitive. Note that a name may start with
space characters or may even contain only spaces;
such names are useable but may be confusing.
Atom Exclusion and Inclusion Types
are used in different arena so there is no problem
with using the same names for both types but that
may be confusing.
There
is no need to arrange the names in any particular
order. Yup.fpf
will sort this list alphabetically and write this
and the Atom Exclusion Type list to the
unformatted file: "Atom
Exclusion and Inclusion
Types".
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