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ANGLe=logical DIHEdral=logical END
works only on regular residues,
not on patched ones. It automatically
generates all possible bond angles based on the connectivity list of the
particular residue. It operates on the residues following the statement
until the
next autogenerate statement appears.
MASS=type=real
adds a default mass assignment for the specified type of
atom to the topology database.
The real number is defined in atomic mass units.
This value will be used by default for all atoms of that type unless an
explicit MASS statement is given in the atom statement (see below).
RESEt
erases all previous entries into the topology database.
RESIdue
residue-name { residue-statement } END
adds a residue to the topology database.
PRESidue
residue-name
{ [ ADD DELEte MODIfy ]
residue-statement } END
adds a patch residue to the topology database.
residue-statement:==
ACCEptor
atom atom adds a hydrogen-bond acceptor
for the explicit hydrogen-bonding energy term or for purposes of analysis
to the residue database. The first atom is acceptor atom;
the second atom is antecedent atom and can be the string NONE.
ANGLe
atom atom atom
adds a bond angle made by
the three atoms to the residue database.
It should not be used if autogenerate angles
are active.
ATOM
[patch-character] atom atom-statement
END
adds an atom to the residue database.
The statement defines atom as a four-character string
specifying the name, and atom statement specifies atom type,
charge, and mass. The patch character is a 1-character string
and may be used only for PRESidue.
BOND
atom atom adds a covalent
bond between the specified atoms to the residue database. The
atoms have
to be
defined previously by atom statements. Parameters for
the bond are specified in Section 3.2.1;
Eq. 4.4 describes the bond energy.
DIHEdral
atom atom atom atom
[MULTiple integer] adds
a dihedral angle to the residue database. The dihedral angle (ijkl)
is defined
by the angle between the plane made by the atoms (ijk) and the plane
made by the atoms (jkl). The dihedral statement
should not be used if autogenerate dihedrals are
active, unless multiple dihedral angles are wanted. MULTiple
specifies dihedral angle entries for the same instance
of four atoms (Eq. 4.6).
This allows one to specify a cosine expansion for the dihedral
angle potential energy.
It must be accompanied by a corresponding DIHEdral angle parameter
entry with appropriate multiplicity. Parameters for
the dihedral angle are specified in Section 3.2.1;
Eq. 4.6 describes the dihedral energy.
DONOr
atom atom adds a hydrogen-bond donor for
the explicit hydrogen-bonding energy term or for purposes of analysis
to the residue database.
The first atom is hydrogen atom, and the second atom is heavy atom; the
first
atom may be the string NONE for extended atom force fields.
Parameters for
the explicit hydrogen bonds are specified in
Section 3.2.1;
Eq. 4.25 describes the hydrogen-bond energy.
GROUp
partitions the atoms into nonbonded groups
(see Section 4.3.3). In addition to use
for nonbonded interactions, grouping has an effect on atom order
for atoms added or modified in PATCh statements (Section 3.8).
IMPRoper
atom atom atom atom
[MULTiple integer] adds
an improper angle to the residue database. The
definition is identical to the DIHEdral angle,
but it uses a different set of parameters
(cf. Section 3.2.1). As in the case of the DIHEdral
angle,
the improper angle (ijkl) is defined by the angle between the plane made by
the atoms (ijk) and the plane made by the atoms (jkl).
MULTiple
specifies improper angle entries for the same
instance of four atoms (Eq. 4.6).
This allows one to specify a cosine expansion for the improper
angle potential energy.
It must be accompanied by a corresponding IMPRoper angle parameter
entry with appropriate multiplicity.
Parameters for
the improper angle are specified in Section 3.2.1;
Eq. 4.6 describes the improper energy.
atom:==
is the name of the atom; it is a four-character string.
atom-statement:==
CHARge=real
specifies an electrostatic charge in
units of
one electron charge. This affects the electrostatic
energy (Eq. 4.16).
EXCLude=( { atom } )
specifies
explicit nonbonded
interaction exclusions (see Section
4.3.3). The
atoms have to have been defined previously by an
atom statement.
MASS=real
overwrites a default given by
mass statement outside
residue statement, in atomic mass units.
TYPE=type
specifies the chemical atom type, a
string with up to four characters. The atom
type is used to retrieve
type-based parameters (see Section 3.2.1).