Syntax

TOPOlogy { <topology-statement> } END

is invoked from the main level of X-PLOR.

<topology-statement>:==

AUTOgenerate

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 m 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).

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 m 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).

<type>:==

is any sequence of four characters.