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Syntax

PARAmeter {$<$parameter-statement$>$ } END is invoked from the main level of X-PLOR.
$<$parameter-statement$>$:==
ANGLe
$<$type$>$ $<$type$>$ $<$type$>$ $<$real$>$ $<$real$>$ [UB $<$real$>$ $<$real$>$] adds a bond angle parameter set for the three atom types to the parameter database. The first real specifies $k_{\phi}$, which has units of kcal mole$^{-1}$ rad$^{-2}$, and the second real specifies $\theta _0$, the equilibrium angle, which has units of degrees (Eq. 4.5). The optional UB specification activates the Urey-Bradley term (Eq. 4.5), where the first real is the Urey-Bradley energy constant $k_{ub}$ and the second real is the Urey-Bradley equilibrium distance $r_{ub}$ between the first and the third atom that define the angle. If UB is not specified, the Urey-Bradley equilibrium distance and energy constant default to zero. The program automatically performs an interchange of the first with the third atom types where this is required.

ANGLe
$<$selection$>$ $<$selection$>$ $<$selection$>$ $<$real$>$ $<$real$>$ [UB $<$real$>$ $<$real$>$] is an atom-based version of the ANGLe statement that specifies the bond angle parameters to be used for any angles in the molecular structure that match the given triple atom selection. It can apply to more than one angle, depending on the number of angles that match the triple atom selection. The definition of the reals is identical to the type-based angle statement. The energy and equilibrium constants can be set to the string TOKEn, which implies that the corresponding parameter will be untouched by this statement.

BOND
$<$type$>$ $<$type$>$ $<$real$>$ $<$real$>$ adds a covalent bond parameter set for the two atom types to the parameter database. The first real specifies $k_b$, which is the energy constant in units of kcal mole$^{-1}$ Å$^{-2}$, and the second real specifies $r{_0}$, which is the equilibrium bond length in Å (Eq. 4.4). The program automatically performs an interchange of the two atom types where this is required.

BOND
$<$selection$>$ $<$selection$>$ $<$real$>$ $<$real$>$ is an atom-based version of the BOND statement. The definition of the reals is identical to the type-based bond statement. It can apply to more than one bond, depending on the number of bonds that match the double atom selection. The energy and equilibrium constants can be set to the string TOKEn, which implies that the corresponding parameter will be untouched by this statement.

DIHEdral
$<$type$>$ $<$type$>$ $<$type$>$ $<$type$>$ [MULT $<$integer$>$] {$<$real$>$ $<$integer$>$ $<$real$>$ } adds a dihedral angle parameter set for the four atom types to the parameter database (see also Eq. 4.6). The MULT option specifies the multiplicity $m$ of the dihedral angle (default: m=1). For multiple dihedrals of multiplicity $m$, there are $m$ groups of $3$ items following the MULT $<$integer$>$ statement. The first real of each group specifies $k_{\theta}$, the integer is the periodicity $n$, and the second real specifies $\delta$, the phase-shift angle, which has units of degrees. If the periodicity $n$ is greater than 0, $k$ has the units of kcal mole$^{-1}$; if the periodicity is 0, $k$ has the units of kcal mol$^{-1}$ rad$^{-2}$ (Eq. 4.6). The special character X is reserved for the following combination: X $<$type$>$ $<$type$>$ X; it acts as a wildcard. The parameter retrieval for a specified dihedral angle proceeds in the following way: first, a match without wildcards is attempted, and second, a match against dihedral parameters containing wildcards is attempted. Some instances (such as sugars) require the mixing of multiple dihedral angle terms with different periodicities. In this case, dihedral statements with the multiple option should be given in the parameter statement and in the topology statement (Section 3.1.1). Wildcards are not allowed for multiple dihedral angles. The program automatically performs the interchange (a b c d) $\rightarrow$ (d c b a) where this is required.

DIHEdral
$<$selection$>$ $<$selection$>$ $<$selection$>$ $<$selection$>$
[MULT $<$integer$>$] { $<$real$>$ $<$integer$>$ $<$real$>$ } is an atom-based version of the DIHEdral statement. The definition of the real and integer numbers is identical to the DIHEdral definition (see also Eq. 4.6). For multiple dihedrals of multiplicity $m$, there are $3m$ items following the MULT $<$integer$>$ statement (i.e., $m$ sets of one energy constant, one periodicity, and one offset). The statement can apply to more than one dihedral angle, depending on the number of bonds that match the quadruple atom selection. An atom-based statement takes priority over any type-based parameter that may have been specified earlier. The energy constants, periodicities, and offsets can be set to the string TOKEn, which implies that the corresponding constant will be untouched by this statement.

HBONded
$<$*type*$>$ $<$*type*$>$ $<$real$>$ $<$real$>$ adds an explicit hydrogen-bonding parameter set for the specified pair of atom types to the parameter database. The first atom type refers to donor (heavy) atoms, whereas the second one refers to the acceptor atoms. Wildcards are allowed for both donor and acceptor atom types. The first real is the well depth $\frac{-B^2}{4A}$ and the second is the distance $\root 6 \of {\frac{2A}{B}}$ (Eq. 4.25).
HBONDS
{ $<$hbonds-statement$>$ } END specifies global hydrogen-bond parameters for the explicit hydrogen-bond energy term (see Eq. 4.25).
IMPRoper
$<$type$>$ $<$type$>$ $<$type$>$ $<$type$>$ [MULT $<$integer$>$] {$<$real$>$ $<$integer$>$ $<$real$>$ } adds an improper angle parameter set for the four atom types to the parameter database. The definition is identical to the DIHEdral definition (see also Eq. 4.6), except for wildcards. The wildcard cascading for improper angles is as follows: (a b c d) $\rightarrow$ (a X X d) $\rightarrow$ (X b c d) $\rightarrow$ (X b c X) $\rightarrow$ (X X c d). The program automatically performs the interchange (a b c d) $\rightarrow$ (d c b a) where this is required.

IMPRoper
$<$selection$>$ $<$selection$>$ $<$selection$>$ $<$selection$>$
[MULT $<$integer$>$] { $<$real$>$ $<$integer$>$ $<$real$>$ } is an atom-based version of the IMPRoper statement. The definition of the real and integer numbers is identical to the DIHEdral definition (see also Eq. 4.6). The statement can apply to more than one improper angle, depending on the number of bonds that match the quadruple atom selection. The energy constants, periodicities, and offsets can be set to the string TOKEn, which implies that the corresponding constant will be untouched by this statement.

LEARn $<$learn-statement$>$ END
learns atom-based parameters from one or more sets of Cartesian coordinates (see Section 3.4).

NBFIx
$<$type$>$ $<$type$>$ $<$real$>$ $<$real$>$ $<$real$>$ $<$real$>$ adds a Lennard-Jones parameter set for the specified pair of atom types to the parameter database. The first two real numbers are the A, B coefficients (Eqs. 4.12 and 4.13) for all nonbonded interactions except the special 1-4 interactions; the second pair of reals is for the 1-4 (NBXMod=$\pm$5) nonbonded interactions. Appropriate NONB statements have to be specified for both atom types before invoking this statement. The NBFIx statement allows one to deviate from the standard combination rule for the Lennard-Jones potential (Eq. 4.14).
NBFIx
$<$selection$>$ $<$selection$>$ $<$real$>$ $<$real$>$ $<$real$>$ $<$real$>$ is an atom-based version of the NBFIx statement that adds a Lennard-Jones parameter set for the selected pairs of atoms to the atom-based parameters. The definition of the reals is identical to the type-based NBFIx statement. Appropriate atom-based NONB statements have to be specified for both atom selections before invoking this statement, e.g., 

NONB ( chemical C* )  0.12  3.74     0.12  3.74
NONB ( chemical N* )  0.24  2.85     0.24  2.85
NBFIx ( chemical C* ) ( chemical N* )  10. 1000. 10. 1000.
Note that the TOKEn keyword is not allowed for the reals.
NBONds { $<$nbonds-statement$>$ } END
applies to both electrostatic and van der Waals energy calculations. It sets up global parameters for the nonbonded interaction list generation and determines the form of subsequent nonbonded energy calculations (see Eq. 4.8).
NONB
$<$type$>$ $<$real$>$ $<$real$>$ $<$real$>$ $<$real$>$ adds a Lennard-Jones parameter set for pairs of atoms of the same specified type to the parameter database. The first pair of reals is $\epsilon$,$\sigma$ (Eq. 4.8) for all nonbonded interactions except the special 1-4 interactions; the second pair is $\epsilon$,$\sigma$ for the 1-4 nonbonded interactions (NBXMod=$\pm$5).
NONB
$<$selection$>$ $<$real$>$ $<$real$>$ $<$real$>$ $<$real$>$ is an atom-based version of the NONB statement that adds a Lennard-Jones parameter set for the selected atoms to the atom-based parameters. The definition of the reals is identical to the type-based NONB statement. Note that the TOKEn keyword is not allowed for the reals.
REDUce { $<$reduce-statement$>$ } END
derives type-based parameters from existing atom-based parameters (see Section 3.5).

RESEt
[ ALL $\vert$ TYPE $\vert$ ATOM ] erases all information about type- and atom-based parameters. The optional specification of ALL erases both databases, TYPE erases just the type base, and ATOM erases just the atom base (default: ALL).
VDWOff
$<$type$>$ turn off all REPEl interactions with atoms of this type. $<$type$>$ must already be defined by a NONB statement.
VERBose
produces a verbose listing of all atom-based parameters.

$<$nbonds-statement$>$:==
CDIE$\vert$RDIE
specifies exclusive flags: constant dielectric (Coulomb's law) or $1/r$-dependent dielectric (Eq. 4.16). RDIE may only be used in combination with VSWItch, SWITch, and REPEl=0. CDIE may be used in combination with VSWItch, SHIFt, and REPEl=0 or in combination with TRUNcation and REPEl=0 (default: CDIE).
CTOFNB=$<$real$>$
specifies the distance $r_{off}$ at which the switching function or shifting function forces the nonbonded energy to zero (Eqs. 4.8, 4.16) (default: 7.5 Å).
CTONNB=$<$real$>$
specifies the distance $r_{on}$ at which the switching function becomes effective (Eq. 4.8) (default: 6.5 Å).
CUTNb=$<$real$>$
specifies the nonbonded interaction cutoff $r_{cut}$ for the nonbonded list generation (default: 8.5 Å).
E14Fac=$<$real$>$
specifies the factor $e_{14}$ for the special 1-4 electrostatic interactions (Eq. 4.17) (default: 1.0).
EPS=$<$real$>$
specifies the dielectric constant $\epsilon$ (Eq. 4.16) (default: 1.0).
GROUp $\vert$ ATOM
specifies exclusive flags: group by group or atom by atom cutoff for nonbonded list generation (default: ATOM).
INHIbit=$<$real$>$
specifies the distance $d_{inhibit}$ (Eq. 4.7) between two atoms below which the van der Waals potential (Eq. 4.8) is truncated (default: 0.25 Å).
IREXponent=$<$integer$>$
specifies the exponent $irexp$ for the repel function (Eq. 4.8) (default: 2).
NBXMod= $+1\vert-1\vert+2\vert-2\vert+3\vert-3\vert+4\vert-4\vert+5\vert-5$
Exclusion list options:
$+-$1
no nonbonded exclusions, that is, all nonbonded interactions are computed regardless of covalent bonds.
$+-$2
excludes nonbonded interactions between bonded atoms.
$+-$3
excludes nonbonded interactions between bonded atoms and atoms that are bonded to a common third atom.
$+-$4
excludes nonbonded interactions between bonded atoms, atoms that are bonded to a common third atom, and or atoms that are connected to each other through three bonds.
$+-$5
same as (+-3), but the 1-4 nonbonded interactions are computed using the 1-4 Lennard-Jones parameters and the electrostatic scale factor $e_{14}$ (Eqs. 4.17 and 4.18).
A positive mode value causes explicit nonbonded exclusions (see exclusion statement, Section 3.1.1) to be taken into account; a negative value causes them to be discarded (default: 5).
RCONst=$<$real$>$
specifies the energy constant $C_{rep}$ for the repel function (Eq. 4.8) (default: 100.0).
REPEl=$<$real$>$
specifies $k_{rep}$: if $>$ 0, this option turns on the repel function (Eq. 4.8) and turns off the electrostatic energy. $k_{rep}$ specifies the factor by which to multiply the van der Waals radius $R_{min}$ (default: 0).
REXPonent=$<$integer$>$
specifies the exponent $rexp$ for the repel function (Eq. 4.8) (default: 2).
SWItch$\vert$SHIFt
specifies exclusive flags: electrostatic switching or shifting. SWITch may only be used in combination with RDIE, VSWItch, and REPEl=0. SHIFt may only be used in combination with CDIE, VSWItch, and REPEl=0 (default: SHIFt).
TOLErance=$<$real$>$
specifies the distance that any atom is allowed to move before the nonbonded list gets updated. Note: if switching or shifting functions are used, the program expects ${\rm CUTNB} \geq {\rm CTOFNB} +2 {\rm TOLErance}$. In this way the nonbonded energy is independent of the update frequency. For the REPEl option, CUTNB and TOLErance should be chosen such that ${\rm CUTNB} \geq r_{\rm max} +2 {\rm TOLErance}$, where $r_{\rm max}$ is the maximum van der Waals radius. TOLErance has no influence on the TRUNcation option. (default: 0.5 Å).
TRUNcation
turns off switching or shifting; i.e., the nonbonded energy functions are “truncated" at CUTNb regardless of the values of CTONNB and CTOFNB. All nonbonded energy terms that are included in the current nonbonded list are computed. May only be used in combination with CDIE. Note: in general, the nonbonded energy will not be conserved before and after nonbonded list updates when using TRUNcation. (default: inactive).
VSWItch
turns on van der Waals switching. May only be used in combination with RDIE, SWITch, and REPEl=0 or in combination with CDIE, SHIFt, and REPEl=0 (default: active).
WMIN=$<$real$>$
specifies the threshold distance for close contact warnings, i.e., a warning is issued when a pair of atoms gets closer than this distance unless the nonbonded interaction is excluded by the NBXMod option (default: 1.5 Å).
$<$hbonds-statement$>$:==
AAEX=$<$real$>$
specifies the exponential for the angle term between the hydrogen, acceptor and acceptor antecedent atoms $n$ (Eq. 4.25) (default: 2).
ACCEptor=$<$logical$>$
is a flag indicating whether to include the acceptor antecedent angular term in Eq. 4.25 (default: TRUE).
ACUT=$<$real$>$
specifies the angular cutoff for the angle between acceptor, hydrogen and donor atoms $\theta_{A-H-D}$ (Eq. 4.25). $0^{\circ}$ corresponds to a linear hydrogen bond (default: $100^{\circ}$).
AEXP=$<$real$>$
specifies the attractive exponential $b$ (Eq. 4.25) (default: 4).
AON=$<$real$>$
specifies $\theta_{h_{on}}$, a switching function parameter for the hydrogen bond angle (Eq. 4.25) (default: $60.0^{\circ}$).
AOFF=$<$real$>$
specifies $\theta_{h_{off}}$, a switching function parameter for the hydrogen bond angle (Eq. 4.25) (default: $80.0^{\circ}$).
DCUT=$<$real$>$
specifies $r_{AD}$, the heavy atom donor to heavy atom acceptor cutoff (Eq. 4.25) (default: 7.5).
DOFF=$<$real$>$
specifies $r_{h_{off}}$, a switching function parameter for the hydrogen bond distance (Eq. 4.25) (default: 6.5).
DON=$<$real$>$
specifies $r_{h_{on}}$, a switching function parameter for the hydrogen bond distance (Eq. 4.25) (default: 5.5).
HAEX=$<$real$>$
specifies the exponential for the angle term between the donor, hydrogen, and acceptor atoms, $m$ (Eq. 4.25) (default: 4).
PRINt=$<$logical$>$
control printing of hydrogen bond neighbor information whenever the neighbor list is updated (default: TRUE).
REXP=$<$real$>$
specifies the repulsive exponential $a$ (Eq. 4.25) (default: 6).
TOLErance=$<$real$>$
specifies how far atoms are allowed to move before the hydrogen-bond list gets updated. Note: the program expects ${\rm DCUT} \geq {\rm DOFF} +2 {\rm TOLErance}$. In this way the hydrogen-bonded energy is independent of the update frequency (default: 0.5).

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Xplor-NIH 2025-03-21