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Potential Function Parameter

angle

Details
Type:         String
Definition:   [3 integers and 4 reals] Provides the values for a single bond angle bending parameter. The integer modifiers give the atom class numbers for the three kinds of atoms involved in the angle which is to be defined. The real number modifiers give the force constant value for the angle and up to three ideal bond angles in degrees. In most cases only one ideal bond angle is given, and that value is used for all occurrences of the specified bond angle. If all three ideal angles are given, the values apply when the central atom of the angle is attached to 0, 1 or 2 additional hydrogen atoms, respectively. This "hydrogen environment" option is provided to implement the corresponding feature of the AMOEBA force field.The default units for the force constant are kcal/mole/radian^2, but this can be controlled via the angleunit keyword.

anglep

Details
Type:         String
Definition:   [3 integers and 3 reals] Provides the values for a single projected in-plane bond angle bending parameter. The integer modifiers give the atom class numbers for the three kinds of atoms involved in the angle which is to be defined. The real number modifiers give the force constant value for the angle and up to two ideal bond angles in degrees. In most cases only one ideal bond angle is given, and that value is used for all occurrences of the specified bond angle. If all two ideal angles are given, the values apply when the central atom of the angle is attached to 0 or 1 additional hydrogen atoms, respectively. This "hydrogen environment" option is provided to implement the corresponding feature of the AMOEBA force field. The default units for the force constant are kcal/mole/radian^2, but this can be controlled via the angleunit keyword.

angtors

Details
Type:         String
Definition:   [4 integers and 6 reals] Provides the values for a single bond angle bending-torsional angle parameter. The integer modifiers give the atom class numbers for the four kinds of atoms involved in the torsion and its contained angles. The real number modifiers give the force constant values for both angles coupled with 1-, 2- and 3-fold torsional terms.The default units for the force constants are kcal/mole/radian, but this can be controlled via the angtorunit keyword.

atom

Details
Type:         String
Definition:   [2 integers, name, quoted string, integer, real and integer] Provides the values needed to define a single force field atom type. The first two integer modifiers denote the atom type and class numbers. If the type and class are identical, only a single integer value is required. The next modifier is a three-character atom name, followed by an 24-character or less atom description contained in single quotes. The next two modifiers are the atomic number and atomic mass. The final integer modifier is the "valence" of the atom, defined as the expected number of attached or bonded atoms.

biotype

Details
Type:         String
Definition:   [integer, name, quoted string and integer] Provides the values to define the correspondence between a single biopolymer atom type and its force field atom type.

bond

Details
Type:         String
Definition:   [2 integers and 2 reals] Provides the values for a single bond stretching parameter. The integer modifiers give the atom class numbers for the two kinds of atoms involved in the bond which is to be defined. The real number modifiers give the force constant value for the bond and the ideal bond length in Angstroms. The default value of 1.0 is used, if the bondunit keyword is not given in the force field parameter file or the keyfile.

charge

Details
Type:         String
Definition:   [1 integer and 1 real] Provides a value for a single atomic partial charge electrostatic parameter. The integer modifier, if positive, gives the atom type number for which the charge parameter is to be defined. Note that charge parameters are given for atom types, not atom classes. If the integer modifier is negative, then the parameter value to follow applies only to the individual atom whose atom number is the negative of the modifier. The real number modifier gives the values of the atomic partial charge in electrons.

forcefield

Details
Type:         String
Definition:   [name] Provides a name for the force field to be used in the current calculation. Its value is usually set in the master force field parameter file for the calculation (see the PARAMETERS keyword) instead of in the property file.

improper

Details
Type:         String
Definition:   [4 integers and 2 reals]Provides the values for a single CHARMM-style improper dihedral angle parameter. The integer modifiers give the atom class numbers for the four kinds of atoms involved in the torsion which is to be defined. The real number modifiers give the force constant value for the deviation from the target improper torsional angle, and the target value for the torsional angle, respectively. The default units for the improper force constant are kcal/mole/radian^2, but this can be controlled via the impropunit keyword.

imptors

Details
Type:         String
Definition:   [4 integers and up to 3 real/real/integer triples] Provides the values for a single AMBER-style improper torsional angle parameter. The first four integer modifiers give the atom class numbers for the atoms involved in the improper torsional angle to be defined. By convention, the third atom class of the four is the trigonal atom on which the improper torsion is centered. The torsional angle computed is literally that defined by the four atom classes in the order specified by the keyword. Each of the remaining triples of real/real/integer modifiers give the half-amplitude, phase offset in degrees and periodicity of a particular improper torsional term, respectively. Periodicities through 3-fold are allowed for improper torsional parameters.

multipole

Details
Type:         String[]
Definition:   [5 lines with: 3 or 4 integers and 1 real; 3 reals; 1 real; 2 reals; 3 reals] Provides the values for a set of atomic multipole parameters at a single site. A complete keyword entry consists of five consecutive lines, the first line containing the multipole keyword and the four following lines. The first line contains three integers which define the atom type on which the multipoles are centered, and the Z-axis and X-axis defining atom types for this center. The optional fourth integer contains the Y-axis defining atom type, and is only required for locally chiral multipole sites. The real number on the first line gives the monopole (atomic charge) in electrons.The second line contains three real numbers which give the X-, Y- and Z-components of the atomic dipole in electron-Ang. The final three lines, consisting of one, two and three real numbers give the upper triangle of the traceless atomic quadrupole tensor in electron-Ang^2.

opbend

Details
Type:         String
Definition:   [4 integers and 1 real] Provides the values for a single out-of-plane bending potential parameter. The first integer modifier is the atom class of the out-of-plane atom and the second integer is the atom class of the central trigonal atom. The third and fourth integers give the atom classes of the two remaining atoms attached to the trigonal atom. Values of zero for the third and fourth integers are treated as wildcards, and can represent any atom type. The real number modifier gives the force constant value for the out-of-plane angle. The default units for the force constant are kcal/mole/radian^2, but this can be controlled via the opbendunit keyword.

pitors

Details
Type:         String
Definition:   [2 integers and 1 real] Provides the values for a single pi-orbital torsional angle potential parameter. The two integer modifiers give the atom class numbers for the atoms involved in the central bond of the torsional angle to be parameterized. The real modifier gives the value of the 2-fold Fourier amplitude for the torsional angle between p-orbitals centered on the defined bond atom classes. The default units for the stretch-torsion force constant can be controlled via the pitorsunit keyword.

polarize

Details
Type:         String
Definition:   [1 integer, up to 3 reals and up to 8 integers] Provides the values for a single atomic dipole polarizability parameter. The initial integer modifier, if positive, gives the atom type number for which a polarizability parameter is to be defined. If the first integer modifier is negative, then the parameter value to follow applies only to the specific atom whose atom number is the negative of the modifier. The first real number modifier gives the value of the dipole polarizability in Ang^3. The second real number modifier, if present, gives the Thole damping value. A Thole value of zero implies undamped polarization. The third real modifier, if present, gives a direct field damping value only used with the AMOEBA+ polarization model. The remaining integer modifiers list the atom type numbers of atoms directly bonded to the current atom and which will be considered to be part of the current atom’s polarization group. If the parameter is for a specific atom, then the integers defining the polarization group are ignored.

solute

Details
Type:         String
Definition:   [integers & 3 reals] Provides values for a single implicit solvation parameter. The integer modifier gives the atom type number for which solvation atom size parameters are to be defined. The three real number modifiers give the values of the atomic diameter in Angstroms, for use in Poisson-Boltzmann (APBS), ddCOSMO and Generalized Kirkwood (GK) calculations, respectively.

strbnd

Details
Type:         String
Definition:   [3 integers and 2 reals] Provides the values for a single stretch-bend cross term potential parameter. The integer modifiers give the atom class numbers for the three kinds of atoms involved in the angle which is to be defined. The real number modifiers give the force constant values for the first bond (first two atom classes) with the angle, and the second bond with the angle, respectively. The default units for the stretch-bend force constant are kcal/mole/Ang-radian, but this can be controlled via the strbndunit keyword.

strtors

Details
Type:         String
Definition:   [2 integers and 1 real] Provides the values for a single stretch-torsion cross term potential parameter. The two integer modifiers give the atom class numbers for the atoms involved in the central bond of the torsional angles to be parameterized. The real modifier gives the value of the stretch-torsion force constant for all torsional angles with the defined atom classes for the central bond. The default units for the stretch-torsion force constant can be controlled via the strtorunit keyword.

torsion

Details
Type:         String
Definition:   [4 integers and up to 6 real/real/integer triples] Provides the values for a single torsional angle parameter. The first four integer modifiers give the atom class numbers for the atoms involved in the torsional angle to be defined. Each of the remaining triples of real/real/integer modifiers give the amplitude, phase offset in degrees and periodicity of a particular torsional function term, respectively. Periodicities through 6-fold are allowed for torsional parameters.

tortors

Details
Type:         String[]
Definition:   [7 integers, then multiple lines of 2 integers and 1 real] Provides the values for a single torsion-torsion parameter. The first five integer modifiers give the atom class numbers for the atoms involved in the two adjacent torsional angles to be defined. The last two integer modifiers contain the number of data grid points that lie along each axis of the torsion-torsion map. For example, this value will be 13 for a 30 degree torsional angle spacing, i.e., 360/30 = 12, but 13 values are required since data values for -180 and +180 degrees must both be supplied. The subsequent lines contain the torsion-torsion map data as the integer values in degrees of each torsional angle and the target energy value in kcal/mole.

ureybrad

Details
Type:         String
Definition:   [3 integers and 2 reals] Provides the values for a single Urey-Bradley cross term potential parameter. The integer modifiers give the atom class numbers for the three kinds of atoms involved in the angle for which a Urey-Bradley term is to be defined. The real number modifiers give the force constant value for the term and the target value for the 1-3 distance in Angstroms. The default units for the force constant are kcal/mole/Ang^2, but this can be controlled via the ureyunit keyword

vdw

Details
Type:         String
Definition:   [1 integer and 3 reals] Provides values for a single van der Waals parameter. The integer modifier, if positive, gives the atom class number for which vdw parameters are to be defined. Note that vdw parameters are given for atom classes, not atom types. The three real number modifiers give the values of the atom size in Angstroms, homoatomic well depth in kcal/mole, and an optional reduction factor for univalent atoms.

vdw14

Details
Type:         String
Definition:   [1 integer and 2 reals] Provides values for a single van der Waals parameter for use in 1-4 nonbonded interactions. The integer modifier, if positive, gives the atom class number for which vdw parameters are to be defined. Note that vdw parameters are given for atom classes, not atom types. The two real number modifiers give the values of the atom size in Angstroms and the homoatomic well depth in kcal/mole. Reduction factors, if used, are carried over from the vdw keyword for the same atom class.

vdwpr

Details
Type:         String
Definition:   [2 integers and 2 reals] Provides the values for the vdw parameters for a single special heteroatomic pair of atoms. The integer modifiers give the pair of atom class numbers for which special vdw parameters are to be defined. The two real number modifiers give the values of the minimum energy contact distance in Angstroms and the well depth at the minimum distance in kcal/mole.