Description of Modules & Global Variables
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The Fortran modules found in the Tinker package are listed below along with a brief description of the variables associated with each module. Each individual module contains a set of globally allocated variables available to any program unit upon inclusion of that module. A source listing containing each of the Tinker functions and subroutines and its included modules can be produced by running the "listing.make" script found in the distribution.

| **ACTION Module - total number of each energy term computed**
| neb	number of bond stretch energy terms computed
| nea	number of angle bend energy terms computed
| neba	number of stretch-bend energy terms computed
| neub	number of Urey-Bradley energy terms computed
| neaa	number of angle-angle energy terms computed
| neopb	number of out-of-plane bend energy terms computed
| neopd	number of out-of-plane distance energy terms computed
| neid	number of improper dihedral energy terms computed
| neit	number of improper torsion energy terms computed
| net	number of torsional energy terms computed
| nept	number of pi-orbital torsion energy terms computed
| nebt	number of stretch-torsion energy terms computed
| nett	number of torsion-torsion energy terms computed
| nev	number of van der Waals energy terms computed
| nec	number of charge-charge energy terms computed
| necd	number of charge-dipole energy terms computed
| ned	number of dipole-dipole energy terms computed
| nem	number of multipole energy terms computed
| nep	number of polarization energy terms computed
| new	number of Ewald summation energy terms computed
| ner	number of reaction field energy terms computed
| nes	number of solvation energy terms computed
| nelf	number of metal ligand field energy terms computed
| neg	number of geometric restraint energy terms computed
| nex	number of extra energy terms computed

| **ALIGN Modules - information for superposition of structures**
| wfit  weights assigned to atom pairs during superposition
| nfit  number of atoms to use in superimposing two structures
| ifit  atom numbers of pairs of atoms to be superimposed

ANALYZ	energy components partitioned over atoms

aesum	total potential energy partitioned over atoms
aeb	bond stretch energy partitioned over atoms
aea	angle bend energy partitioned over atoms
aeba	stretch-bend energy partitioned over atoms
aeub	Urey-Bradley energy partitioned over atoms
aeaa	angle-angle energy partitioned over atoms
aeopb	out-of-plane bend energy partitioned over atoms
aeopd	out-of-plane distance energy partitioned over atoms
aeid	improper dihedral energy partitioned over atoms
aeit	improper torsion energy partitioned over atoms
aet	torsional energy partitioned over atoms
aept	pi-orbital torsion energy partitioned over atoms
aebt	stretch-torsion energy partitioned over atoms
aett	torsion-torsion energy partitioned over atoms
aev	van der Waals energy partitioned over atoms
aec	charge-charge energy partitioned over atoms
aecd	charge-dipole energy partitioned over atoms
aed	dipole-dipole energy partitioned over atoms
aem	multipole energy partitioned over atoms
aep	polarization energy partitioned over atoms
aer	reaction field energy partitioned over atoms
aes	solvation energy partitioned over atoms
aelf	metal ligand field energy partitioned over atoms
aeg	geometric restraint energy partitioned over atoms
aex	extra energy term partitioned over atoms

ANGANG	angle-angle terms in current structure

kaa	force constant for angle-angle cross terms
nangang	total number of angle-angle interactions
iaa	angle numbers used in each angle-angle term

ANGLE	bond angles within the current structure

ak	harmonic angle force constant (kcal/mole/rad**2)
anat	ideal bond angle or phase shift angle (degrees)
afld	periodicity for Fourier bond angle term
nangle	total number of bond angles in the system
iang	numbers of the atoms in each bond angle
angtyp	potential energy function type for each bond angle

ANGPOT	specifics of bond angle functional forms

cang	cubic coefficient in angle bending potential
qang	quartic coefficient in angle bending potential
pang	quintic coefficient in angle bending potential
sang	sextic coefficient in angle bending potential
angunit	convert angle bending energy to kcal/mole
stbnunit	convert stretch-bend energy to kcal/mole
aaunit	convert angle-angle energy to kcal/mole
opbunit	convert out-of-plane bend energy to kcal/mole
opdunit	convert out-of-plane distance energy to kcal/mole
mm2stbn	logical flag governing use of MM2-style stretch-bend

ARGUE	command line arguments at program startup

maxarg	maximum number of command line arguments
narg	number of command line arguments to the program
listarg	flag to mark available command line arguments
arg	strings containing the command line arguments

ATMLST	local geometry terms involving each atom

bndlist	list of the bond numbers involving each atom
anglist	list of the angle numbers centered on each atom

ATMTYP	atomic properties for each current atom

mass	atomic weight for each atom in the system
tag	integer atom labels from input coordinates file
class	atom class number for each atom in the system
atomic	atomic number for each atom in the system
valence	valence number for each atom in the system
name	atom name for each atom in the system
story	descriptive type for each atom in system

ATOMS	number, position and type of current atoms

x	current x-coordinate for each atom in the system
y	current y-coordinate for each atom in the system
z	current z-coordinate for each atom in the system
n	total number of atoms in the current system
type	atom type number for each atom in the system

BATH	temperature and pressure control parameters

maxnose	maximum length of the Nose-Hoover chain
kelvin0	target value for the system temperature (K)
kelvin	variable target temperature for thermostat (K)
atmsph	target value for the system pressure (atm)
tautemp	time constant for Berendsen thermostat (psec)
taupres	time constant for Berendsen barostat (psec)
compress	isothermal compressibility of medium (atm-1)
collide	collision frequency for Andersen thermostat
xnh	position of each chained Nose-Hoover thermostat
vnh	velocity of each chained Nose-Hoover thermostat
qnh	mass for each chained Nose-Hoover thermostat
gnh	coupling between chained Nose-Hoover thermostats
isothermal	logical flag governing use of temperature control
isobaric	logical flag governing use of pressure control
tempvary	logical flag to enable variable target thermostat
thermostat	choice of temperature control method to be used
barostat	choice of pressure control method to be used

BITOR	bitorsions within the current structure

nbitor	total number of bitorsions in the system
ibitor	numbers of the atoms in each bitorsion

BNDPOT	specifics of bond stretch functional forms

cbnd	cubic coefficient in bond stretch potential
qbnd	quartic coefficient in bond stretch potential
bndunit	convert bond stretch energy to kcal/mole
bndtyp	type of bond stretch potential energy function

BOND	covalent bonds in the current structure

bk	bond stretch force constants (kcal/mole/Ang**2)
bl	ideal bond length values in Angstroms
nbond	total number of bond stretches in the system
ibnd	numbers of the atoms in each bond stretch

BORDER	bond orders for a conjugated pisystem

pbpl	pi-bond orders for bonds in "planar" pisystem
pnpl	pi-bond orders for bonds in "nonplanar" pisystem

BOUND	control of periodic boundary conditions

polycut	cutoff distance for infinite polymer nonbonds
polycut2	square of infinite polymer nonbond cutoff
use_bounds	flag to use periodic boundary conditions
use_image	flag to use images for periodic system
use_replica	flag to use replicates for periodic system
use_polymer	flag to mark presence of infinite polymer

BOXES	parameters for periodic boundary conditions

xbox	length in Angs of a-axis of periodic box
ybox	length in Angs of b-axis of periodic box
zbox	length in Angs of c-axis of periodic box
alpha	angle in degrees between b- and c-axes of box
beta	angle in degrees between a- and c-axes of box
gamma	angle in degrees between a- and b-axes of box
xbox2	half of the a-axis length of periodic box
ybox2	half of the b-axis length of periodic box
zbox2	half of the c-axis length of periodic box
box34	three-fourths axis length of truncated octahedron
recip	reciprocal lattice vectors as matrix columns
volbox	volume in Ang**3 of the periodic box
beta_sin	sine of the beta periodic box angle
beta_cos	cosine of the beta periodic box angle
gamma_sin	sine of the gamma periodic box angle
gamma_cos	cosine of the gamma periodic box angle
beta_term	term used in generating triclinic box
gamma_term	term used in generating triclinic box
orthogonal	flag to mark periodic box as orthogonal
monoclinic	flag to mark periodic box as monoclinic
triclinic	flag to mark periodic box as triclinic
octahedron	flag to mark box as truncated octahedron
spacegrp	space group symbol for the unitcell type

CELL	periodic boundaries using replicated cells

xcell	length of the a-axis of the complete replicated cell
ycell	length of the b-axis of the complete replicated cell
zcell	length of the c-axis of the complete replicated cell
xcell2	half the length of the a-axis of the replicated cell
ycell2	half the length of the b-axis of the replicated cell
zcell2	half the length of the c-axis of the replicated cell
ncell	total number of cell replicates for periodic boundaries
icell	offset along axes for each replicate periodic cell

CHARGE	partial charges for the current structure

pchg	magnitude of the partial charges (e-)
nion	total number of partial charges in system
iion	number of the atom site for each partial charge
jion	neighbor generation site for each partial charge
kion	cutoff switching site for each partial charge
chglist	partial charge site for each atom (0=no charge)

CHGPOT	specifics of charge-charge functional form

dielec	dielectric constant for electrostatic interactions
c2scale	factor by which 1-2 charge interactions are scaled
c3scale	factor by which 1-3 charge interactions are scaled
c4scale	factor by which 1-4 charge interactions are scaled
c5scale	factor by which 1-5 charge interactions are scaled
neutnbr	logical flag governing use of neutral group neighbors
neutcut	logical flag governing use of neutral group cutoffs

CHRONO	timing statistics for the current program

cputim	elapsed cpu time in seconds since start of program

COUPLE	near-neighbor atom connectivity lists

maxn13	maximum number of atoms 1-3 connected to an atom
maxn14	maximum number of atoms 1-4 connected to an atom
maxn15	maximum number of atoms 1-5 connected to an atom
n12	number of atoms directly bonded to each atom
i12	atom numbers of atoms 1-2 connected to each atom
n13	number of atoms in a 1-3 relation to each atom
i13	atom numbers of atoms 1-3 connected to each atom
n14	number of atoms in a 1-4 relation to each atom
i14	atom numbers of atoms 1-4 connected to each atom
n15	number of atoms in a 1-5 relation to each atom
i15	atom numbers of atoms 1-5 connected to each atom

CUTOFF	cutoff distances for energy interactions

vdwcut	cutoff distance for van der Waals interactions
chgcut	cutoff distance for charge-charge interactions
dplcut	cutoff distance for dipole-dipole interactions
mpolecut	cutoff distance for atomic multipole interactions
vdwtaper	distance at which van der Waals switching begins
chgtaper	distance at which charge-charge switching begins
dpltaper	distance at which dipole-dipole switching begins
mpoletaper	distance at which atomic multipole switching begins
ewaldcut	cutoff distance for direct space Ewald summation
use_ewald	logical flag governing use of Ewald summation term
use_lights	logical flag to use method of lights neighbors

DERIV	Cartesian coordinate derivative components

desum	total energy Cartesian coordinate derivatives
deb	bond stretch Cartesian coordinate derivatives
dea	angle bend Cartesian coordinate derivatives
deba	stretch-bend Cartesian coordinate derivatives
deub	Urey-Bradley Cartesian coordinate derivatives
deaa	angle-angle Cartesian coordinate derivatives
deopb	out-of-plane bend Cartesian coordinate derivatives
deopd	out-of-plane distance Cartesian coordinate derivatives
deid	improper dihedral Cartesian coordinate derivatives
deit	improper torsion Cartesian coordinate derivatives
det	torsional Cartesian coordinate derivatives
dept	pi-orbital torsion Cartesian coordinate derivatives
debt	stretch-torsion Cartesian coordinate derivatives
dett	torsion-torsion Cartesian coordinate derivatives
dev	van der Waals Cartesian coordinate derivatives
dec	charge-charge Cartesian coordinate derivatives
decd	charge-dipole Cartesian coordinate derivatives
ded	dipole-dipole Cartesian coordinate derivatives
dem	multipole Cartesian coordinate derivatives
dep	polarization Cartesian coordinate derivatives
der	reaction field Cartesian coordinate derivatives
des	solvation Cartesian coordinate derivatives
delf	metal ligand field Cartesian coordinate derivatives
deg	geometric restraint Cartesian coordinate derivatives
dex	extra energy term Cartesian coordinate derivatives

DIPOLE	atom & bond dipoles for current structure

bdpl	magnitude of each of the dipoles (Debyes)
sdpl	position of each dipole between defining atoms
ndipole	total number of dipoles in the system
idpl	numbers of atoms that define each dipole

DISGEO	distance geometry bounds and parameters

bnd	distance geometry upper and lower bounds matrix
vdwrad	hard sphere radii for distance geometry atoms
vdwmax	maximum value of hard sphere sum for an atom pair
compact	index of local distance compaction on embedding
pathmax	maximum value of upper bound after smoothing
use_invert	flag to use enantiomer closest to input structure
use_anneal	flag to use simulated annealing refinement

DOMEGA	derivative components over torsions

tesum	total energy derivatives over torsions
teb	bond stretch derivatives over torsions
tea	angle bend derivatives over torsions
teba	stretch-bend derivatives over torsions
teub	Urey-Bradley derivatives over torsions
teaa	angle-angle derivatives over torsions
teopb	out-of-plane bend derivatives over torsions
teopd	out-of-plane distance derivatives over torsions
teid	improper dihedral derivatives over torsions
teit	improper torsion derivatives over torsions
tet	torsional derivatives over torsions
tept	pi-orbital torsion derivatives over torsions
tebt	stretch-torsion derivatives over torsions
tett	torsion-torsion derivatives over torsions
tev	van der Waals derivatives over torsions
tec	charge-charge derivatives over torsions
tecd	charge-dipole derivatives over torsions
ted	dipole-dipole derivatives over torsions
tem	atomic multipole derivatives over torsions
tep	polarization derivatives over torsions
ter	reaction field derivatives over torsions
tes	solvation derivatives over torsions
telf	metal ligand field derivatives over torsions
teg	geometric restraint derivatives over torsions
tex	extra energy term derivatives over torsions

ENERGI	individual potential energy components

esum	total potential energy of the system
eb	bond stretch potential energy of the system
ea	angle bend potential energy of the system
eba	stretch-bend potential energy of the system
eub	Urey-Bradley potential energy of the system
eaa	angle-angle potential energy of the system
eopb	out-of-plane bend potential energy of the system
eopd	out-of-plane distance potential energy of the system
eid	improper dihedral potential energy of the system
eit	improper torsion potential energy of the system
et	torsional potential energy of the system
ept	pi-orbital torsion potential energy of the system
ebt	stretch-torsion potential energy of the system
ett	torsion-torsion potential energy of the system
ev	van der Waals potential energy of the system
ec	charge-charge potential energy of the system
ecd	charge-dipole potential energy of the system
ed	dipole-dipole potential energy of the system
em	atomic multipole potential energy of the system
ep	polarization potential energy of the system
er	reaction field potential energy of the system
es	solvation potential energy of the system
elf	metal ligand field potential energy of the system
eg	geometric restraint potential energy of the system
ex	extra term potential energy of the system

EWALD	parameters for regular or PM Ewald summation

aewald	Ewald convergence coefficient value (Ang-1)
frecip	fractional cutoff value for reciprocal sphere
tinfoil	flag governing use of tinfoil boundary conditions

EWREG	exponential factors for regular Ewald sum

maxvec	maximum number of k-vectors per reciprocal axis
ejc	exponental factors for cosine along the j-axis
ejs	exponental factors for sine along the j-axis
ekc	exponental factors for cosine along the k-axis
eks	exponental factors for sine along the k-axis
elc	exponental factors for cosine along the l-axis
els	exponental factors for sine along the l-axis

FACES	variables for Connolly area and volume

maxnbr	maximum number of neighboring atom pairs
maxtt	maximum number of temporary tori
maxt	maximum number of total tori
maxp	maximum number of probe positions
maxv	maximum number of vertices
maxen	maximum number of concave edges
maxfn	maximum number of concave faces
maxc	maximum number of circles
maxep	maximum number of convex edges
maxfs	maximum number of saddle faces
maxcy	maximum number of cycles
mxcyep	maximum number of cycle convex edges
maxfp	maximum number of convex faces
mxfpcy	maximum number of convex face cycles

FIELDS	molecular mechanics force field description

biotyp	force field atom type of each biopolymer type
forcefield	string used to describe the current forcefield

FILES	name and number of current structure files

nprior	number of previously existing cycle files
ldir	length in characters of the directory name
leng	length in characters of the base filename
filename	base filename used by default for all files
outfile	output filename used for intermediate results

FRACS	atom distances to molecular center of mass

xfrac	fractional coordinate along a-axis of center of mass
yfrac	fractional coordinate along b-axis of center of mass
zfrac	fractional coordinate along c-axis of center of mass

GROUP	partitioning of system into atom groups

grpmass	total mass of all the atoms in each group
wgrp	weight for each set of group-group interactions
ngrp	total number of atom groups in the system
kgrp	contiguous list of the atoms in each group
igrp	first and last atom of each group in the list
grplist	number of the group to which each atom belongs
use_group	flag to use partitioning of system into groups
use_intra	flag to include only intragroup interactions
use_inter	flag to include only intergroup interactions

HESCUT	cutoff value for Hessian matrix elements

hesscut	magnitude of smallest allowed Hessian element

HESSN	Cartesian Hessian elements for a single atom

hessx	Hessian elements for x-component of current atom
hessy	Hessian elements for y-component of current atom
hessz	Hessian elements for z-component of current atom

IMPROP	improper dihedrals in the current structure

kprop	force constant values for improper dihedral angles
vprop	ideal improper dihedral angle value in degrees
niprop	total number of improper dihedral angles in the system
iiprop	numbers of the atoms in each improper dihedral angle

IMPTOR	improper torsions in the current structure

itors1	1-fold amplitude and phase for each improper torsion
itors2	2-fold amplitude and phase for each improper torsion
itors3	3-fold amplitude and phase for each improper torsion
nitors	total number of improper torsional angles in the system
iitors	numbers of the atoms in each improper torsional angle

INFORM	control values for I/O and program flow

digits	decimal places output for energy and coordinates
iprint	steps between status printing (0=no printing)
iwrite	steps between coordinate dumps (0=no dumps)
isend	steps between socket communication (0=no sockets)
verbose	logical flag to turn on extra information
debug	logical flag to turn on full debug printing
holdup	logical flag to wait for carriage return on exit
abort	logical flag to stop execution at next chance

INTER	sum of intermolecular energy components

einter	total intermolecular potential energy

IOUNIT	Fortran input/output (I/O) unit numbers

iout	Fortran I/O unit for major output (default=6)
input	Fortran I/O unit for major input (default=5)

KANANG	forcefield parameters for angle-angle terms

anan	angle-angle cross term parameters for each atom class

KANGS	forcefield parameters for bond angle bending

maxna	maximum number of harmonic angle bend parameter entries
maxna5	maximum number of 5-membered ring angle bend entries
maxna4	maximum number of 4-membered ring angle bend entries
maxna3	maximum number of 3-membered ring angle bend entries
maxnaf	maximum number of Fourier angle bend parameter entries
acon	force constant parameters for harmonic angle bends
acon5	force constant parameters for 5-ring angle bends
acon4	force constant parameters for 4-ring angle bends
acon3	force constant parameters for 3-ring angle bends
aconf	force constant parameters for Fourier angle bends
ang	bond angle parameters for harmonic angle bends
ang5	bond angle parameters for 5-ring angle bends
ang4	bond angle parameters for 4-ring angle bends
ang3	bond angle parameters for 3-ring angle bends
angf	phase shift angle and periodicity for Fourier bends
ka	string of atom classes for harmonic angle bends
ka5	string of atom classes for 5-ring angle bends
ka4	string of atom classes for 4-ring angle bends
ka3	string of atom classes for 3-ring angle bends
kaf	string of atom classes for Fourier angle bends

KATOMS	forcefield parameters for the atom types

weight	average atomic mass of each atom type
atmcls	atom class number for each of the atom types
atmnum	atomic number for each of the atom types
ligand	number of atoms to be attached to each atom type
symbol	modified atomic symbol for each atom type
describe	string identifing each of the atom types

KBONDS	forcefield parameters for bond stretching

maxnb	maximum number of bond stretch parameter entries
maxnb5	maximum number of 5-membered ring bond stretch entries
maxnb4	maximum number of 4-membered ring bond stretch entries
maxnb3	maximum number of 3-membered ring bond stretch entries
maxnel	maximum number of electronegativity bond corrections
bcon	force constant parameters for harmonic bond stretch
bcon5	force constant parameters for 5-ring bond stretch
bcon4	force constant parameters for 4-ring bond stretch
bcon3	force constant parameters for 3-ring bond stretch
blen	bond length parameters for harmonic bond stretch
blen5	bond length parameters for 5-ring bond stretch
blen4	bond length parameters for 4-ring bond stretch
blen3	bond length parameters for 3-ring bond stretch
dlen	electronegativity bond length correction parameters
kb	string of atom classes for harmonic bond stretch
kb5	string of atom classes for 5-ring bond stretch
kb4	string of atom classes for 4-ring bond stretch
kb3	string of atom classes for 3-ring bond stretch
kel	string of atom classes for electronegativity corrections

KCHRGE	forcefield parameters for partial charges

chg	partial charge parameters for each atom type

KDIPOL	forcefield parameters for bond dipoles

maxnd	maximum number of bond dipole parameter entries
maxnd5	maximum number of 5-membered ring dipole entries
maxnd4	maximum number of 4-membered ring dipole entries
maxnd3	maximum number of 3-membered ring dipole entries
dpl	dipole moment parameters for bond dipoles
dpl5	dipole moment parameters for 5-ring dipoles
dpl4	dipole moment parameters for 4-ring dipoles
dpl3	dipole moment parameters for 3-ring dipoles
pos	dipole position parameters for bond dipoles
pos5	dipole position parameters for 5-ring dipoles
pos4	dipole position parameters for 4-ring dipoles
pos3	dipole position parameters for 3-ring dipoles
kd	string of atom classes for bond dipoles
kd5	string of atom classes for 5-ring dipoles
kd4	string of atom classes for 4-ring dipoles
kd3	string of atom classes for 3-ring dipoles

KEYS	contents of current keyword parameter file

nkey	number of nonblank lines in the keyword file
keyline	contents of each individual keyword file line

KGEOMS	parameters for the geometrical restraints

xpfix	x-coordinate target for each restrained position
ypfix	y-coordinate target for each restrained position
zpfix	z-coordinate target for each restrained position
pfix	force constant and flat-well range for each position
dfix	force constant and target range for each distance
afix	force constant and target range for each angle
tfix	force constant and target range for each torsion
gfix	force constant and target range for each group distance
chir	force constant and target range for chiral centers
depth	depth of shallow Gaussian basin restraint
width	exponential width coefficient of Gaussian basin
rwall	radius of spherical droplet boundary restraint
npfix	number of position restraints to be applied
ipfix	atom number involved in each position restraint
kpfix	flags to use x-, y-, z-coordinate position restraints
ndfix	number of distance restraints to be applied
idfix	atom numbers defining each distance restraint
nafix	number of angle restraints to be applied
iafix	atom numbers defining each angle restraint
ntfix	number of torsional restraints to be applied
itfix	atom numbers defining each torsional restraint
ngfix	number of group distance restraints to be applied
igfix	group numbers defining each group distance restraint
nchir	number of chirality restraints to be applied
ichir	atom numbers defining each chirality restraint
use_basin	logical flag governing use of Gaussian basin
use_wall	logical flag governing use of droplet boundary

KHBOND	forcefield parameters for H-bonding terms

maxnhb	maximum number of hydrogen bonding pair entries
radhb	radius parameter for hydrogen bonding pairs
epshb	well depth parameter for hydrogen bonding pairs
khb	string of atom types for hydrogen bonding pairs

KIPROP	forcefield parameters for improper dihedral

maxndi	maximum number of improper dihedral parameter entries
dcon	force constant parameters for improper dihedrals
tdi	ideal dihedral angle values for improper dihedrals
kdi	string of atom classes for improper dihedral angles

KITORS	forcefield parameters for improper torsions

maxnti	maximum number of improper torsion parameter entries
ti1	torsional parameters for improper 1-fold rotation
ti2	torsional parameters for improper 2-fold rotation
ti3	torsional parameters for improper 3-fold rotation
kti	string of atom classes for improper torsional parameters

KMULTI	forcefield parameters for atomic multipoles

maxnmp	maximum number of atomic multipole parameter entries
multip	atomic monopole, dipole and quadrupole values
mpaxis	type of local axis definition for atomic multipoles
kmp	string of atom types for atomic multipoles

KOPBND	forcefield parameters for out-of-plane bend

maxnopb	maximum number of out-of-plane bending entries
copb	force constant parameters for out-of-plane bending
kaopb	string of atom classes for out-of-plane bending

KOPDST	forcefield parameters for out-plane distance

maxnopb	maximum number of out-of-plane distance entries
copb	force constant parameters for out-of-plane distance
kaopb	string of atom classes for out-of-plane distance

KORBS	forcefield parameters for pisystem orbitals

maxnpi	maximum number of pisystem bond parameter entries
electron	number of pi-electrons for each atom class
ionize	ionization potential for each atom class
repulse	repulsion integral value for each atom class
sslope	slope for bond stretch vs. pi-bond order
tslope	slope for 2-fold torsion vs. pi-bond order
kpi	string of atom classes for pisystem bonds

KPITOR	forcefield parameters for pi-orbit torsions

maxnpt	maximum number of pi-orbital torsion parameter entries
ptcon	force constant parameters for pi-orbital torsions
kpt	string of atom classes for pi-orbital torsion terms

KPOLR	forcefield parameters for polarizability

polr	dipole polarizability parameters for each atom type
pgrp	connected types in polarization group of each atom type

KSTBND	forcefield parameters for stretch-bending

stbn	stretch-bending parameters for each atom class

KSTTOR	forcefield parameters for stretch-torsions

maxnbt	maximum number of stretch-torsion parameter entries
btcon	force constant parameters for stretch-torsion
kbt	string of atom classes for bonds in stretch-torsion

KTORSN	forcefield parameters for torsional angles

maxnt	maximum number of torsional angle parameter entries
maxnt5	maximum number of 5-membered ring torsion entries
maxnt4	maximum number of 4-membered ring torsion entries
t1	torsional parameters for standard 1-fold rotation
t2	torsional parameters for standard 2-fold rotation
t3	torsional parameters for standard 3-fold rotation
t4	torsional parameters for standard 4-fold rotation
t5	torsional parameters for standard 5-fold rotation
t6	torsional parameters for standard 6-fold rotation
t15	torsional parameters for 1-fold rotation in 5-ring
t25	torsional parameters for 2-fold rotation in 5-ring
t35	torsional parameters for 3-fold rotation in 5-ring
t45	torsional parameters for 4-fold rotation in 5-ring
t55	torsional parameters for 5-fold rotation in 5-ring
t65	torsional parameters for 6-fold rotation in 5-ring
t14	torsional parameters for 1-fold rotation in 4-ring
t24	torsional parameters for 2-fold rotation in 4-ring
t34	torsional parameters for 3-fold rotation in 4-ring
t44	torsional parameters for 4-fold rotation in 4-ring
t54	torsional parameters for 5-fold rotation in 4-ring
t64	torsional parameters for 6-fold rotation in 4-ring
kt	string of atom classes for torsional angles
kt5	string of atom classes for 5-ring torsions
kt4	string of atom classes for 4-ring torsions

KTRTOR	forcefield parameters for torsion-torsions

maxntt	maximum number of torsion-torsion parameter entries
maxtgrd	maximum dimension of torsion-torsion spline grid
maxtgrd2	maximum number of torsion-torsion spline grid points
ttx	angle values for first torsion of spline grid
tty	angle values for second torsion of spline grid
tbf	function values at points on spline grid
tbx	gradient over first torsion of spline grid
tby	gradient over second torsion of spline grid
tbxy	Hessian cross components over spline grid
tnx	number of columns in torsion-torsion spline grid
tny	number of rows in torsion-torsion spline grid
ktt	string of torsion-torsion atom classes

KURYBR	forcefield parameters for Urey-Bradley terms

maxnu	maximum number of Urey-Bradley parameter entries
ucon	force constant parameters for Urey-Bradley terms
dst13	ideal 1-3 distance parameters for Urey-Bradley terms
ku	string of atom classes for Urey-Bradley terms

KVDWPR	forcefield parameters for special vdw terms

maxnvp	maximum number of special van der Waals pair entries
radpr	radius parameter for special van der Waals pairs
epspr	well depth parameter for special van der Waals pairs
kvpr	string of atom classes for special van der Waals pairs

KVDWS	forcefield parameters for van der Waals terms

rad	van der Waals radius parameter for each atom class
eps	van der Waals well depth parameter for each atom class
rad4	van der Waals radius parameter in 1-4 interactions
eps4	van der Waals well depth parameter in 1-4 interactions
reduct	van der Waals reduction factor for each atom class

LIGHT	indices for method of lights pair neighbors

nlight	total number of sites for method of lights calculation
kbx	low index of neighbors of each site in the x-sorted list
kby	low index of neighbors of each site in the y-sorted list
kbz	low index of neighbors of each site in the z-sorted list
kex	high index of neighbors of each site in the x-sorted list
key	high index of neighbors of each site in the y-sorted list
kez	high index of neighbors of each site in the z-sorted list
locx	pointer from x-sorted list into original interaction list
locy	pointer from y-sorted list into original interaction list
locz	pointer from z-sorted list into original interaction list
rgx	pointer from original interaction list into x-sorted list
rgy	pointer from original interaction list into y-sorted list
rgz	pointer from original interaction list into z-sorted list

LINMIN	parameters for line search minimization

stpmin	minimum step length in current line search direction
stpmax	maximum step length in current line search direction
cappa	stringency of line search (0=tight < cappa < 1=loose)
slpmax	projected gradient above which stepsize is reduced
angmax	maximum angle between search direction and -gradient
intmax	maximum number of interpolations during line search

MATH	mathematical and geometrical constants

radian	conversion factor from radians to degrees
pi	numerical value of the geometric constant
sqrtpi	numerical value of the square root of Pi
logten	numerical value of the natural log of ten
sqrttwo	numerical value of the square root of two
twosix	numerical value of the sixth root of two

MDSTUF	control of molecular dynamics trajectory

nfree	total number of degrees of freedom for a system
velsave	flag to save velocity vector components to a file
frcsave	flag to save force vector components to a file
uindsave	flag to save induced atomic dipoles to a file
integrate	type of molecular dynamics integration algorithm

MINIMA	general parameters for minimizations

fctmin	value below which function is deemed optimized
hguess	initial value for the H-matrix diagonal elements
maxiter	maximum number of iterations during optimization
nextiter	iteration number to use for the first iteration

MOLCUL	individual molecules within current system

molmass	molecular weight for each molecule in the system
totmass	total weight of all the molecules in the system
nmol	total number of separate molecules in the system
kmol	contiguous list of the atoms in each molecule
imol	first and last atom of each molecule in the list
molcule	number of the molecule to which each atom belongs

MOLDYN	velocity and acceleration on MD trajectory

v	current velocity of each atom along the x,y,z-axes
a	current acceleration of each atom along x,y,z-axes
aold	previous acceleration of each atom along x,y,z-axes

MOMENT	components of electric multipole moments

netchg	net electric charge for the total system
netdpl	dipole moment magnitude for the total system
netqdp	diagonal quadrupole (Qxx, Qyy, Qzz) for system
xdpl	dipole vector x-component in the global frame
ydpl	dipole vector y-component in the global frame
zdpl	dipole vector z-component in the global frame
xxqdp	quadrupole tensor xx-component in global frame
xyqdp	quadrupole tensor xy-component in global frame
xzqdp	quadrupole tensor xz-component in global frame
yxqdp	quadrupole tensor yx-component in global frame
yyqdp	quadrupole tensor yy-component in global frame
yzqdp	quadrupole tensor yz-component in global frame
zxqdp	quadrupole tensor zx-component in global frame
zyqdp	quadrupole tensor zy-component in global frame
zzqdp	quadrupole tensor zz-component in global frame

MPLPOT	specifics of atomic multipole functions

m2scale	factor by which 1-2 multipole interactions are scaled
m3scale	factor by which 1-3 multipole interactions are scaled
m4scale	factor by which 1-4 multipole interactions are scaled
m5scale	factor by which 1-5 multipole interactions are scaled

MPOLE	multipole components for current structure

maxpole	max components (monopole=1,dipole=4,quadrupole=13)
pole	multipole values for each site in the local frame
rpole	multipoles rotated to the global coordinate system
npole	total number of multipole sites in the system
ipole	number of the atom for each multipole site
polsiz	number of mutipole components at each multipole site
zaxis	number of the z-axis defining atom for each site
xaxis	number of the x-axis defining atom for each site
yaxis	number of the y-axis defining atom for each site
polaxe	local axis type for each multipole site

MUTANT	hybrid atoms for free energy perturbation

lambda	weighting of initial state in hybrid Hamiltonian
nhybrid	number of atoms mutated from initial to final state
ihybrid	atomic sites differing in initial and final state
type0	atom type of each atom in the initial state system
class0	atom class of each atom in the initial state system
type1	atom type of each atom in the final state system
class1	atom class of each atom in the final state system
alter	true if an atom is to be mutated, false otherwise

NUCLEO	parameters for nucleic acid structure

bkbone	phosphate backbone angles for each nucleotide
glyco	glycosidic torsional angle for each nucleotide
pucker	sugar pucker, either 2=2'-endo or 3=3'-endo
dblhlx	flag to mark system as nucleic acid double helix
deoxy	flag to mark deoxyribose or ribose sugar units
hlxform	helix form (A, B or Z) of polynucleotide strands

OMEGA	dihedrals for torsional space computations

dihed	current value in radians of each dihedral angle
nomega	number of dihedral angles allowed to rotate
iomega	numbers of two atoms defining rotation axis
zline	line number in Z-matrix of each dihedral angle

OPBEND	out-of-plane bends in the current structure

kopb	force constant values for out-of-plane bending
nopbend	total number of out-of-plane bends in the system
iopb	bond angle numbers used in out-of-plane bending

OPDIST	out-of-plane distances in current structure

kopd	force constant values for out-of-plane distance
nopdist	total number of out-of-plane distances in the system
iopb	numbers of the atoms in each out-of-plane distance

ORBITS	orbital energies for conjugated pisystem

q	number of pi-electrons contributed by each atom
w	ionization potential of each pisystem atom
em	repulsion integral for each pisystem atom
nfill	number of filled pisystem molecular orbitals

OUTPUT	control of coordinate output file format

archive	logical flag to save structures in an archive
noversion	logical flag governing use of filename versions
overwrite	logical flag to overwrite intermediate files inplace
cyclesave	logical flag to mark use of numbered cycle files
coordtype	selects Cartesian, internal, rigid body or none

PARAMS	contents of force field parameter file

nprm	number of nonblank lines in the parameter file
prmline	contents of each individual parameter file line

PATHS	parameters for Elber reaction path method

p0	reactant Cartesian coordinates as variables
p1	product Cartesian coordinates as variables
pmid	midpoint between the reactant and product
pvect	vector connecting the reactant and product
pstep	step per cycle along reactant-product vector
pzet	current projection on reactant-product vector
pnorm	length of the reactant-product vector
acoeff	transformation matrix 'A' from Elber paper
gc	gradients of the path constraints

PDB	definition of a Protein Data Bank structure

xpdb	x-coordinate of each atom stored in PDB format
ypdb	y-coordinate of each atom stored in PDB format
zpdb	z-coordinate of each atom stored in PDB format
npdb	number of atoms stored in Protein Data Bank format
resnum	number of the residue to which each atom belongs
npdb12	number of atoms directly bonded to each CONECT atom
ipdb12	atom numbers of atoms connected to each CONECT atom
pdblist	list of the Protein Data Bank atom number of each atom
pdbtyp	Protein Data Bank record type assigned to each atom
atmnam	Protein Data Bank atom name assigned to each atom
resnam	Protein Data Bank residue name assigned to each atom

PHIPSI	phi-psi-omega-chi angles for a protein

phi	value of the phi angle for each amino acid residue
psi	value of the psi angle for each amino acid residue
omega	value of the omega angle for each amino acid residue
chi	values of the chi angles for each amino acid residue
chiral	chirality of each amino acid residue (1=L, -1=D)
disulf	residue joined to each residue via a disulfide link

PIORBS	conjugated system in the current structure

norbit	total number of pisystem orbitals in the system
iorbit	numbers of the atoms containing pisystem orbitals
reorbit	number of evaluations between orbital updates
piperp	atoms defining a normal plane to each orbital
nbpi	total number of bonds affected by the pisystem
bpi	bond and piatom numbers for each pisystem bond
ntpi	total number of torsions affected by the pisystem
tpi	torsion and pibond numbers for each pisystem torsion
listpi	atom list indicating whether each atom has an orbital

PISTUF	bonds and torsions in the current pisystem

bkpi	bond stretch force constants for pi-bond order of 1.0
blpi	ideal bond length values for a pi-bond order of 1.0
kslope	rate of force constant decrease with bond order decrease
lslope	rate of bond length increase with a bond order decrease
torsp2	2-fold torsional energy barrier for pi-bond order of 1.0

PITORS	pi-orbital torsions in the current structure

kpit	2-fold pi-orbital torsional force constants
npitors	total number of pi-orbital torsional interactions
ipit	numbers of the atoms in each pi-orbital torsion

PME	parameters for particle mesh Ewald summation

maxfft	maximum number of points along each FFT direction
maxorder	maximum order of the B-spline approximation
maxtable	maximum size of the FFT table array
maxgrid	maximum dimension of the PME charge grid array
bsmod1	B-spline moduli along the a-axis direction
bsmod2	B-spline moduli along the b-axis direction
bsmod3	B-spline moduli along the c-axis direction
table	intermediate array used by the FFT calculation
nfft1	number of grid points along the a-axis direction
nfft2	number of grid points along the b-axis direction
nfft3	number of grid points along the c-axis direction
bsorder	order of the PME B-spline approximation

POLAR	polarizabilities and induced dipole moments

polarity	dipole polarizability for each multipole site (Ang**3)
pdamp	value of polarizability damping factor for each site
uind	induced dipole components at each multipole site
uinp	induced dipoles in field used for energy interactions
npolar	total number of polarizable sites in the system

POLGRP	polarizable site group connectivity lists

maxp11	maximum number of atoms in a polarization group
maxp12	maximum number of atoms in groups 1-2 to an atom
maxp13	maximum number of atoms in groups 1-3 to an atom
maxp14	maximum number of atoms in groups 1-4 to an atom
np11	number of atoms in polarization group of each atom
ip11	atom numbers of atoms in same group as each atom
np12	number of atoms in groups 1-2 to each atom
ip12	atom numbers of atoms in groups 1-2 to each atom
np13	number of atoms in groups 1-3 to each atom
ip13	atom numbers of atoms in groups 1-3 to each atom
np14	number of atoms in groups 1-4 to each atom
ip14	atom numbers of atoms in groups 1-4 to each atom

POLPOT	specifics of polarization functional form

poleps	induced dipole convergence criterion (rms Debyes/atom)
polsor	induced dipole SOR convergence acceleration factor
pgamma	prefactor in exponential polarization damping term
p2scale	field 1-2 scale factor for energy evaluations
p3scale	field 1-3 scale factor for energy evaluations
p4scale	field 1-4 scale factor for energy evaluations
p5scale	field 1-5 scale factor for energy evaluations
d1scale	field intra-group scale factor for direct induced
d2scale	field 1-2 group scale factor for direct induced
d3scale	field 1-3 group scale factor for direct induced
d4scale	field 1-4 group scale factor for direct induced
u1scale	field intra-group scale factor for mutual induced
u2scale	field 1-2 group scale factor for mutual induced
u3scale	field 1-3 group scale factor for mutual induced
u4scale	field 1-4 group scale factor for mutual induced
poltyp	type of polarization potential (direct or mutual)

POTENT	usage of each potential energy component

use_bond	logical flag governing use of bond stretch potential
use_angle	logical flag governing use of angle bend potential
use_strbnd	logical flag governing use of stretch-bend potential
use_urey	logical flag governing use of Urey-Bradley potential
use_angang	logical flag governing use of angle-angle cross term
use_opbend	logical flag governing use of out-of-plane bend term
use_opdist	logical flag governing use of out-of-plane distance
use_improp	logical flag governing use of improper dihedral term
use_imptor	logical flag governing use of improper torsion term
use_tors	logical flag governing use of torsional potential
use_pitors	logical flag governing use of pi-orbital torsion term
use_strtor	logical flag governing use of stretch-torsion term
use_tortor	logical flag governing use of torsion-torsion term
use_vdw	logical flag governing use of vdw der Waals potential
use_charge	logical flag governing use of charge-charge potential
use_chgdpl	logical flag governing use of charge-dipole potential
use_dipole	logical flag governing use of dipole-dipole potential
use_mpole	logical flag governing use of multipole potential
use_polar	logical flag governing use of polarization term
use_rxnfld	logical flag governing use of reaction field term
use_solv	logical flag governing use of surface area solvation
use_gbsa	logical flag governing use of GB/SA solvation term
use_metal	logical flag governing use of ligand field term
use_geom	logical flag governing use of geometric restraints
use_extra	logical flag governing use of extra potential term
use_orbit	logical flag governing use of pisystem computation

PRECIS	values of machine precision tolerances

tiny	the smallest positive floating point value
small	the smallest relative floating point spacing
huge	the largest relative floating point spacing

REFER	storage of reference atomic coordinate set

xref	reference x-coordinate for each atom in the system
yref	reference y-coordinate for each atom in the system
zref	reference z-coordinate for each atom in the system
nref	total number of atoms in the reference system
reftyp	atom type for each atom in the reference system
n12ref	number of atoms bonded to each reference atom
i12ref	atom numbers of atoms 1-2 connected to each atom
refleng	length in characters of the reference filename
refltitle	length in characters of the reference title string
refnam	atom name for each atom in the reference system
reffile	base filename for the reference structure
reftitle	title used to describe the reference structure

RESDUE	standard biopolymer residue abbreviations

amino	three-letter abbreviations for amino acids types
nuclz	three-letter abbreviations for nucleic acids types
amino1	one-letter abbreviations for amino acids types
nuclz1	one-letter abbreviations for nucleic acids types

RGDDYN	velocities and momenta for rigid body MD

vcm	current translational velocity of each rigid body
wcm	current angular velocity of each rigid body
lm	current angular momentum of each rigid body
linear	logical flag to mark group as linear or nonlinear

RIGID	rigid body coordinates for atom groups

xrb	rigid body reference x-coordinate for each atom
yrb	rigid body reference y-coordinate for each atom
zrb	rigid body reference z-coordinate for each atom
rbc	current rigid body coordinates for each group
use_rigid	flag to mark use of rigid body coordinate system

RING	number and location of small ring structures

nring3	total number of 3-membered rings in the system
iring3	numbers of the atoms involved in each 3-ring
nring4	total number of 4-membered rings in the system
iring4	numbers of the atoms involved in each 4-ring
nring5	total number of 5-membered rings in the system
iring5	numbers of the atoms involved in each 5-ring
nring6	total number of 6-membered rings in the system
iring6	numbers of the atoms involved in each 6-ring

ROTATE	molecule partitions for rotation of a bond

nrot	total number of atoms moving when bond rotates
rot	atom numbers of atoms moving when bond rotates
use_short	logical flag governing use of shortest atom list

RXNFLD	reaction field matrix elements and indices

b1	first reaction field matrix element array
b2	second reaction field matrix element array
ijk	indices into the reaction field element arrays

RXNPOT	specifics of reaction field functional form

rfsize	radius of reaction field sphere centered at origin
rfbulkd	bulk dielectric constant of reaction field continuum
rfterms	number of terms to use in reaction field summation

SCALES	parameter scale factors for optimization

scale	multiplicative factor for each optimization parameter
set_scale	logical flag to show if scale factors have been set

SEQUEN	sequence information for a biopolymer

nseq	total number of residues in biopolymer sequences
nchain	number of separate biopolymer sequence chains
ichain	first and last residue in each biopolymer chain
seqtyp	residue type for each residue in the sequence
seq	three-letter code for each residue in the sequence
chnnam	one-letter identifier for each sequence chain

SHAKE	definition of Shake/Rattle constraints

krat	ideal distance value for rattle constraint
nrat	number of rattle distance constraints to apply
nratx	number of atom group spatial constraints to apply
irat	atom numbers of atoms in a rattle constraint
iratx	group number of group in a spatial constraint
kratx	spatial constraint type (1=plane, 2=line, 3=point)
ratimage	flag to use minimum image for rattle constraint
use_rattle	logical flag to set use of rattle contraints

SHUNT	polynomial switching function coefficients

off	distance at which the potential energy goes to zero
off2	square of distance at which the potential goes to zero
cut	distance at which switching of the potential begins
cut2	square of distance at which the switching begins
c0	zeroth order coefficient of multiplicative switch
c1	first order coefficient of multiplicative switch
c2	second order coefficient of multiplicative switch
c3	third order coefficient of multiplicative switch
c4	fourth order coefficient of multiplicative switch
c5	fifth order coefficient of multiplicative switch
f0	zeroth order coefficient of additive switch function
f1	first order coefficient of additive switch function
f2	second order coefficient of additive switch function
f3	third order coefficient of additive switch function
f4	fourth order coefficient of additive switch function
f5	fifth order coefficient of additive switch function
f6	sixth order coefficient of additive switch function
f7	seventh order coefficient of additive switch function

SIZES	parameter values to set array dimensions

"sizes.i" sets values for critical array dimensions used throughout the software; these parameters will fix the size of the largest systems that can be handled; values too large for	the computer's memory and/or swap space to accomodate will result in poor performance or outright failure

parameter:	maximum allowed number of:

maxatm	atoms in the molecular system
maxval	atoms directly bonded to an atom
maxgrp	user-defined groups of atoms
maxtyp	force field atom type definitions
maxclass	force field atom class definitions
maxprm	lines in the parameter file
maxkey	lines in the keyword file
maxrot	bonds for torsional rotation
maxvar	optimization variables (vector storage)
maxopt	optimization variables (matrix storage)
maxhess	off-diagonal Hessian elements
maxlight	sites for method of lights neighbors
maxvib	vibrational frequencies
maxgeo	distance geometry points
maxcell	unit cells in replicated crystal
maxring	3-, 4-, or 5-membered rings
maxfix	geometric constraints and restraints
maxbio	biopolymer atom definitions
maxres	residues in the macromolecule
maxamino	amino acid residue types
maxnuc	nucleic acid residue types
maxbnd	covalent bonds in molecular system
maxang	bond angles in molecular system
maxtors	torsional angles in molecular system
maxbitor	bitorsions in molecular system
maxpi	atoms in conjugated pisystem
maxpib	covalent bonds involving pisystem
maxpit	torsional angles involving pisystem

SOCKET	control parameters for socket communication

runtyp	calculation type for passing socket information
cstep	current optimization or dynamics step number
cdt	current dynamics cumulative simulation time
cenergy	current potential energy from simulation
cdx	current gradient components along the x-axis
cdy	current gradient components along the y-axis
cdz	current gradient components along the z-axis
skt_init	logical flag set to true after socket initialization
use_socket	logical flag governing use of external sockets
use_gui	logical flag to show Tinker was invoked from GUI
closing	logical flag to indicate JVM and server shutdown

SOLUTE	parameters for continuum solvation models

rsolv	atomic radius of each atom for continuum solvation
vsolv	atomic volume of each atom for continuum solvation
asolv	atomic solvation parameters (kcal/mole/Ang**2)
rborn	Born radius of each atom for GB/SA solvation
drb	solvation derivatives with respect to Born radii
doffset	dielectric offset to continuum solvation atomic radii
p1	single-atom scale factor for analytical Still GB/SA
p2	1-2 interaction scale factor for analytical Still GB/SA
p3	1-3 interaction scale factor for analytical Still GB/SA
p4	nonbonded scale factor for analytical Still GB/SA
p5	soft cutoff parameter for analytical Still GB/SA
gpol	polarization self-energy values for each atom
shct	overlap scaling factors for Hawkins-Cramer-Truhlar GB/SA
wace	"omega" values for atom class pairs for use with ACE
s2ace	"sigma^2" values for atom class pairs for use with ACE
uace	"mu" values for atom class pairs for use with ACE
solvtyp	solvation model (ASP, SASA, ONION, STILL, HCT, ACE)

STODYN	frictional coefficients for SD trajectory

friction	global frictional coefficient for exposed particle
gamma	atomic frictional coefficients for each atom
use_sdarea	logical flag to use surface area friction scaling

STRBND	stretch-bends in the current structure

ksb	force constant for stretch-bend terms
nstrbnd	total number of stretch-bend interactions
isb	angle and bond numbers used in stretch-bend

STRTOR	stretch-torsions in the current structure

kst	1-, 2- and 3-fold stretch-torsion force constants
nstrtor	total number of stretch-torsion interactions
ist	torsion and bond numbers used in stretch-torsion

SYNTRN	definition of synchronous transit path

t	value of the path coordinate (0=reactant, 1=product)
pm	path coordinate for extra point in quadratic transit
xmin1	reactant coordinates as array of optimization variables
xmin2	product coordinates as array of optimization variables
xm	extra coordinate set for quadratic synchronous transit

TITLES	title for the current molecular system

ltitle	length in characters of the nonblank title string
title	title used to describe the current structure

TORPOT	specifics of torsional functional forms

idihunit	convert improper dihedral energy to kcal/mole
itorunit	convert improper torsion amplitudes to kcal/mole
torsunit	convert torsional parameter amplitudes to kcal/mole
ptorunit	convert pi-orbital torsion energy to kcal/mole
storunit	convert stretch-torsion energy to kcal/mole
ttorunit	convert stretch-torsion energy to kcal/mole

TORS	torsional angles within the current structure

tors1	1-fold amplitude and phase for each torsional angle
tors2	2-fold amplitude and phase for each torsional angle
tors3	3-fold amplitude and phase for each torsional angle
tors4	4-fold amplitude and phase for each torsional angle
tors5	5-fold amplitude and phase for each torsional angle
tors6	6-fold amplitude and phase for each torsional angle
ntors	total number of torsional angles in the system
itors	numbers of the atoms in each torsional angle

TORTOR	torsion-torsions in the current structure

ntortor	total number of torsion-torsion interactions
itt	atoms and parameter indices for torsion-torsion

TREE	potential smoothing & search tree levels

maxpss	maximum number of potential smoothing levels
etree	energy reference value at the top of the tree
ilevel	smoothing deformation value at each tree level
nlevel	number of levels of potential smoothing used

UNITS	physical constants and unit conversions

avogadro	Avogadro's number (N) in particles/mole
boltzmann	Boltzmann constant (kB) in g*Ang**2/ps**2/K/mole
gasconst	ideal gas constant (R) in kcal/mole/K
lightspd	speed of light in vacuum (c) in cm/ps
bohr	conversion from Bohrs to Angstroms
joule	conversion from calories to joules
evolt	conversion from Hartree to electron-volts
hartree	conversion from Hartree to kcal/mole
electric	conversion from electron**2/Ang to kcal/mole
debye	conversion from electron-Ang to Debyes
prescon	conversion from kcal/mole/Ang**3 to Atm
convert	conversion from kcal to g*Ang**2/ps**2

UREY	Urey-Bradley interactions in the structure

uk	Urey-Bradley force constants (kcal/mole/Ang**2)
ul	ideal 1-3 distance values in Angstroms
nurey	total number of Urey-Bradley terms in the system
iury	numbers of the atoms in each Urey-Bradley interaction

URYPOT	specifics of Urey-Bradley functional form

cury	cubic coefficient in Urey-Bradley potential
qury	quartic coefficient in Urey-Bradley potential
ureyunit	convert Urey-Bradley energy to kcal/mole

USAGE	atoms active during energy computation

nuse	number of active atoms used in energy calculation
use	true if an atom is active, false if inactive

VDW	van der Waals parameters for current structure

radmin	minimum energy distance for each atom class pair
epsilon	well depth parameter for each atom class pair
radmin4	minimum energy distance for 1-4 interaction pairs
epsilon4	well depth parameter for 1-4 interaction pairs
radhbnd	minimum energy distance for hydrogen bonding pairs
epshbnd	well depth parameter for hydrogen bonding pairs
kred	value of reduction factor parameter for each atom
ired	attached atom from which reduction factor is applied
nvdw	total number van der Waals active sites in the system
ivdw	number of the atom for each van der Waals active site

VDWPOT	specifics of van der Waals functional form

abuck	value of "A" constant in Buckingham vdw potential
bbuck	value of "B" constant in Buckingham vdw potential
cbuck	value of "C" constant in Buckingham vdw potential
ghal	value of "gamma" in buffered 14-7 vdw potential
dhal	value of "delta" in buffered 14-7 vdw potential
v2scale	factor by which 1-2 vdw interactions are scaled
v3scale	factor by which 1-3 vdw interactions are scaled
v4scale	factor by which 1-4 vdw interactions are scaled
v5scale	factor by which 1-5 vdw interactions are scaled
igauss	coefficients of Gaussian fit to vdw potential
ngauss	number of Gaussians used in fit to vdw potential
vdwtyp	type of van der Waals potential energy function
radtyp	type of parameter (sigma or R-min) for atomic size
radsiz	atomic size provided as radius or diameter
radrule	combining rule for atomic size parameters
epsrule	combining rule for vdw well depth parameters
gausstyp	type of Gaussian fit to van der Waals potential

VIRIAL	components of internal virial tensor

vir	total internal virial Cartesian tensor components

WARP	parameters for potential surface smoothing

m2	second moment of the GDA gaussian for each atom
deform	value of the smoothing deformation parameter
difft	diffusion coefficient for torsional potential
diffv	diffusion coefficient for van der Waals potential
diffc	diffusion coefficient for charge-charge potential
use_smooth	flag to use a potential energy smoothing method
use_dem	flag to use diffusion equation method potential
use_gda	flag to use gaussian density annealing potential
use_tophat	flag to use analytical tophat smoothed potential
use_stophat	flag to use shifted tophat smoothed potential

XTALS	crystal structures for parameter fitting

e0_lattice	ideal lattice energy for the current crystal
moment_0	ideal dipole moment for monomer from crystal
nxtal	number of crystal structures to be stored
nvary	number of potential parameters to optimize
ivary	index for the types of potential parameters
vary	atom numbers involved in potential parameters
iresid	crystal structure to which each residual refers
rsdtyp	experimental variable for each of the residuals
vartyp	type of potential parameter to be optimized

ZCLOSE	ring openings and closures for Z-matrix

nadd	number of added bonds between Z-matrix atoms
iadd	numbers of the atom pairs defining added bonds
ndel	number of bonds between Z-matrix bonds to delete
idel	numbers of the atom pairs defining deleted bonds

ZCOORD	Z-matrix internal coordinate definitions

zbond	bond length used to define each Z-matrix atom
zang	bond angle used to define each Z-matrix atom
ztors	angle or torsion used to define Z-matrix atom
iz	defining atom numbers for each Z-matrix atom
