the goodman group
university of cambridge  


   contents of common block variables

Tinker


10. Contents of Common Block Variables

The Fortran common blocks found in the TINKER package are listed below along with a brief description of the contents of each variable in each common block. Each individual common block is present as a separate ".i" file in the /source subdirectory. A source code listing containing each of the source code modules and each of the common blocks can be produced by running the "listing.make" script found in the distribution.

ACTION
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

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

ne14
number of 1-4 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
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

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

aebt
stretch-torsion energy partitioned over atoms

aett
torsion-torsion energy partitioned over atoms

aev
van der Waals energy partitioned over atoms

ae14
1-4 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 force constant to kcal/mole/deg**2

stbnunit
convert str-bend constant to kcal/mole/deg-Ang**2

aaunit
convert angle-angle constant to kcal/mole/deg**2

opbunit
convert out-of-plane bend force to kcal/mole/deg**2

opdunit
convert out-of-plane distance to kcal/mole/Ang**2

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

arg
strings containing the command line arguments

listarg
flag to mark available 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 bath control values

kelvin
target value for the system temperature (K)

atmsph
target value for the system pressure (atm)

tautemp
time constant in psec for temperature bath coupling

taupres
time constant in psec for pressure bath coupling

compress
isothermal compressibility of medium (atm-1)

isothermal
logical flag geverning use of temperature bath

isobaric
logical flag governing use of pressure bath

BNDPOT
specifics of bond stretch functional forms

cbnd
cubic coefficient in bond stretch potential

qbnd
quartic coefficient in bond stretch potential

bndunit
convert bond force constant to kcal/mole/Ang**2

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 pi-system

pbpl
pi-bond orders for bonds in "planar" pi-system

pnpl
pi-bond orders for bonds in "nonplanar" pi-system

BOUND
control of periodic boundary conditions

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

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 Angs**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

CENTRE
coordinates relative to molecule centroid

xcm
x-offset of atom from molecular center of mass

ycm
y-offset of atom from molecular center of mass

zcm
z-offset of atom from molecular center of mass

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 electrostatics functional form

dielec
dielectric constant for electrostatic interactions

chgscale
factor by which 1-4 electrostatic terms are scaled

chg12use
usage of 1-2 electrostatics (0=use, 1=omit, -1=scale)

chg13use
usage of 1-3 electrostatics (0=use, 1=omit, -1=scale)

chg14use
usage of 1-4 electrostatics (0=use, 1=omit, -1=scale)

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

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

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_lights
logical flag to use method of lights neighbors

use_ewald
logical flag governing use of Ewald summation term

DERIV
Cartesian coordinate derivative components

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

debt
stretch-torsion Cartesian coordinate derivatives

dett
torsion-torsion Cartesian coordinate derivatives

dev
van der Waals Cartesian coordinate derivatives

de14
1-4 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

vchir
signed volume values for chirality constraints

compact
index of local distance compaction on embedding

pathmax
maximum value of upper bound after smoothing

vdwmax
maximum value of hard sphere sum for an atom pair

nchir
total number of chirality constraints

ichir
numbers of atoms in each chirality constraint

use_invert
flag to use enantiomer closest to input structure

use_anneal
flag to use simulated annealing refinement

DOMEGA
derivative components over dihedrals

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

tebt
stretch-torsion derivatives over torsions

tett
torsion-torsion derivatives over torsions

tev
van der Waals derivatives over torsions

te14
1-4 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

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

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

e14
1-4 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 standard Ewald summation

aewald
Ewald convergence coefficient value (Ang-1)

frecip
percentage cutoff value for reciprocal sphere

kvec
number of standard Ewald reciprocal space vectors

tinfoil
flag governing use of tinfoil boundary conditions

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

wgrp
energetic weight of a group-group interaction

grpnum
original group number for each nonempty group

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

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 flags for I/O and program flow

digits
decimal places output for energy and coordinates

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

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 pi-system orbitals

maxnpi
maximum number of pi-system 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 pi-system bonds

KPOLR
forcefield parameters for polarizability

polr
dipole polarizability parameters for 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

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

cappa
stringency of line search (0=tight < cappa < 1=loose)

stpmin
minimum step length in current line search direction

stpmax
maximum step length in current line search direction

angmax
maximum angle between search direction and -gradient

intmax
maximum number of inner iterations 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

twosix
numerical value of the sixth root of two

MDSTUF
control of molecular dynamics trajectory

velsave
flag to save atomic velocity 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

iprint
iterations between status printing (0=no printing)

iwrite
iterations between coordinate dumps (0=no dumps)

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

a_old
previous acceleration of each atom along x,y,z-axes

MOMENT
components of the net multipole moments

netchg
net electric charge on the total system

xdipole
dipole moment of the system along the x-axis

ydipole
dipole moment of the system along the y-axis

zdipole
dipole moment of the system along the z-axis

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

dpole
derivative rotation matrix for each multipole

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

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 pi-system

q
number of pi-electrons contributed by each atom

w
ionization potential of each pi-system atom

em
repulsion integral for each pi-system atom

nfill
number of filled pi-system molecular orbitals

OUTPUT
control of coordinate output file format

archive
logical flag to save structures in an archive

binary
logical flag to substitute binary for ASCII format

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

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

npibond
total number of bonds affected by the pisystem

pibond
bond and piatom numbers for each pisystem bond

npitors
total number of torsions affected by the pisystem

pitors
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 pi-system

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

torspi
2-fold torsional energy barrier for pi-bond order of 1.0

PME
parameters specific for particle mesh Ewald

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

order
order of the PME B-spline approximation

POLAR
polarizabilities and induced dipole moments

polarize
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

npolar
total number of polarizable sites in the system

POLPOT
specifics of polarization functional form

poleps
induced dipole convergence criterion (rms Debyes/atom)

pradius
radius of an idealized atom with unit polarizability

pgamma
prefactor in exponential polarization damping term

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_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 pi-system 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

RESTRN
definition of the geometrical restraints

depth
depth of shallow Gaussian basin restraint

width
exponential width coefficient of Gaussian basin

rwall
radius of spherical droplet boundary restraint

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
flat-well range and force constant for each position

dfix
target range and force constant for each distance

tfix
target range and force constant for each torsion

npfix
number of position restraints to be applied

ipfix
atom number involved in each position restraint

ndfix
number of distance restraints to be applied

idfix
atom numbers defining each distance restraint

ntfix
number of torsional restraints to be applied

itfix
atom numbers defining each torsional restraint

use_basin
logical flag governing use of Gaussian basin

use_wall
logical flag governing use of droplet boundary

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 atom group

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

b2

ijk

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
one-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 constraints to be applied

irat
atom numbers of atoms in a rattle constraint

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

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 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
dihedral angles in molecular system

maxpi
atoms in conjugated pisystem

maxpib
covalent bonds in pisystem

maxpit
dihedrals involving pisystem

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

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 force to kcal/mole/deg**2

itorunit
convert improper torsion amplitudes to kcal/mole

torsunit
convert torsional parameter amplitudes to kcal/mole

storunit
convert stretch-torsion force to kcal/mole/Ang

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

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 constant to kcal/mole/Ang**2

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

vdwscale
factor by which 1-4 vdw interactions are scaled

igauss
coefficients of Gaussian fit to vdw potential

ngauss
number of Gaussians used in fit to vdw potential

vdw12use
usage of 1-2 vdw terms (1=omit, -1=use scaled value)

vdw13use
usage of 1-3 vdw terms (1=omit, -1=use scaled value)

vdw14use
usage of 1-4 vdw terms (1=omit, -1=use scaled value)

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 the internal virial

virx
x-component of the total internal virial

viry
y-component of the total internal virial

virz
z-component of the total internal virial

WARP
parameters for potential surface smoothing

m2
second moment of Gaussian representing each atom

deform
value of diffusional smoothing deformation parameter

diffb
diffusion coefficient for bond stretch potential

diffa
diffusion coefficient for angle bend potential

diffid
diffusion coefficient for improper dihedral potential

difft
diffusion coefficient for torsional potential

diffv
diffusion coefficient for van der Waals potential

diffc
diffusion coefficient for charge-charge potential

use_deform
flag to use diffusion smoothed potential terms

use_gda
flag to use Straub's GDA instead of Scheraga's DEM

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



© Goodman Group, 2005-2017; privacy; last updated November 16, 2017

department of chemistry University of Cambridge