

 

contents of common block variables

 
 

 
 

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 stretchbend energy terms computed
 neub
 number of UreyBradley energy terms computed
 neaa
 number of angleangle energy terms computed
 neopb
 number of outofplane bend energy terms computed
 neopd
 number of outofplane 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 stretchtorsion energy terms computed
 nett
 number of torsiontorsion energy terms computed
 nev
 number of van der Waals energy terms computed
 ne14
 number of 14 van der Waals energy terms computed
 nec
 number of chargecharge energy terms computed
 necd
 number of chargedipole energy terms computed
 ned
 number of dipoledipole 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
 stretchbend energy partitioned over atoms
 aeub
 UreyBradley energy partitioned over atoms
 aeaa
 angleangle energy partitioned over atoms
 aeopb
 outofplane bend energy partitioned over atoms
 aeopd
 outofplane 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
 stretchtorsion energy partitioned over atoms
 aett
 torsiontorsion energy partitioned over atoms
 aev
 van der Waals energy partitioned over atoms
 ae14
 14 van der Waals energy partitioned over atoms
 aec
 chargecharge energy partitioned over atoms
 aecd
 chargedipole energy partitioned over atoms
 aed
 dipoledipole 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
 angleangle terms in current structure
 kaa
 force constant for angleangle cross terms
 nangang
 total number of angleangle interactions
 iaa
 angle numbers used in each angleangle 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 strbend constant to kcal/mole/degAng**2
 aaunit
 convert angleangle constant to kcal/mole/deg**2
 opbunit
 convert outofplane bend force to kcal/mole/deg**2
 opdunit
 convert outofplane distance to kcal/mole/Ang**2
 mm2stbn
 logical flag governing use of MM2style stretchbend
 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 xcoordinate for each atom in the system
 y
 current ycoordinate for each atom in the system
 z
 current zcoordinate 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 (atm1)
 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 pisystem
 pbpl
 pibond orders for bonds in "planar" pisystem
 pnpl
 pibond orders for bonds in "nonplanar" pisystem
 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 aaxis of periodic box
 ybox
 length in Angs of baxis of periodic box
 zbox
 length in Angs of caxis of periodic box
 alpha
 angle in degrees between b and caxes of box
 beta
 angle in degrees between a and caxes of box
 gamma
 angle in degrees between a and baxes of box
 xbox2
 half of the aaxis length of periodic box
 ybox2
 half of the baxis length of periodic box
 zbox2
 half of the caxis length of periodic box
 box34
 threefourths 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 aaxis of the complete replicated cell
 ycell
 length of the baxis of the complete replicated cell
 zcell
 length of the caxis of the complete replicated cell
 xcell2
 half the length of the aaxis of the replicated cell
 ycell2
 half the length of the baxis of the replicated cell
 zcell2
 half the length of the caxis 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
 xoffset of atom from molecular center of mass
 ycm
 yoffset of atom from molecular center of mass
 zcm
 zoffset 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 14 electrostatic terms are scaled
 chg12use
 usage of 12 electrostatics (0=use, 1=omit, 1=scale)
 chg13use
 usage of 13 electrostatics (0=use, 1=omit, 1=scale)
 chg14use
 usage of 14 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
 nearneighbor atom connectivity lists
 n12
 number of atoms directly bonded to each atom
 i12
 atom numbers of atoms 12 connected to each atom
 n13
 number of atoms in a 13 relation to each atom
 i13
 atom numbers of atoms 13 connected to each atom
 n14
 number of atoms in a 14 relation to each atom
 i14
 atom numbers of atoms 14 connected to each atom
 CUTOFF
 cutoff distances for energy interactions
 vdwcut
 cutoff distance for van der Waals interactions
 chgcut
 cutoff distance for chargecharge interactions
 dplcut
 cutoff distance for dipoledipole interactions
 mpolecut
 cutoff distance for atomic multipole interactions
 vdwtaper
 distance at which van der Waals switching begins
 chgtaper
 distance at which chargecharge switching begins
 dpltaper
 distance at which dipoledipole 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
 stretchbend Cartesian coordinate derivatives
 deub
 UreyBradley Cartesian coordinate derivatives
 deaa
 angleangle Cartesian coordinate derivatives
 deopb
 outofplane bend Cartesian coordinate derivatives
 deopd
 outofplane distance Cartesian coordinate derivatives
 deid
 improper dihedral Cartesian coordinate derivatives
 deit
 improper torsion Cartesian coordinate derivatives
 det
 torsional Cartesian coordinate derivatives
 debt
 stretchtorsion Cartesian coordinate derivatives
 dett
 torsiontorsion Cartesian coordinate derivatives
 dev
 van der Waals Cartesian coordinate derivatives
 de14
 14 van der Waals Cartesian coordinate derivatives
 dec
 chargecharge Cartesian coordinate derivatives
 decd
 chargedipole Cartesian coordinate derivatives
 ded
 dipoledipole 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
 stretchbend derivatives over torsions
 teub
 UreyBradley derivatives over torsions
 teaa
 angleangle derivatives over torsions
 teopb
 outofplane bend derivatives over torsions
 teopd
 outofplane distance derivatives over torsions
 teid
 improper dihedral derivatives over torsions
 teit
 improper torsion derivatives over torsions
 tet
 torsional derivatives over torsions
 tebt
 stretchtorsion derivatives over torsions
 tett
 torsiontorsion derivatives over torsions
 tev
 van der Waals derivatives over torsions
 te14
 14 van der Waals derivatives over torsions
 tec
 chargecharge derivatives over torsions
 tecd
 chargedipole derivatives over torsions
 ted
 dipoledipole 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
 stretchbend potential energy of the system
 eub
 UreyBradley potential energy of the system
 eaa
 angleangle potential energy of the system
 eopb
 outofplane bend potential energy of the system
 eopd
 outofplane 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
 stretchtorsion potential energy of the system
 ett
 torsiontorsion potential energy of the system
 ev
 van der Waals potential energy of the system
 e14
 14 van der Waals potential energy of the system
 ec
 chargecharge potential energy of the system
 ecd
 chargedipole potential energy of the system
 ed
 dipoledipole 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 (Ang1)
 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 aaxis of center of mass
 yfrac
 fractional coordinate along baxis of center of mass
 zfrac
 fractional coordinate along caxis of center of mass
 GROUP
 partitioning of system into atom groups
 wgrp
 energetic weight of a groupgroup 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 xcomponent of current atom
 hessy
 Hessian elements for ycomponent of current atom
 hessz
 Hessian elements for zcomponent 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
 1fold amplitude and phase for each improper torsion
 itors2
 2fold amplitude and phase for each improper torsion
 itors3
 3fold 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 angleangle terms
 anan
 angleangle 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 5membered ring angle bend entries
 maxna4
 maximum number of 4membered ring angle bend entries
 maxna3
 maximum number of 3membered 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 5ring angle bends
 acon4
 force constant parameters for 4ring angle bends
 acon3
 force constant parameters for 3ring angle bends
 aconf
 force constant parameters for Fourier angle bends
 ang
 bond angle parameters for harmonic angle bends
 ang5
 bond angle parameters for 5ring angle bends
 ang4
 bond angle parameters for 4ring angle bends
 ang3
 bond angle parameters for 3ring 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 5ring angle bends
 ka4
 string of atom classes for 4ring angle bends
 ka3
 string of atom classes for 3ring 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 5membered ring bond stretch entries
 maxnb4
 maximum number of 4membered ring bond stretch entries
 maxnb3
 maximum number of 3membered ring bond stretch entries
 maxnel
 maximum number of electronegativity bond corrections
 bcon
 force constant parameters for harmonic bond stretch
 bcon5
 force constant parameters for 5ring bond stretch
 bcon4
 force constant parameters for 4ring bond stretch
 bcon3
 force constant parameters for 3ring bond stretch
 blen
 bond length parameters for harmonic bond stretch
 blen5
 bond length parameters for 5ring bond stretch
 blen4
 bond length parameters for 4ring bond stretch
 blen3
 bond length parameters for 3ring bond stretch
 dlen
 electronegativity bond length correction parameters
 kb
 string of atom classes for harmonic bond stretch
 kb5
 string of atom classes for 5ring bond stretch
 kb4
 string of atom classes for 4ring bond stretch
 kb3
 string of atom classes for 3ring 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 5membered ring dipole entries
 maxnd4
 maximum number of 4membered ring dipole entries
 maxnd3
 maximum number of 3membered ring dipole entries
 dpl
 dipole moment parameters for bond dipoles
 dpl5
 dipole moment parameters for 5ring dipoles
 dpl4
 dipole moment parameters for 4ring dipoles
 dpl3
 dipole moment parameters for 3ring dipoles
 pos
 dipole position parameters for bond dipoles
 pos5
 dipole position parameters for 5ring dipoles
 pos4
 dipole position parameters for 4ring dipoles
 pos3
 dipole position parameters for 3ring dipoles
 kd
 string of atom classes for bond dipoles
 kd5
 string of atom classes for 5ring dipoles
 kd4
 string of atom classes for 4ring dipoles
 kd3
 string of atom classes for 3ring 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 Hbonding 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 1fold rotation
 ti2
 torsional parameters for improper 2fold rotation
 ti3
 torsional parameters for improper 3fold 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 outofplane bend
 maxnopb
 maximum number of outofplane bending entries
 copb
 force constant parameters for outofplane bending
 kaopb
 string of atom classes for outofplane bending
 KOPDST
 forcefield parameters for outplane distance
 maxnopb
 maximum number of outofplane distance entries
 copb
 force constant parameters for outofplane distance
 kaopb
 string of atom classes for outofplane distance
 KORBS
 forcefield parameters for pisystem orbitals
 maxnpi
 maximum number of pisystem bond parameter entries
 electron
 number of pielectrons 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. pibond order
 tslope
 slope for 2fold torsion vs. pibond order
 kpi
 string of atom classes for pisystem bonds
 KPOLR
 forcefield parameters for polarizability
 polr
 dipole polarizability parameters for each atom type
 KSTBND
 forcefield parameters for stretchbending
 stbn
 stretchbending parameters for each atom class
 KSTTOR
 forcefield parameters for stretchtorsions
 maxnbt
 maximum number of stretchtorsion parameter entries
 btcon
 force constant parameters for stretchtorsion
 kbt
 string of atom classes for bonds in stretchtorsion
 KTORSN
 forcefield parameters for torsional angles
 maxnt
 maximum number of torsional angle parameter entries
 maxnt5
 maximum number of 5membered ring torsion entries
 maxnt4
 maximum number of 4membered ring torsion entries
 t1
 torsional parameters for standard 1fold rotation
 t2
 torsional parameters for standard 2fold rotation
 t3
 torsional parameters for standard 3fold rotation
 t4
 torsional parameters for standard 4fold rotation
 t5
 torsional parameters for standard 5fold rotation
 t6
 torsional parameters for standard 6fold rotation
 t15
 torsional parameters for 1fold rotation in 5ring
 t25
 torsional parameters for 2fold rotation in 5ring
 t35
 torsional parameters for 3fold rotation in 5ring
 t45
 torsional parameters for 4fold rotation in 5ring
 t55
 torsional parameters for 5fold rotation in 5ring
 t65
 torsional parameters for 6fold rotation in 5ring
 t14
 torsional parameters for 1fold rotation in 4ring
 t24
 torsional parameters for 2fold rotation in 4ring
 t34
 torsional parameters for 3fold rotation in 4ring
 t44
 torsional parameters for 4fold rotation in 4ring
 t54
 torsional parameters for 5fold rotation in 4ring
 t64
 torsional parameters for 6fold rotation in 4ring
 kt
 string of atom classes for torsional angles
 kt5
 string of atom classes for 5ring torsions
 kt4
 string of atom classes for 4ring torsions
 KURYBR
 forcefield parameters for UreyBradley terms
 maxnu
 maximum number of UreyBradley parameter entries
 ucon
 force constant parameters for UreyBradley terms
 dst13
 ideal 13 distance parameters for UreyBradley terms
 ku
 string of atom classes for UreyBradley 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 14 interactions
 eps4
 van der Waals well depth parameter in 14 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 xsorted list
 kby
 low index of neighbors of each site in the ysorted list
 kbz
 low index of neighbors of each site in the zsorted list
 kex
 high index of neighbors of each site in the xsorted list
 key
 high index of neighbors of each site in the ysorted list
 kez
 high index of neighbors of each site in the zsorted list
 locx
 pointer from xsorted list into original interaction list
 locy
 pointer from ysorted list into original interaction list
 locz
 pointer from zsorted list into original interaction list
 rgx
 pointer from original interaction list into xsorted list
 rgy
 pointer from original interaction list into ysorted list
 rgz
 pointer from original interaction list into zsorted 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 Hmatrix 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,zaxes
 a
 current acceleration of each atom along x,y,zaxes
 a_old
 previous acceleration of each atom along x,y,zaxes
 MOMENT
 components of the net multipole moments
 netchg
 net electric charge on the total system
 xdipole
 dipole moment of the system along the xaxis
 ydipole
 dipole moment of the system along the yaxis
 zdipole
 dipole moment of the system along the zaxis
 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 zaxis defining atom for each site
 xaxis
 number of the xaxis 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 Zmatrix of each dihedral angle
 OPBEND
 outofplane bends in the current structure
 kopb
 force constant values for outofplane bending
 nopbend
 total number of outofplane bends in the system
 iopb
 bond angle numbers used in outofplane bending
 OPDIST
 outofplane distances in current structure
 kopd
 force constant values for outofplane distance
 nopdist
 total number of outofplane distances in the system
 iopb
 numbers of the atoms in each outofplane distance
 ORBITS
 orbital energies for conjugated pisystem
 q
 number of pielectrons 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
 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 reactantproduct vector
 pzet
 current projection on reactantproduct vector
 pnorm
 length of the reactantproduct vector
 acoeff
 transformation matrix 'A' from Elber paper
 gc
 gradients of the path constraints
 PDB
 definition of a Protein Data Bank structure
 xpdb
 xcoordinate of each atom stored in PDB format
 ypdb
 ycoordinate of each atom stored in PDB format
 zpdb
 zcoordinate 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
 phipsiomegachi 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 pisystem
 bkpi
 bond stretch force constants for pibond order of 1.0
 blpi
 ideal bond length values for a pibond 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
 2fold torsional energy barrier for pibond 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 Bspline approximation
 maxtable
 maximum size of the FFT table array
 maxgrid
 maximum dimension of the PME charge grid array
 bsmod1
 Bspline moduli along the aaxis direction
 bsmod2
 Bspline moduli along the baxis direction
 bsmod3
 Bspline moduli along the caxis direction
 table
 intermediate array used by the FFT calculation
 nfft1
 number of grid points along the aaxis direction
 nfft2
 number of grid points along the baxis direction
 nfft3
 number of grid points along the caxis direction
 order
 order of the PME Bspline 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 stretchbend potential
 use_urey
 logical flag governing use of UreyBradley potential
 use_angang
 logical flag governing use of angleangle cross term
 use_opbend
 logical flag governing use of outofplane bend term
 use_opdist
 logical flag governing use of outofplane 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 stretchtorsion term
 use_tortor
 logical flag governing use of torsiontorsion term
 use_vdw
 logical flag governing use of vdw der Waals potential
 use_charge
 logical flag governing use of chargecharge potential
 use_chgdpl
 logical flag governing use of chargedipole potential
 use_dipole
 logical flag governing use of dipoledipole 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 xcoordinate for each atom in the system
 yref
 reference ycoordinate for each atom in the system
 zref
 reference zcoordinate 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 12 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
 threeletter abbreviations for amino acids types
 nuclz
 threeletter abbreviations for nucleic acids types
 amino1
 oneletter abbreviations for amino acids types
 nuclz1
 oneletter 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
 xcoordinate target for each restrained position
 ypfix
 ycoordinate target for each restrained position
 zpfix
 zcoordinate target for each restrained position
 pfix
 flatwell 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 xcoordinate for each atom
 yrb
 rigid body reference ycoordinate for each atom
 zrb
 rigid body reference zcoordinate for each atom
 rbc
 current rigid body coordinates for each atom group
 RING
 number and location of small ring structures
 nring3
 total number of 3membered rings in the system
 iring3
 numbers of the atoms involved in each 3ring
 nring4
 total number of 4membered rings in the system
 iring4
 numbers of the atoms involved in each 4ring
 nring5
 total number of 5membered rings in the system
 iring5
 numbers of the atoms involved in each 5ring
 nring6
 total number of 6membered rings in the system
 iring6
 numbers of the atoms involved in each 6ring
 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
 oneletter code for each residue in the sequence
 chnnam
 oneletter 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
 userdefined 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
 offdiagonal 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 5membered 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
 singleatom scale factor for analytical Still GB/SA
 p2
 12 interaction scale factor for analytical Still GB/SA
 p3
 13 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 selfenergy values for each atom
 shct
 overlap scaling factors for HawkinsCramerTruhlar 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
 stretchbends in the current structure
 ksb
 force constant for stretchbend terms
 nstrbnd
 total number of stretchbend interactions
 isb
 angle and bond numbers used in stretchbend
 STRTOR
 stretchtorsions in the current structure
 kst
 1, 2 and 3fold stretchtorsion force constants
 nstrtor
 total number of stretchtorsion interactions
 ist
 torsion and bond numbers used in stretchtorsion
 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 stretchtorsion force to kcal/mole/Ang
 TORS
 torsional angles within the current structure
 tors1
 1fold amplitude and phase for each torsional angle
 tors2
 2fold amplitude and phase for each torsional angle
 tors3
 3fold amplitude and phase for each torsional angle
 tors4
 4fold amplitude and phase for each torsional angle
 tors5
 5fold amplitude and phase for each torsional angle
 tors6
 6fold 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 electronvolts
 hartree
 conversion from Hartree to kcal/mole
 electric
 conversion from electron**2/Ang to kcal/mole
 debye
 conversion from electronAng to Debyes
 prescon
 conversion from kcal/mole/Ang**3 to Atm
 convert
 conversion from kcal to g*Ang**2/ps**2
 UREY
 UreyBradley interactions in the structure
 uk
 UreyBradley force constants (kcal/mole/Ang**2)
 ul
 ideal 13 distance values in Angstroms
 nurey
 total number of UreyBradley terms in the system
 iury
 numbers of the atoms in each UreyBradley interaction
 URYPOT
 specifics of UreyBradley functional form
 cury
 cubic coefficient in UreyBradley potential
 qury
 quartic coefficient in UreyBradley potential
 ureyunit
 convert UreyBradley 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 14 interaction pairs
 epsilon4
 well depth parameter for 14 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 147 vdw potential
 dhal
 value of "delta" in buffered 147 vdw potential
 vdwscale
 factor by which 14 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 12 vdw terms (1=omit, 1=use scaled value)
 vdw13use
 usage of 13 vdw terms (1=omit, 1=use scaled value)
 vdw14use
 usage of 14 vdw terms (1=omit, 1=use scaled value)
 vdwtyp
 type of van der Waals potential energy function
 radtyp
 type of parameter (sigma or Rmin) 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
 xcomponent of the total internal virial
 viry
 ycomponent of the total internal virial
 virz
 zcomponent 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 chargecharge 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 Zmatrix
 nadd
 number of added bonds between Zmatrix atoms
 iadd
 numbers of the atom pairs defining added bonds
 ndel
 number of bonds between Zmatrix bonds to delete
 idel
 numbers of the atom pairs defining deleted bonds
 ZCOORD
 Zmatrix internal coordinate definitions
 zbond
 bond length used to define each Zmatrix atom
 zang
 bond angle used to define each Zmatrix atom
 ztors
 angle or torsion used to define Zmatrix atom
 iz
 defining atom numbers for each Zmatrix atom

  
 
 
 
 

