Descriptions of Tinker Routines¶
The distribution version of the Tinker package contains over 700 separate programs, subroutines and functions. This section contains a brief description of the purpose of most of these code units. Further information can be found in the comments located at the top of each source code file.
ACTIVE Subroutine
“active” sets the list of atoms that are used during each potential energy Function** calculation
ADDBASE Subroutine
“addbase” builds the Cartesian coordinates for a single nucleic acid base; coordinates are read from the Protein Data Bank file or found from internal coordinates, then atom types are assigned and connectivity data generated
ADDBOND Subroutine
“addbond” adds entries to the attached atoms list in order to generate a direct connection between two atoms
ADDSIDE Subroutine
“addside” builds the Cartesian coordinates for a single amino acid side chain; coordinates are read from the Protein Data Bank file or found from internal coordinates, then atom types are assigned and connectivity data generated
ADJACENT Function
“adjacent” finds an atom connected to atom “i1” other than atom “i2”; if no such atom exists, then the closest atom in space is returned
ALCHEMY Program
“alchemy” computes the free energy difference corresponding to a small perturbation by Boltzmann weighting the potential energy difference over a number of sample states; current version (incorrectly) considers the charge energy to be intermolecular in finding the perturbation energies
ANALYSIS Subroutine
“analysis” calls the series of routines needed to calculate the potential energy and perform energy partitioning analysis in terms of type of interaction or atom number
ANALYZ4 Subroutine
“analyz4” prints the energy to 4 decimal places and number of interactions for each component of the potential energy
ANALYZ6 Subroutine
“analyz6” prints the energy to 6 decimal places and number of interactions for each component of the potential energy
ANALYZ8 Subroutine
“analyz8” prints the energy to 8 decimal places and number of interactions for each component of the potential energy
ANALYZE Program
“analyze” computes and displays the total potential; options are provided to partition the energy by atom or by potential Function** type; parameters used in computing interactions can also be displayed by atom; output of large energy interactions and of electrostatic and inertial properties is available
ANGLES Subroutine
“angles” finds the total number of bond angles and stores the atom numbers of the atoms defining each angle; for each angle to a trivalent central atom, the third bonded atom is stored for use in out-of-plane bending
ANNEAL Program
“anneal” performs a simulated annealing protocol by means of variable temperature molecular dynamics using either linear, exponential or sigmoidal cooling schedules
ANORM Function
“anorm” finds the norm (length) of a vector; used as a service routine by the Connolly surface area and volume computation
ARCHIVE Program
“archive” is a utility Program** for coordinate files which concatenates multiple coordinate sets into a single archive file, or extracts individual coordinate sets from an archive
ASET Subroutine
“aset” computes by recursion the A Function**s used in the evaluation of Slater-type (STO) overlap integrals
ATOMYZE Subroutine
“atomyze” prints the potential energy components broken down by atom and to a choice of precision
ATTACH Subroutine
“attach” generates lists of 1-3, 1-4 and 1-5 connectivities starting from the previously determined list of attached atoms (ie, 1-2 connectivity)
BASEFILE Subroutine
“basefile” extracts from an input filename the portion consisting of any directory name and the base filename
BCUCOF Subroutine
“bcucof” determines the coefficient matrix needed for bicubic interpolation of a Function**, gradients and cross derivatives
BCUINT Subroutine
“bcuint” performs a bicubic interpolation of the Function** value on a 2D spline grid
BCUINT1 Subroutine
“bcuint1” performs a bicubic interpolation of the Function** value and gradient along the directions of a 2D spline grid
BCUINT2 Subroutine
“bcuint2” performs a bicubic interpolation of the Function** value, gradient and Hessain along the directions of a 2D spline grid
BEEMAN Subroutine
“beeman” performs a single molecular dynamics time step by means of a Beeman multistep recursion formula; the actual coefficients are Brooks’ “Better Beeman” values
BETACF Function
“betacf” computes a rapidly convergent continued fraction needed by routine “betai” to evaluate the cumulative Beta distribution
BETAI Function
“betai” evaluates the cumulative Beta distribution Function** as the probability that a random variable from a distribution with Beta parameters “a” and “b” will be less than “x”
BIGBLOCK Subroutine
“bigblock” replicates the coordinates of a single unit cell to give a larger block of repeated units
BITORS Subroutine
“bitors” finds the total number of bitorsions, pairs of overlapping dihedral angles, and the numbers of the five atoms defining each bitorsion
BMAX Function
“bmax” computes the maximum order of the B Function**s needed for evaluation of Slater-type (STO) overlap integrals
BNDERR Function
“bnderr” is the distance bound error Function** and derivatives; this version implements the original and Havel’s normalized lower bound penalty, the normalized version is preferred when lower bounds are small (as with NMR NOE restraints), the original penalty is needed if large lower bounds are present
BONDS Subroutine
“bonds” finds the total number of covalent bonds and stores the atom numbers of the atoms defining each bond
BORN Subroutine
“born” computes the Born radius of each atom for use with the various GB/SA solvation models
BORN1 Subroutine
“born1” computes derivatives of the Born radii with respect to atomic coordinates and increments total energy derivatives and virial components for potentials involving Born radii
BOUNDS Subroutine
“bounds” finds the center of mass of each molecule and translates any stray molecules back into the periodic box
BSET Subroutine
“bset” computes by downward recursion the B Function**s used in the evaluation of Slater-type (STO) overlap integrals
BSPLINE Subroutine
“bspline” calculates the coefficients for an n-th order B-spline approximation
BSPLINE1 Subroutine
“bspline1” calculates the coefficients and derivative coefficients for an n-th order B-spline approximation
BSSTEP Subroutine
“bsstep” takes a single Bulirsch-Stoer step with monitoring of local truncation error to ensure accuracy
CALENDAR Subroutine
“calendar” returns the current time as a set of integer values representing the year, month, day, hour, minute and second
CELLATOM Subroutine
“cellatom” completes the addition of a symmetry related atom to a unit cell by updating the atom type and attachment arrays
CENTER Subroutine
“center” moves the weighted centroid of each coordinate set to the origin during least squares superposition
CERROR Subroutine
“cerror” is the error handling routine for the Connolly surface area and volume computation
CFFTB Subroutine
“cfftb” computes the backward complex discrete Fourier transform, the Fourier synthesis
CFFTB1 Subroutine
CFFTF Subroutine
“cfftf” computes the forward complex discrete Fourier transform, the Fourier analysis
CFFTF1 Subroutine
CFFTI Subroutine
“cffti” initializes the array “wsave” which is used in both forward and backward transforms; the prime factorization of “n” together with a tabulation of the trigonometric Function**s are computed and stored in “wsave”
CFFTI1 Subroutine
CHIRER Function
“chirer” computes the chirality error and its derivatives with respect to atomic Cartesian coordinates as a sum the squares of deviations of chiral volumes from target values
CHKCLASH Subroutine
“chkclash” determines if there are any atom clashes which might cause trouble on subsequent energy evaluation
CHKPOLE Subroutine
“chkpole” inverts atomic multipole moments as necessary at sites with chiral local reference frame definitions
CHKRING Subroutine
“chkring” tests angles to be constrained for their presence in small rings and removes constraints that are redundant
CHKSIZE Subroutine
“chksize” computes a measure of overall global structural expansion or compaction from the number of excess upper or lower bounds matrix violations
CHKTREE Subroutine
“chktree” tests a minimum energy structure to see if it belongs to the correct progenitor in the existing map
CHKXYZ Subroutine
“chkxyz” finds any pairs of atoms with identical Cartesian coordinates, and prints a warning message
CHOLESKY Subroutine
“cholesky” uses a modified Cholesky method to solve the linear system Ax = b, returning “x” in “b”; “A” is assumed to be a real symmetric positive definite matrix with its diagonal and upper triangle stored by rows
CIRPLN Subroutine
CJKM Function
“cjkm” computes the coefficients of spherical harmonics expressed in prolate spheroidal coordinates
CLIMBER Subroutine
CLIMBRGD Subroutine
CLIMBROT Subroutine
CLIMBTOR Subroutine
CLIMBXYZ Subroutine
CLOCK Subroutine
“clock” determines elapsed CPU time in seconds since the start of the job
CLUSTER Subroutine
“cluster” gets the partitioning of the system into groups and stores a list of the group to which each atom belongs
COLUMN Subroutine
“column” takes the off-diagonal Hessian elements stored as sparse rows and sets up indices to allow column access
COMMAND Subroutine
“command” uses the standard Unix-like iargc/getarg routines to get the number and values of arguments specified on the command line at Program** runtime
COMPRESS Subroutine
“compress” transfers only the non-buried tori from the temporary tori arrays to the final tori arrays
CONNECT Subroutine
“connect” sets up the attached atom arrays starting from a set of internal coordinates
CONNOLLY Subroutine
“connolly” uses the algorithms from the AMS/VAM Program**s of Michael Connolly to compute the analytical molecular surface area and volume of a collection of spherical atoms; thus it implements Fred Richards’ molecular surface definition as a set of analytically defined spherical and toroidal polygons
CONTACT Subroutine
“contact” constructs the contact surface, cycles and convex faces
CONTROL Subroutine
“control” gets initial values for parameters that determine the output style and information level provided by Tinker
COORDS Subroutine
“coords” converts the three principal eigenvalues/vectors from the metric matrix into atomic coordinates, and calls a routine to compute the rms deviation from the bounds
CORRELATE Program
“correlate” computes the time correlation Function** of some user-supplied property from individual snapshot frames taken from a molecular dynamics or other trajectory
CREATEJVM Subroutine
CREATESERVER Subroutine
CREATESYSTEM Subroutine
CREATEUPDATE Subroutine
CRYSTAL Program
“crystal” is a utility Program** which converts between fractional and Cartesian coordinates, and can generate full unit cells from asymmetric units
CUTOFFS Subroutine
“cutoffs” initializes and stores spherical energy cutoff distance windows, Hessian element and Ewald sum cutoffs, and the pairwise neighbor generation method
CYTSY Subroutine
“cytsy” solves a system of linear equations for a cyclically tridiagonal, symmetric, positive definite matrix
CYTSYP Subroutine
“cytsyp” finds the Cholesky factors of a cyclically tridiagonal symmetric, positive definite matrix given by two vectors
CYTSYS Subroutine
“cytsys” solves a cyclically tridiagonal linear system given the Cholesky factors
D1D2 Function
“d1d2” is a utility Function** used in computation of the reaction field recursive summation elements
DELETE Subroutine
“delete” removes a specified atom from the Cartesian coordinates list and shifts the remaining atoms
DEPTH Function
DESTROYJVM Subroutine
DESTROYSERVER Subroutine
DFTMOD Subroutine
“dftmod” computes the modulus of the discrete Fourier transform of “bsarray”, storing it into “bsmod”
DIAGQ Subroutine
“diagq” is a matrix diagonalization routine which is derived from the classical given, housec, and eigen algorithms with several modifications to increase the efficiency and accuracy
DIFFEQ Subroutine
“diffeq” performs the numerical integration of an ordinary differential equation using an adaptive stepsize method to solve the corresponding coupled first-order equations of the general form dyi/dx = f(x,y1,…,yn) for yi = y1,…,yn
DIFFUSE Program
“diffuse” finds the self-diffusion constant for a homogeneous liquid via the Einstein relation from a set of stored molecular dynamics frames; molecular centers of mass are unfolded and mean squared displacements are computed versus time separation
DIST2 Function
“dist2” finds the distance squared between two points; used as a service routine by the Connolly surface area and volume computation
DISTGEOM Program
“distgeom” uses a metric matrix distance geometry procedure to generate structures with interpoint distances that lie within specified bounds, with chiral centers that maintain chirality, and with torsional angles restrained to desired values; the user also has the ability to interactively inspect and alter the triangle smoothed bounds matrix prior to embedding
DMDUMP Subroutine
“dmdump” puts the distance matrix of the final structure into the upper half of a matrix, the distance of each atom to the centroid on the diagonal, and the individual terms of the bounds errors into the lower half of the matrix
DOCUMENT Program
“document” generates a formatted description of all the code modules or common blocks, an index of routines called by each source code module, a listing of all valid keywords, a list of include file dependencies as needed by a Unix-style Makefile, or a formatted force field parameter set summary
DOT Function
“dot” finds the dot product of two vectors
DSTMAT Subroutine
“dstmat” selects a distance matrix containing values between the previously smoothed upper and lower bounds; the distance values are chosen from uniform distributions, in a triangle correlated fashion, or using random partial metrization
DYNAMIC Program
“dynamic” computes a molecular dynamics trajectory in any of several statistical mechanical ensembles with optional periodic boundaries and optional coupling to temperature and pressure baths alternatively a stochastic dynamics trajectory can be generated
EANGANG Subroutine
“eangang” calculates the angle-angle potential energy
EANGANG1 Subroutine
“eangang1” calculates the angle-angle potential energy and first derivatives with respect to Cartesian coordinates
EANGANG2 Subroutine
“eangang2” calculates the angle-angle potential energy second derivatives with respect to Cartesian coordinates using finite difference methods
EANGANG2A Subroutine
“eangang2a” calculates the angle-angle first derivatives for a single interaction with respect to Cartesian coordinates; used in computation of finite difference second derivatives
EANGANG3 Subroutine
“eangang3” calculates the angle-angle potential energy; also partitions the energy among the atoms
EANGLE Subroutine
“eangle” calculates the angle bending potential energy; projected in-plane angles at trigonal centers or Fourier angle bending terms are optionally used
EANGLE1 Subroutine
“eangle1” calculates the angle bending potential energy and the first derivatives with respect to Cartesian coordinates; projected in-plane angles at trigonal centers or Fourier angle bending terms are optionally used
EANGLE2 Subroutine
“eangle2” calculates second derivatives of the angle bending energy for a single atom using a mixture of analytical and finite difference methods; projected in-plane angles at trigonal centers or Fourier angle bending terms are optionally used
EANGLE2A Subroutine
“eangle2a” calculates bond angle bending potential energy second derivatives with respect to Cartesian coordinates
EANGLE2B Subroutine
“eangle2b” computes projected in-plane bending first derivatives for a single angle with respect to Cartesian coordinates; used in computation of finite difference second derivatives
EANGLE3 Subroutine
“eangle3” calculates the angle bending potential energy, also partitions the energy among the atoms; projected in-plane angles at trigonal centers or Fourier angle bending terms are optionally used
EBOND Subroutine
“ebond” calculates the bond stretching energy
EBOND1 Subroutine
“ebond1” calculates the bond stretching energy and first derivatives with respect to Cartesian coordinates
EBOND2 Subroutine
“ebond2” calculates second derivatives of the bond stretching energy for a single atom at a time
EBOND3 Subroutine
“ebond3” calculates the bond stretching energy; also partitions the energy among the atoms
EBUCK Subroutine
“ebuck” calculates the Buckingham exp-6 van der Waals energy
EBUCK0A Subroutine
“ebuck0a” calculates the Buckingham exp-6 van der Waals energy using a pairwise double loop
EBUCK0B Subroutine
“ebuck0b” calculates the Buckingham exp-6 van der Waals energy using the method of lights to locate neighboring atoms
EBUCK0C Subroutine
“ebuck0c” calculates the Buckingham exp-6 van der Waals energy via a Gaussian approximation for potential energy smoothing
EBUCK1 Subroutine
“ebuck1” calculates the Buckingham exp-6 van der Waals energy and its first derivatives with respect to Cartesian coordinates
EBUCK1A Subroutine
“ebuck1a” calculates the Buckingham exp-6 van der Waals energy and its first derivatives using a pairwise double loop
EBUCK1B Subroutine
“ebuck1b” calculates the Buckingham exp-6 van der Waals energy and its first derivatives using the method of lights to locate neighboring atoms
EBUCK1C Subroutine
“ebuck1c” calculates the Buckingham exp-6 van der Waals energy and its first derivatives via a Gaussian approximation for potential energy smoothing
EBUCK2 Subroutine
“ebuck2” calculates the Buckingham exp-6 van der Waals second derivatives for a single atom at a time
EBUCK2A Subroutine
“ebuck2a” calculates the Buckingham exp-6 van der Waals second derivatives using a double loop over relevant atom pairs
EBUCK2B Subroutine
“ebuck2b” calculates the Buckingham exp-6 van der Waals second derivatives via a Gaussian approximation for use with potential energy smoothing
EBUCK3 Subroutine
“ebuck3” calculates the Buckingham exp-6 van der Waals energy and partitions the energy among the atoms
EBUCK3A Subroutine
“ebuck3a” calculates the Buckingham exp-6 van der Waals energy and partitions the energy among the atoms using a pairwise double loop
EBUCK3B Subroutine
“ebuck3b” calculates the Buckingham exp-6 van der Waals energy and also partitions the energy among the atoms using the method of lights to locate neighboring atoms
EBUCK3C Subroutine
“ebuck3c” calculates the Buckingham exp-6 van der Waals energy via a Gaussian approximation for potential energy smoothing
ECHARGE Subroutine
“echarge” calculates the charge-charge interaction energy
ECHARGE0A Subroutine
“echarge0a” calculates the charge-charge interaction energy using a pairwise double loop
ECHARGE0B Subroutine
“echarge0b” calculates the charge-charge interaction energy using the method of lights to locate neighboring atoms
ECHARGE0C Subroutine
“echarge0c” calculates the charge-charge interaction energy for use with potential smoothing methods
ECHARGE0D Subroutine
“echarge0d” calculates the charge-charge interaction energy using a particle mesh Ewald summation
ECHARGE0E Subroutine
“echarge0e” calculates the charge-charge interaction energy using a particle mesh Ewald summation and the method of lights to locate neighboring atoms
ECHARGE1 Subroutine
“echarge1” calculates the charge-charge interaction energy and first derivatives with respect to Cartesian coordinates
ECHARGE1A Subroutine
“echarge1a” calculates the charge-charge interaction energy and first derivatives with respect to Cartesian coordinates using a pairwise double loop
ECHARGE1B Subroutine
“echarge1b” calculates the charge-charge interaction energy and first derivatives with respect to Cartesian coordinates using the method of lights to locate neighboring atoms
ECHARGE1C Subroutine
“echarge1c” calculates the charge-charge interaction energy and first derivatives with respect to Cartesian coordinates for use with potential smoothing methods
ECHARGE1D Subroutine
“echarge1d” calculates the charge-charge interaction energy and first derivatives with respect to Cartesian coordinates using a particle mesh Ewald summation
ECHARGE2 Subroutine
“echarge2” calculates second derivatives of the charge-charge interaction energy for a single atom
ECHARGE2A Subroutine
“echarge2a” calculates second derivatives of the charge-charge interaction energy for a single atom using a pairwise double loop
ECHARGE2B Subroutine
“echarge2b” calculates second derivatives of the charge-charge interaction energy for a single atom for use with potential smoothing methods
ECHARGE2C Subroutine
“echarge2c” calculates second derivatives of the charge-charge interaction energy for a single atom using a particle mesh Ewald summation
ECHARGE3 Subroutine
“echarge3” calculates the charge-charge interaction energy and partitions the energy among the atoms
ECHARGE3A Subroutine
“echarge3a” calculates the charge-charge interaction energy and partitions the energy among the atoms using a pairwise double loop
ECHARGE3B Subroutine
“echarge3b” calculates the charge-charge interaction energy and partitions the energy among the atoms using the method of lights to locate neighboring atoms
ECHARGE3C Subroutine
“echarge3c” calculates the charge-charge interaction energy and partitions the energy among the atoms for use with potential smoothing methods
ECHARGE3D Subroutine
“echarge3d” calculates the charge-charge interaction energy and partitions the energy among the atoms using a particle mesh Ewald summation
ECHARGE3E Subroutine
“echarge3e” calculates the charge-charge interaction energy and partitions the energy among the atoms using a particle mesh Ewald summation and the method of lights to locate neighboring atoms
ECHGDPL Subroutine
“echgdpl” calculates the charge-dipole interaction energy
ECHGDPL1 Subroutine
“echgdpl1” calculates the charge-dipole interaction energy and first derivatives with respect to Cartesian coordinates
ECHGDPL2 Subroutine
“echgdpl2” calculates second derivatives of the charge-dipole interaction energy for a single atom
ECHGDPL3 Subroutine
“echgdpl3” calculates the charge-dipole interaction energy; also partitions the energy among the atoms
EDIPOLE Subroutine
“edipole” calculates the dipole-dipole interaction energy
EDIPOLE1 Subroutine
“edipole1” calculates the dipole-dipole interaction energy and first derivatives with respect to Cartesian coordinates
EDIPOLE2 Subroutine
“edipole2” calculates second derivatives of the dipole-dipole interaction energy for a single atom
EDIPOLE3 Subroutine
“edipole3” calculates the dipole-dipole interaction energy; also partitions the energy among the atoms
EGAUSS Subroutine
“egauss” calculates the Gaussian expansion van der Waals interaction energy
EGAUSS0A Subroutine
“egauss0a” calculates the Gaussian expansion van der Waals interaction energy using a pairwise double loop
EGAUSS0B Subroutine
“egauss0b” calculates the Gaussian expansion van der Waals interaction energy for use with potential energy smoothing
EGAUSS1 Subroutine
“egauss1” calculates the Gaussian expansion van der Waals interaction energy and its first derivatives with respect to Cartesian coordinates
EGAUSS1A Subroutine
“egauss1a” calculates the Gaussian expansion van der Waals interaction energy and its first derivatives using a pairwise double loop
EGAUSS1B Subroutine
“egauss1b” calculates the Gaussian expansion van der Waals interaction energy and its first derivatives for use with stophat potential energy smoothing
EGAUSS2 Subroutine
“egauss2” calculates the Gaussian expansion van der Waals second derivatives for a single atom at a time
EGAUSS2A Subroutine
“egauss2a” calculates the Gaussian expansion van der Waals second derivatives using a pairwise double loop
EGAUSS2B Subroutine
“egauss2b” calculates the Gaussian expansion van der Waals second derivatives for stophat potential energy smoothing
EGAUSS3 Subroutine
“egauss3” calculates the Gaussian expansion van der Waals interaction energy and partitions the energy among the atoms
EGAUSS3A Subroutine
“egauss3a” calculates the Gaussian expansion van der Waals interaction energy and partitions the energy among the atoms using a pairwise double loop
EGAUSS3B Subroutine
“egauss3b” calculates the Gaussian expansion van der Waals interaction energy and partitions the energy among the atoms using a pairwise double loop
EGBSA0A Subroutine
“egbsa0a” calculates the generalized Born polarization energy for the GB/SA solvation models
EGBSA0B Subroutine
“egbsa0b” calculates the generalized Born polarization energy for the GB/SA solvation models for use with potential smoothing methods via analogy to the smoothing of Coulomb’s law
EGBSA1A Subroutine
“egbsa1a” calculates the generalized Born energy and first derivatives of the GB/SA solvation models
EGBSA1B Subroutine
“egbsa1b” calculates the generalized Born energy and first derivatives of the GB/SA solvation models for use with potential smoothing methods
EGBSA2A Subroutine
“egbsa2a” calculates second derivatives of the generalized Born energy term for the GB/SA solvation models
EGBSA2B Subroutine
“egbsa2b” calculates second derivatives of the generalized Born energy term for the GB/SA solvation models for use with potential smoothing methods
EGBSA3A Subroutine
“egbsa3a” calculates the generalized Born energy term for the GB/SA solvation models; also partitions the energy among the atoms
EGBSA3B Subroutine
“egbsa3b” calculates the generalized Born polarization energy for the GB/SA solvation models for use with potential smoothing methods via analogy to the smoothing of Coulomb’s law; also partitions the energy among the atoms
EGEOM Subroutine
“egeom” calculates the energy due to restraints on positions, distances, angles and torsions as well as Gaussian basin and spherical droplet restraints
EGEOM1 Subroutine
“egeom1” calculates the energy and first derivatives with respect to Cartesian coordinates due to restraints on positions, distances, angles and torsions as well as Gaussian basin and spherical droplet restraints
EGEOM2 Subroutine
“egeom2” calculates second derivatives of restraints on positions, distances, angles and torsions as well as Gaussian basin and spherical droplet restraints
EGEOM3 Subroutine
“egeom3” calculates the energy due to restraints on positions, distances, angles and torsions as well as Gaussian basin and droplet restraints; also partitions energy among the atoms
EHAL Subroutine
“ehal” calculates the buffered 14-7 van der Waals energy
EHAL0A Subroutine
“ehal0a” calculates the buffered 14-7 van der Waals energy using a pairwise double loop
EHAL0B Subroutine
“ehal0a” calculates the buffered 14-7 van der Waals energy using the method of lights to locate neighboring atoms
EHAL1 Subroutine
“ehal1” calculates the buffered 14-7 van der Waals energy and its first derivatives with respect to Cartesian coordinates
EHAL1A Subroutine
“ehal1a” calculates the buffered 14-7 van der Waals energy and its first derivatives with respect to Cartesian coordinates using a pairwise double loop
EHAL1B Subroutine
“ehal1b” calculates the buffered 14-7 van der Waals energy and its first derivatives with respect to Cartesian coordinates using the method of lights to locate neighboring atoms
EHAL2 Subroutine
“ehal2” calculates the buffered 14-7 van der Waals second derivatives for a single atom at a time
EHAL3 Subroutine
“ehal3” calculates the buffered 14-7 van der Waals energy and partitions the energy among the atoms
EHAL3A Subroutine
“ehal3a” calculates the buffered 14-7 van der Waals energy and partitions the energy among the atoms using a pairwise double loop
EHAL3B Subroutine
“ehal3b” calculates the buffered 14-7 van der Waals energy and also partitions the energy among the atoms using the method of lights to locate neighboring atoms
EIGEN Subroutine
“eigen” uses the power method to compute the largest eigenvalues and eigenvectors of the metric matrix, “valid” is set true if the first three eigenvalues are positive
EIGENRGD Subroutine
EIGENROT Subroutine
EIGENROT Subroutine
EIGENTOR Subroutine
EIGENXYZ Subroutine
EIMPROP Subroutine
“eimprop” calculates the improper dihedral potential energy
EIMPROP1 Subroutine
“eimprop1” calculates improper dihedral energy and its first derivatives with respect to Cartesian coordinates
EIMPROP2 Subroutine
“eimprop2” calculates second derivatives of the improper dihedral angle energy for a single atom
EIMPROP3 Subroutine
“eimprop3” calculates the improper dihedral potential energy; also partitions the energy terms among the atoms
EIMPTOR Subroutine
“eimptor” calculates the improper torsion potential energy
EIMPTOR1 Subroutine
“eimptor1” calculates improper torsion energy and its first derivatives with respect to Cartesian coordinates
EIMPTOR2 Subroutine
“eimptor2” calculates second derivatives of the improper torsion energy for a single atom
EIMPTOR3 Subroutine
“eimptor3” calculates the improper torsion potential energy; also partitions the energy terms among the atoms
ELJ Subroutine
“elj” calculates the Lennard-Jones 6-12 van der Waals energy
ELJ0A Subroutine
“elj0a” calculates the Lennard-Jones 6-12 van der Waals energy using a pairwise double loop
ELJ0B Subroutine
“elj0b” calculates the Lennard-Jones 6-12 van der Waals energy using the method of lights to locate neighboring atoms
ELJ0C Subroutine
“elj0c” calculates the Lennard-Jones 6-12 van der Waals energy via a Gaussian approximation for potential energy smoothing
ELJ0D Subroutine
“elj0d” calculates the Lennard-Jones 6-12 van der Waals energy for use with stophat potential energy smoothing
ELJ1 Subroutine
“elj1” calculates the Lennard-Jones 6-12 van der Waals energy and its first derivatives with respect to Cartesian coordinates
ELJ1A Subroutine
“elj1a” calculates the Lennard-Jones 6-12 van der Waals energy and its first derivatives using a pairwise double loop
ELJ1B Subroutine
“elj1b” calculates the Lennard-Jones 6-12 van der Waals energy and its first derivatives using the method of lights to locate neighboring atoms
ELJ1C Subroutine
“elj1c” calculates the Lennard-Jones 6-12 van der Waals energy and its first derivatives via a Gaussian approximation for potential energy smoothing
ELJ1D Subroutine
“elj1d” calculates the van der Waals interaction energy and its first derivatives for use with stophat potential energy smoothing
ELJ2 Subroutine
“elj2” calculates the Lennard-Jones 6-12 van der Waals second derivatives for a single atom at a time
ELJ2A Subroutine
“elj2a” calculates the Lennard-Jones 6-12 van der Waals second derivatives using a double loop over relevant atom pairs
ELJ2B Subroutine
“elj2b” calculates the Lennard-Jones 6-12 van der Waals second derivatives via a Gaussian approximation for use with potential energy smoothing
ELJ2C Subroutine
“elj2c” calculates the Lennard-Jones 6-12 van der Waals second derivatives for use with stophat potential energy smoothing
ELJ3 Subroutine
“elj3” calculates the Lennard-Jones 6-12 van der Waals energy and also partitions the energy among the atoms
ELJ3A Subroutine
“elj3a” calculates the Lennard-Jones 6-12 van der Waals energy and also partitions the energy among the atoms using a pairwise double loop
ELJ3B Subroutine
“elj3b” calculates the Lennard-Jones 6-12 van der Waals energy and also partitions the energy among the atoms using the method of lights to locate neighboring atoms
ELJ3C Subroutine
“elj3c” calculates the Lennard-Jones 6-12 van der Waals energy and also partitions the energy among the atoms via a Gaussian approximation for potential energy smoothing
ELJ3D Subroutine
“elj3d” calculates the Lennard-Jones 6-12 van der Waals energy and also partitions the energy among the atoms for use with stophat potential energy smoothing
EMBED Subroutine
“embed” is a distance geometry routine patterned after the ideas of Gordon Crippen, Irwin Kuntz and Tim Havel; it takes as input a set of upper and lower bounds on the interpoint distances, chirality restraints and torsional restraints, and attempts to generate a set of coordinates that satisfy the input bounds and restraints
EMETAL Subroutine
“emetal” calculates the transition metal ligand field energy
EMETAL1 Subroutine
“emetal1” calculates the transition metal ligand field energy and its first derivatives with respect to Cartesian coordinates
EMETAL2 Subroutine
“emetal2” calculates the transition metal ligand field second derivatives for a single atom at a time
EMETAL3 Subroutine
“emetal3” calculates the transition metal ligand field energy and also partitions the energy among the atoms
EMM3HB Subroutine
“emm3hb” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen bonding energy
EMM3HB0A Subroutine
“emm3hb0a” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen bonding energy using a pairwise double loop
EMM3HB0B Subroutine
“emm3hb0b” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen bonding energy using the method of lights to locate neighboring atoms
EMM3HB1 Subroutine
“emm3hb1” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen bonding energy with respect to Cartesian coordinates
EMM3HB1A Subroutine
“emm3hb1a” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen bonding energy with respect to Cartesian coordinates using a pairwise double loop
EMM3HB1B Subroutine
“emm3hb1b” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen bonding energy with respect to Cartesian coordinates using the method of lights to locate neighboring atoms
EMM3HB2 Subroutine
“emm3hb2” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen bonding second derivatives for a single atom at a time
EMM3HB3 Subroutine
“emm3hb3” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen bonding energy, and partitions the energy among the atoms
EMM3HB3A Subroutine
“emm3hb3” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen bonding energy, and partitions the energy among the atoms
EMM3HB3B Subroutine
“emm3hb3b” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen bonding energy using the method of lights to locate neighboring atoms
EMPOLE Subroutine
“empole” calculates the electrostatic energy due to atomic multipole interactions and dipole polarizability
EMPOLE0A Subroutine
“empole0a” calculates the electrostatic energy due to atomic multipole interactions and dipole polarizability using a pairwise double loop
EMPOLE0B Subroutine
“empole0b” calculates the electrostatic energy due to atomic multipole interactions and dipole polarizability using a regular Ewald summation
EMPOLE1 Subroutine
“empole1” calculates the multipole and dipole polarization energy and derivatives with respect to Cartesian coordinates
EMPOLE1A Subroutine
“empole1a” calculates the multipole and dipole polarization energy and derivatives with respect to Cartesian coordinates using a pairwise double loop
EMPOLE1B Subroutine
“empole1b” calculates the multipole and dipole polarization energy and derivatives with respect to Cartesian coordinates using a regular Ewald summation
EMPOLE2 Subroutine
“empole2” calculates second derivatives of the multipole and dipole polarization energy for a single atom at a time
EMPOLE2A Subroutine
“empole2a” computes multipole and dipole polarization first derivatives for a single atom with respect to Cartesian coordinates; used to get finite difference second derivatives
EMPOLE3 Subroutine
“empole3” calculates the electrostatic energy due to atomic multipole interactions and dipole polarizability, and partitions the energy among the atoms
EMPOLE3A Subroutine
“empole3a” calculates the electrostatic energy due to atomic multipole interactions and dipole polarizability, and partitions the energy among the atoms using a double loop
EMPOLE3B Subroutine
“empole3b” calculates the electrostatic energy due to atomic multipole interactions and dipole polarizability, and partitions the energy among the atoms using a regular Ewald summation
ENERGY Function
“energy” calls the Subroutine**s to calculate the potential energy terms and sums up to form the total energy
ENRGYZE Subroutine
“energyze” is an auxiliary routine for the analyze Program** that performs the energy analysis and prints the total and intermolecular energies
EOPBEND Subroutine
“eopbend” computes the out-of-plane bend potential energy at trigonal centers via a Wilson-Decius-Cross angle bend
EOPBEND1 Subroutine
“eopbend1” computes the out-of-plane bend potential energy and first derivatives at trigonal centers via a Wilson-Decius-Cross angle bend
EOPBEND2 Subroutine
“eopbend2” calculates second derivatives of the out-of-plane bend energy via a Wilson-Decius-Cross angle bend for a single atom using finite difference methods
EOPBEND2A Subroutine
“eopbend2a” calculates out-of-plane bending first derivatives at a trigonal center via a Wilson-Decius-Cross angle bend; used in computation of finite difference second derivatives
EOPBEND3 Subroutine
“eopbend3” computes the out-of-plane bend potential energy at trigonal centers via a Wilson-Decius-Cross angle bend; also partitions the energy among the atoms
EOPDIST Subroutine
“eopdist” computes the out-of-plane distance potential energy at trigonal centers via the central atom height
EOPDIST1 Subroutine
“eopdist1” computes the out-of-plane distance potential energy and first derivatives at trigonal centers via the central atom height
EOPDIST2 Subroutine
“eopdist2” calculates second derivatives of the out-of-plane distance energy for a single atom via the central atom height
EOPDIST3 Subroutine
“eopdist3” computes the out-of-plane distance potential energy at trigonal centers via the central atom height; also partitions the energy among the atoms
EPITORS Subroutine
“epitors” calculates the pi-orbital torsion potential energy
EPITORS1 Subroutine
“epitors1” calculates the pi-orbital torsion potential energy and first derivatives with respect to Cartesian coordinates
EPITORS2 Subroutine
“epitors2” calculates the second derivatives of the pi-orbital torsion energy for a single atom using finite difference methods
EPITORS2A Subroutine
“epitors2a” calculates the pi-orbital torsion first derivatives; used in computation of finite difference second derivatives
EPITORS3 Subroutine
“epitors3” calculates the pi-orbital torsion potential energy; also partitions the energy terms among the atoms
EPME Subroutine
“epme” computes the reciprocal space energy for a particle mesh Ewald summation over partial charges
EPME1 Subroutine
“epme1” computes the reciprocal space energy and first derivatives for a particle mesh Ewald summation
EPME3 Subroutine
“epme3” computes the reciprocal space energy for a particle mesh Ewald summation over partial charges and prints information about the energy over the charge grid points
EPUCLC Subroutine
EREAL Subroutine
“ereal” evaluates the real space portion of the regular Ewald summation energy due to atomic multipole interactions and dipole polarizability
EREAL1 Subroutine
“ereal1” evaluates the real space portion of the regular Ewald summation energy and gradient due to atomic multipole interactions and dipole polarizability
EREAL3 Subroutine
“ereal3” evaluates the real space portion of the regular Ewald summation energy due to atomic multipole interactions and dipole polarizability and partitions the energy among the atoms
ERECIP Subroutine
“erecip” evaluates the reciprocal space portion of the regular Ewald summation energy due to atomic multipole interactions and dipole polarizability
ERECIP1 Subroutine
“erecip1” evaluates the reciprocal space portion of the regular Ewald summation energy and gradient due to atomic multipole interactions and dipole polarizability
ERECIP3 Subroutine
“erecip3” evaluates the reciprocal space portion of the regular Ewald summation energy due to atomic multipole interactions and dipole polarizability, and prints information about the energy over the reciprocal lattice vectors
ERF Function
“erf” computes a numerical approximation to the value of the error Function** via a Chebyshev approximation
ERFC Function
“erfc” computes a numerical approximation to the value of the complementary error Function** via a Chebyshev approximation
ERFCORE Subroutine
“erfcore” evaluates erf(x) or erfc(x) for a real argument x; when called with mode set to 0 it returns erf, a mode of 1 returns erfc; uses rational Function**s that approximate erf(x) and erfc(x) to at least 18 significant decimal digits
ERFIK Subroutine
“erfik” compute the reaction field energy due to a single pair of atomic multipoles
ERFINV Function
“erfinv” evaluates the inverse of the error Function** erf for a real argument in the range (-1,1) using a rational Function** approximation followed by cycles of Newton-Raphson correction
ERXNFLD Subroutine
“erxnfld” calculates the macroscopic reaction field energy arising from a set of atomic multipoles
ERXNFLD1 Subroutine
“erxnfld1” calculates the macroscopic reaction field energy and derivatives with respect to Cartesian coordinates
ERXNFLD2 Subroutine
“erxnfld2” calculates second derivatives of the macroscopic reaction field energy for a single atom at a time
ERXNFLD3 Subroutine
“erxnfld3” calculates the macroscopic reaction field energy, and also partitions the energy among the atoms
ESOLV Subroutine
“esolv” calculates the continuum solvation energy via either the Eisenberg-McLachlan ASP model, Ooi-Scheraga SASA model, various GB/SA methods or the ACE model
ESOLV1 Subroutine
“esolv1” calculates the continuum solvation energy and first derivatives with respect to Cartesian coordinates using either the Eisenberg-McLachlan ASP, Ooi-Scheraga SASA or various GB/SA solvation models
ESOLV2 Subroutine
“esolv2” calculates second derivatives of the continuum solvation energy using either the Eisenberg-McLachlan ASP, Ooi-Scheraga SASA or various GB/SA solvation models
ESOLV3 Subroutine
“esolv3” calculates the continuum solvation energy using either the Eisenberg-McLachlan ASP model, Ooi-Scheraga SASA model, various GB/SA methods or the ACE model; also partitions the energy among the atoms
ESTRBND Subroutine
“estrbnd” calculates the stretch-bend potential energy
ESTRBND1 Subroutine
“estrbnd1” calculates the stretch-bend potential energy and first derivatives with respect to Cartesian coordinates
ESTRBND2 Subroutine
“estrbnd2” calculates the stretch-bend potential energy second derivatives with respect to Cartesian coordinates
ESTRBND3 Subroutine
“estrbnd3” calculates the stretch-bend potential energy; also partitions the energy among the atoms
ESTRTOR Subroutine
“estrtor” calculates the stretch-torsion potential energy
ESTRTOR1 Subroutine
“estrtor1” calculates the stretch-torsion energy and first derivatives with respect to Cartesian coordinates
ESTRTOR2 Subroutine
“estrtor2” calculates the stretch-torsion potential energy second derivatives with respect to Cartesian coordinates
ESTRTOR3 Subroutine
“estrtor3” calculates the stretch-torsion potential energy; also partitions the energy terms among the atoms
ETORS Subroutine
“etors” calculates the torsional potential energy
ETORS0A Subroutine
“etors0a” calculates the torsional potential energy using a standard sum of Fourier terms
ETORS0B Subroutine
“etors0b” calculates the torsional potential energy for use with potential energy smoothing methods
ETORS1 Subroutine
“etors1” calculates the torsional potential energy and first derivatives with respect to Cartesian coordinates
ETORS1A Subroutine
“etors1a” calculates the torsional potential energy and first derivatives with respect to Cartesian coordinates using a standard sum of Fourier terms
ETORS1B Subroutine
“etors1b” calculates the torsional potential energy and first derivatives with respect to Cartesian coordinates for use with potential energy smoothing methods
ETORS2 Subroutine
“etors2” calculates the second derivatives of the torsional energy for a single atom
ETORS2A Subroutine
“etors2a” calculates the second derivatives of the torsional energy for a single atom using a standard sum of Fourier terms
ETORS2B Subroutine
“etors2b” calculates the second derivatives of the torsional energy for a single atom for use with potential energy smoothing methods
ETORS3 Subroutine
“etors3” calculates the torsional potential energy; also partitions the energy among the atoms
ETORS3A Subroutine
“etors3a” calculates the torsional potential energy using a standard sum of Fourier terms and partitions the energy among the atoms
ETORS3B Subroutine
“etors3b” calculates the torsional potential energy for use with potential energy smoothing methods and partitions the energy among the atoms
ETORTOR Subroutine
“etortor” calculates the torsion-torsion potential energy
ETORTOR1 Subroutine
“etortor1” calculates the torsion-torsion energy and first derivatives with respect to Cartesian coordinates
ETORTOR2 Subroutine
“etortor2” calculates the torsion-torsion potential energy second derivatives with respect to Cartesian coordinates
ETORTOR3 Subroutine
“etortor3” calculates the torsion-torsion potential energy; also partitions the energy terms among the atoms
EUREY Subroutine
“eurey” calculates the Urey-Bradley 1-3 interaction energy
EUREY1 Subroutine
“eurey1” calculates the Urey-Bradley interaction energy and its first derivatives with respect to Cartesian coordinates
EUREY2 Subroutine
“eurey2” calculates second derivatives of the Urey-Bradley interaction energy for a single atom at a time
EUREY3 Subroutine
“eurey3” calculates the Urey-Bradley energy; also partitions the energy among the atoms
EWALDCOF Subroutine
“ewaldcof” finds a value of the Ewald coefficient such that all terms beyond the specified cutoff distance will have an value less than a specified tolerance
EXPLORE Subroutine
“explore” uses simulated annealing on an initial crude embedded distance geoemtry structure to refine versus the bound, chirality, planarity and torsional error Function**s
EXTRA Subroutine
“extra” calculates any additional user defined potential energy contribution
EXTRA1 Subroutine
“extra1” calculates any additional user defined potential energy contribution and its first derivatives
EXTRA2 Subroutine
“extra2” calculates second derivatives of any additional user defined potential energy contribution for a single atom at a time
EXTRA3 Subroutine
“extra3” calculates any additional user defined potential contribution and also partitions the energy among the atoms
FATAL Subroutine
“fatal” terminates execution due to a user request, a severe error or some other nonstandard condition
FFTBACK Subroutine
FFTFRONT Subroutine
FFTSETUP Subroutine
FIELD Subroutine
“field” sets the force field potential energy Function**s from a parameter file and modifications specified in a keyfile
FINAL Subroutine
“final” performs any final Program** actions, prints a status message, and then pauses if necessary to avoid closing the execution window
FINDATM Subroutine
“findatm” locates a specific PDB atom name type within a range of atoms from the PDB file, returns zero if the name type was not found
FIXPDB Subroutine
“fixpdb” corrects problems with PDB files by converting residue and atom names to the forms used by Tinker
FRACDIST Subroutine
“fracdist” computes a normalized distribution of the pairwise fractional distances between the smoothed upper and lower bounds
FREEUNIT Function
“freeunit” finds an unopened Fortran I/O unit and returns its numerical value from 1 to 99; the units already assigned to “input” and “iout” (usually 5 and 6) are skipped since they have special meaning as the default I/O units
GAMMLN Function
“gammln” uses a series expansion due to Lanczos to compute the natural logarithm of the Gamma Function** at “x” in [0,1]
GDA Program
“gda” implements Gaussian Density Annealing (GDA) algorithm for global optimization via simulated annealing
GDA1 Subroutine
GDA2 Function
GDA3 Subroutine
GDASTAT Subroutine
GENDOT Subroutine
“gendot” finds the coordinates of a specified number of surface points for a sphere with the input radius and coordinate center
GEODESIC Subroutine
“geodesic” smooths the upper and lower distance bounds via the triangle inequality using a sparse matrix version of a shortest path algorithm
GEOMETRY Function
“geometry” finds the value of the interatomic distance, angle or dihedral angle defined by two to four input atoms
GETBASE Subroutine
“getbase” finds the base heavy atoms for a single nucleotide residue and copies the names and coordinates to the Protein Data Bank file
GETIME Subroutine
“getime” gets elapsed CPU time in seconds for an interval
GETINT Subroutine
“getint” asks for an internal coordinate file name, then reads the internal coordinates and computes Cartesian coordinates
GETKEY Subroutine
“getkey” finds a valid keyfile and stores its contents as line images for subsequent keyword parameter searching
GETMOL2 Subroutine
“getmol2” asks for a Sybyl MOL2 molecule file name, then reads the coordinates from the file
GETMONITOR Subroutine
GETNUCH Subroutine
“getnuch” finds the nucleotide hydrogen atoms for a single residue and copies the names and coordinates to the Protein Data Bank file
GETNUMB Subroutine
“getnumb” searchs an input string from left to right for an integer and puts the numeric value in “number”; returns zero with “next” unchanged if no integer value is found
GETPDB Subroutine
“getpdb” asks for a Protein Data Bank file name, then reads in the coordinates file
GETPRB Subroutine
“getprb” tests for a possible probe position at the interface between three neighboring atoms
GETPRM Subroutine
“getprm” finds the potential energy parameter file and then opens and reads the parameters
GETPROH Subroutine
“getproh” finds the hydrogen atoms for a single amino acid residue and copies the names and coordinates to the Protein Data Bank file
GETREF Subroutine
“getref” copies structure information from the reference area into the standard variables for the current system structure
GETSEQ Subroutine
“getseq” asks the user for the amino acid sequence and torsional angle values needed to define a peptide
GETSEQN Subroutine
“getseqn” asks the user for the nucleotide sequence and torsional angle values needed to define a nucleic acid
GETSIDE Subroutine
“getside” finds the side chain heavy atoms for a single amino acid residue and copies the names and coordinates to the Protein Data Bank file
GETSTRING Subroutine
“getstring” searchs for a quoted text string within an input character string; the region between the first and second quotes is returned as the “text”; if the actual text is too long, only the first part is returned
GETTEXT Subroutine
“gettext” searchs an input string for the first string of non-blank characters; the region from a non-blank character to the first blank space is returned as “text”; if the actual text is too long, only the first part is returned
GETTOR Subroutine
“gettor” tests for a possible torus position at the interface between two atoms, and finds the torus radius, center and axis
GETWORD Subroutine
“getword” searchs an input string for the first alphabetic character (A-Z or a-z); the region from this first character to the first blank space or comma is returned as a “word”; if the actual word is too long, only the first part is returned
GETXYZ Subroutine
“getxyz” asks for a Cartesian coordinate file name, then reads in the coordinates file
GRADIENT Subroutine
“gradient” calls Subroutine**s to calculate the potential energy and first derivatives with respect to Cartesian coordinates
GRADRGD Subroutine
“gradrgd” calls Subroutine**s to calculate the potential energy and first derivatives with respect to rigid body coordinates
GRADROT Subroutine
“gradrot” calls Subroutine**s to calculate the potential energy and its torsional first derivatives
GRAFIC Subroutine
“grafic” outputs the upper & lower triangles and diagonal of a square matrix in a schematic form for visual inspection
GROUPS Subroutine
“groups” tests a set of atoms to see if all are members of a single atom group or a pair of atom groups; if so, then the correct intra- or intergroup weight is assigned
GRPLINE Subroutine
“grpline” tests each atom group for linearity of the sites contained in the group
GYRATE Subroutine
“gyrate” computes the radius of gyration of a molecular system from its atomic coordinates
HANGLE Subroutine
“hangle” constructs hybrid angle bending parameters given an initial state, final state and “lambda” value
HATOM Subroutine
“hatom” assigns a new atom type to each hybrid site
HBOND Subroutine
“hbond” constructs hybrid bond stretch parameters given an initial state, final state and “lambda” value
HCHARGE Subroutine
“hcharge” constructs hybrid charge interaction parameters given an initial state, final state and “lambda” value
HDIPOLE Subroutine
“hdipole” constructs hybrid dipole interaction parameters given an initial state, final state and “lambda” value
HESSIAN Subroutine
“hessian” calls Subroutine**s to calculate the Hessian elements for each atom in turn with respect to Cartesian coordinates
HESSRGD Subroutine
“hessrgd” computes the numerical Hessian elements with respect to rigid body coordinates via 6*ngroup+1 gradient evaluations
HESSROT Subroutine
“hessrot” computes the numerical Hessian elements with respect to torsional angles; either the full matrix or just the diagonal can be calculated; the full matrix needs nomega+1 gradient evaluations while the diagonal requires just two gradient calls
HIMPTOR Subroutine
“himptor” constructs hybrid improper torsional parameters given an initial state, final state and “lambda” value
HSTRBND Subroutine
“hstrbnd” constructs hybrid stretch-bend parameters given an initial state, final state and “lambda” value
HSTRTOR Subroutine
“hstrtor” constructs hybrid stretch-torsion parameters given an initial state, final state and “lambda” value
HTORS Subroutine
“htors” constructs hybrid torsional parameters for a given initial state, final state and “lambda” value
HVDW Subroutine
“hvdw” constructs hybrid van der Waals parameters given an initial state, final state and “lambda” value
HYBRID Subroutine
“hybrid” constructs the hybrid hamiltonian for a specified initial state, final state and mutation parameter “lambda”
IJKPTS Subroutine
“ijkpts” stores a set of indices used during calculation of macroscopic reaction field energetics
IMAGE Subroutine
“image” takes the components of pairwise distance between two points in the same or neighboring periodic boxes and converts to the components of the minimum image distance
IMPOSE Subroutine
“impose” performs the least squares best superposition of two atomic coordinate sets via a quaternion method; upon return, the first coordinate set is unchanged while the second set is translated and rotated to give best fit; the final root mean square fit is returned in “rmsvalue”
INDUCE Subroutine
“induce” computes the induced dipole moment at each polarizable site due to direct or mutual polarization; assumes that multipole components have already been rotated into the global coordinate frame
INDUCE0A Subroutine
“induce0a” computes the induced dipole moment at each polarizable site using a pairwise double loop
INDUCE0B Subroutine
“induce0b” computes the induced dipole moment at each polarizable site using a regular Ewald summation
INEDGE Subroutine
“inedge” inserts a concave edge into the linked list for its temporary torus
INERTIA Subroutine
“inertia” computes the principal moments of inertia for the system, and optionally translates the center of mass to the origin and rotates the principal axes onto the global axes
INITERR Function
“initerr” is the initial error Function** and derivatives for a distance geometry embedding; it includes components from the local geometry and torsional restraint errors
INITIAL Subroutine
“initial” sets up original values for some parameters and variables that might not otherwise get initialized
INITPRM Subroutine
“initprm” completely initializes a force field by setting all parameters to zero and using defaults for control values
INITRES Subroutine
“initres” sets names for biopolymer residue types used in PDB file conversion and automated generation of structures
INITROT Subroutine
“initrot” sets the torsional angles which are to be rotated in subsequent computation, by default automatically selects all rotatable single bonds; assumes internal coordinates have already been setup
INSERT Subroutine
“insert” adds the specified atom to the Cartesian coordinates list and shifts the remaining atoms
INTEDIT Program
“intedit” allows the user to extract information from or alter the values within an internal coordinates file
INTXYZ Program
“intxyz” takes as input an internal coordinates file, converts to and then writes out Cartesian coordinates
INVBETA Function
“invbeta” computes the inverse Beta distribution Function** via a combination of Newton iteration and bisection search
INVERT Subroutine
“invert” inverts a matrix using the Gauss-Jordan method
IPEDGE Subroutine
“ipedge” inserts convex edge into linked list for atom
ISPLPE Subroutine
“isplpe” computes the coefficients for a cubic periodic interpolating spline
JACOBI Subroutine
“jacobi” performs a matrix diagonalization of a real symmetric matrix by the method of Jacobi rotations
KANGANG Subroutine
“kangang” assigns the parameters for angle-angle cross term interactions and processes new or changed parameter values
KANGLE Subroutine
“kangle” assigns the force constants and ideal angles for the bond angles; also processes new or changed parameters
KATOM Subroutine
“katom” assigns an atom type definitions to each atom in the structure and processes any new or changed values
KBOND Subroutine
“kbond” assigns a force constant and ideal bond length to each bond in the structure and processes any new or changed parameter values
KCHARGE Subroutine
“kcharge” assigns partial charges to the atoms within the structure and processes any new or changed values
KCHIRAL Subroutine
“kchiral” determines the target value for each chirality and planarity restraint as the signed volume of the parallelpiped spanned by vectors from a common atom to each of three other atoms
KDIPOLE Subroutine
“kdipole” assigns bond dipoles to the bonds within the structure and processes any new or changed values
KENEG Subroutine
“keneg” applies primary and secondary electronegativity bond length corrections to applicable bond parameters
KEWALD Subroutine
“kewald” assigns both regular Ewald summation and particle mesh Ewald parameters for a periodic box
KGEOM Subroutine
“kgeom” asisgns parameters for geometric restraint terms to be included in the potential energy calculation
KIMPROP Subroutine
“kimprop” assigns potential parameters to each improper dihedral in the structure and processes any changed values
KIMPTOR Subroutine
“kimptor” assigns torsional parameters to each improper torsion in the structure and processes any changed values
KINETIC Subroutine
“kinetic” computes the total kinetic energy and kinetic energy contributions to the pressure tensor by summing over velocities
KMETAL Subroutine
“kmetal” assigns ligand field parameters to transition metal atoms and processes any new or changed parameter values
KMPOLE Subroutine
“kmpole” assigns atomic multipole moments to the atoms of the structure and processes any new or changed values
KOPBEND Subroutine
“kopbend” assigns the force constants for out-of-plane bending at trigonal centers via Wilson-Decius-Cross angle bends; also processes any new or changed parameter values
KOPDIST Subroutine
“kopdist” assigns the force constants for out-of-plane distance at trigonal centers via the central atom height; also processes any new or changed parameter values
KORBIT Subroutine
“korbit” assigns pi-orbital parameters to conjugated systems and processes any new or changed parameters
KPITORS Subroutine
“kpitors” assigns pi-orbital torsion parameters to torsions needing them, and processes any new or changed values
KPOLAR Subroutine
“kpolar” assigns atomic dipole polarizabilities to the atoms within the structure and processes any new or changed values
KSOLV Subroutine
“ksolv” assigns continuum solvation energy parameters for the Eisenberg-McLachlan ASP, Ooi-Scheraga SASA or various GB/SA solvation models
KSTRBND Subroutine
“kstrbnd” assigns the parameters for the stretch-bend interactions and processes new or changed parameter values
KSTRTOR Subroutine
“kstrtor” assigns stretch-torsion parameters to torsions needing them, and processes any new or changed values
KTORS Subroutine
“ktors” assigns torsional parameters to each torsion in the structure and processes any new or changed values
KTORTOR Subroutine
“ktortor” assigns torsion-torsion parameters to adjacent torsion pairs and processes any new or changed values
KUREY Subroutine
“kurey” assigns the force constants and ideal distances for the Urey-Bradley 1-3 interactions; also processes any new or changed parameter values
KVDW Subroutine
“kvdw” assigns the parameters to be used in computing the van der Waals interactions and processes any new or changed values for these parameters
LATTICE Subroutine
“lattice” stores the periodic box dimensions and sets angle values to be used in computing fractional coordinates
LBFGS Subroutine
“lbfgs” is a limited memory BFGS quasi-newton nonlinear optimization routine
LIGASE Subroutine
“ligase” translates a nucleic acid structure in Protein Data Bank format to a Cartesian coordinate file and sequence file
LIGHTS Subroutine
“lights” computes the set of nearest neighbor interactions using the method of lights algorithm
LINBODY Subroutine
“linbody” finds the angular velocity of a linear rigid body given the inertia tensor and angular momentum
LMSTEP Subroutine
“lmstep” computes the Levenberg-Marquardt step during a nonlinear least squares calculation; this version is based upon ideas from the Minpack routine LMPAR together with with the internal doubling strategy of Dennis and Schnabel
LOCALMIN Subroutine
“localmin” is used during normal mode local search to perform a Cartesian coordinate energy minimization
LOCALRGD Subroutine
“localrgd” is used during the PSS local search procedure to perform a rigid body energy minimization
LOCALROT Subroutine
“localrot” is used during the PSS local search procedure to perform a torsional space energy minimization
LOCALXYZ Subroutine
“localxyz” is used during the potential smoothing and search procedure to perform a local optimization at the current smoothing level
LOCERR Function
“locerr” is the local geometry error Function** and derivatives including the 1-2, 1-3 and 1-4 distance bound restraints
LOWCASE Subroutine
“lowcase” converts a text string to all lower case letters
MAJORIZE Subroutine
“majorize” refines the projected coordinates by attempting to minimize the least square residual between the trial distance matrix and the distances computed from the coordinates
MAKEINT Subroutine
“makeint” converts Cartesian to internal coordinates where selection of internal coordinates is controlled by “mode”
MAKEPDB Subroutine
“makexyz” converts a set of Cartesian coordinates to Protein Data Bank format with special handling for systems consisting of polypeptide chains, ligands and water molecules
MAKEREF Subroutine
“makeref” copies the information contained in the “xyz” file of the current structure into corresponding reference areas
MAKEXYZ Subroutine
“makexyz” generates a complete set of Cartesian coordinates for a full structure from the internal coordinate values
MAPCHECK Subroutine
“mapcheck” checks the current minimum energy structure for possible addition to the master list of local minima
MAXWELL Function
“maxwell” returns a speed in Angstroms/picosecond randomly selected from a 3-D Maxwell-Boltzmann distribution for the specified particle mass and system temperature
MCM1 Function
“mcm1” is a service routine that computes the energy and gradient for truncated Newton optimization in Cartesian coordinate space
MCM2 Subroutine
“mcm2” is a service routine that computes the sparse matrix Hessian elements for truncated Newton optimization in Cartesian coordinate space
MCMSTEP Function
“mcmstep” implements the minimization phase of an MCM step via Cartesian minimization following a Monte Carlo step
MDINIT Subroutine
“mdinit” initializes the velocities and accelerations for a molecular dynamics trajectory, including restarts
MDREST Subroutine
“mdrest” finds and removes any translational or rotational kinetic energy of the overall system center of mass
MDSAVE Subroutine
“mdsave” writes molecular dynamics trajectory snapshots and auxiliary files with velocity and induced dipole information; also checks for user requested termination of a simulation
MDSTAT Subroutine
“mdstat” is called at each molecular dynamics time step to form statistics on various average values and fluctuations, and to periodically save the state of the trajectory
MEASFN Subroutine
MEASFP Subroutine
MEASFS Subroutine
MEASPM Subroutine
“measpm” computes the volume of a single prism section of the full interior polyhedron
MECHANIC Subroutine
“mechanic” sets up needed parameters for the potential energy calculation and reads in many of the user selectable options
MERGE Subroutine
“merge” combines the reference and current structures into a single new “current” structure containing the reference atoms followed by the atoms of the current structure
METRIC Subroutine
“metric” takes as input the trial distance matrix and computes the metric matrix of all possible dot products between the atomic vectors and the center of mass using the law of cosines and the following formula for the distances to the center of mass:
MIDERR Function
“miderr” is the secondary error Function** and derivatives for a distance geometry embedding; it includes components from the distance bounds, local geometry, chirality and torsional restraint errors
MINIMIZ1 Function
“minimiz1” is a service routine that computes the energy and gradient for a low storage BFGS optimization in Cartesian coordinate space
MINIMIZE Program
“minimize” performs energy minimization in Cartesian coordinate space using a low storage BFGS nonlinear optimization
MINIROT Program
“minirot” performs an energy minimization in torsional angle space using a low storage BFGS nonlinear optimization
MINIROT1 Function
“minirot1” is a service routine that computes the energy and gradient for a low storage BFGS nonlinear optimization in torsional angle space
MINPATH Subroutine
“minpath” is a routine for finding the triangle smoothed upper and lower bounds of each atom to a specified root atom using a sparse variant of the Bellman-Ford shortest path algorithm
MINRIGID Program
“minrigid” performs an energy minimization of rigid body atom groups using a low storage BFGS nonlinear optimization
MINRIGID1 Function
“minrigid1” is a service routine that computes the energy and gradient for a low storage BFGS nonlinear optimization of rigid bodies
MMID Subroutine
“mmid” implements a modified midpoint method to advance the integration of a set of first order differential equations
MODECART Subroutine
MODEROT Subroutine
MODESRCH Subroutine
MODETORS Subroutine
MODULI Subroutine
“moduli” sets the moduli of the inverse discrete Fourier transform of the B-splines; bsmod[1-3] hold these values, nfft[1-3] are the grid dimensions, bsorder is the order of B-spline approximation
MOLECULE Subroutine
“molecule” counts the molecules, assigns each atom to its molecule and computes the mass of each molecule
MOLUIND Subroutine
“moluind” computes the molecular induced dipole components in the presence of an external electric field
MOMENTS Subroutine
“moments” computes the total electric charge, dipole and quadrupole moments for the entire system as a sum over the partial charges, bond dipoles and atomic multipole moments
MONTE Program
“monte” performs a Monte Carlo/MCM conformational search using either Cartesian single atom or torsional move sets
MUTATE Subroutine
“mutate” constructs the hybrid hamiltonian for a specified initial state, final state and mutation parameter “lambda”
NEEDUPDATE Subroutine
NEIGHBOR Subroutine
“neighbor” finds all of the neighbors of each atom
NEWATM Subroutine
“newatm” creates and defines an atom needed for the Cartesian coordinates file, but which may not present in the original Protein Data Bank file
NEWTON Program
“newton” performs an energy minimization in Cartesian coordinate space using a truncated Newton method
NEWTON1 Function
“newton1” is a service routine that computes the energy and gradient for truncated Newton optimization in Cartesian coordinate space
NEWTON2 Subroutine
“newton2” is a service routine that computes the sparse matrix Hessian elements for truncated Newton optimization in Cartesian coordinate space
NEWTROT Program
“newtrot” performs an energy minimization in torsional angle space using a truncated Newton conjugate gradient method
NEWTROT1 Function
“newtrot1” is a service routine that computes the energy and gradient for truncated Newton conjugate gradient optimization in torsional angle space
NEWTROT2 Subroutine
“newtrot2” is a service routine that computes the sparse matrix Hessian elements for truncated Newton optimization in torsional angle space
NEXTARG Subroutine
“nextarg” finds the next unused command line argument and returns it in the input character string
NEXTTEXT Function
“nexttext” finds and returns the location of the first non-blank character within an input text string; zero is returned if no such character is found
NORMAL Function
“normal” generates a random number from a normal Gaussian distribution with a mean of zero and a variance of one
NUCBASE Subroutine
“nucbase” builds the side chain for a single nucleotide base in terms of internal coordinates
NUCCHAIN Subroutine
“nucchain” builds up the internal coordinates for a nucleic acid sequence from the sugar type, backbone and glycosidic torsional values
NUCLEIC Program
“nucleic” builds the internal and Cartesian coordinates of a polynucleotide from nucleic acid sequence and torsional angle values for the nucleic acid backbone and side chains
NUMBER Function
“number” converts a text numeral into an integer value; the input string must contain only numeric characters
NUMERAL Subroutine
“numeral” converts an input integer number into the corresponding right- or left-justified text numeral
NUMGRAD Subroutine
“numgrad” computes the gradient of the objective Function** “fvalue” with respect to Cartesian coordinates of the atoms via a two-sided numerical differentiation
OCVM Subroutine
“ocvm” is an optimally conditioned variable metric nonlinear optimization routine without line searches
OLDATM Subroutine
“oldatm” get the Cartesian coordinates for an atom from the Protein Data Bank file, then assigns the atom type and atomic connectivities
OPENEND Subroutine
“openend” opens a file on a Fortran unit such that the position is set to the bottom for appending to the end of the file
OPTIMIZ1 Function
“optimiz1” is a service routine that computes the energy and gradient for optimally conditioned variable metric optimization in Cartesian coordinate space
OPTIMIZE Program
“optimize” performs energy minimization in Cartesian coordinate space using an optimally conditioned variable metric method
OPTIROT Program
“optirot” performs an energy minimization in torsional angle space using an optimally conditioned variable metric method
OPTIROT1 Function
“optirot1” is a service routine that computes the energy and gradient for optimally conditioned variable metric optimization in torsional angle space
OPTRIGID Program
“optrigid” performs an energy minimization of rigid body atom groups using an optimally conditioned variable metric method
OPTRIGID1 Function
“optrigid1” is a service routine that computes the energy and gradient for optimally conditioned variable metric optimization of rigid bodies
OPTSAVE Subroutine
“optsave” is used by the optimizers to write imtermediate coordinates and other relevant information; also checks for user requested termination of an optimization
ORBITAL Subroutine
“orbital” finds and organizes lists of atoms in a pisystem, bonds connecting pisystem atoms and torsions whose two central atoms are both pisystem atoms
ORIENT Subroutine
“orient” computes a set of reference Cartesian coordinates in standard orientation for each rigid body atom group
ORTHOG Subroutine
“orthog” performs an orthogonalization of an input matrix via the modified Gram-Schmidt algorithm
OVERLAP Subroutine
“overlap” computes the overlap for two parallel p-orbitals given the atomic numbers and distance of separation
PARAMYZE Subroutine
“paramyze” prints the force field parameters used in the computation of each of the potential energy terms
PASSB Subroutine
PASSB2 Subroutine
PASSB3 Subroutine
PASSB4 Subroutine
PASSB5 Subroutine
PASSF Subroutine
PASSF2 Subroutine
PASSF3 Subroutine
PASSF4 Subroutine
PASSF5 Subroutine
PATH Program
“path” locates a series of structures equally spaced along a conformational pathway connecting the input reactant and product structures; a series of constrained optimizations orthogonal to the path is done via Lagrangian multipliers
PATH1 Function
PATHPNT Subroutine
“pathpnt” finds a structure on the synchronous transit path with the specified path value “t”
PATHSCAN Subroutine
“pathscan” makes a scan of a synchronous transit pathway by computing structures and energies for specific path values
PATHVAL Subroutine
“pathval” computes the synchronous transit path value for the specified structure
PDBATM Subroutine
“pdbatm” adds an atom to the Protein Data Bank file
PDBXYZ Program
“pdbxyz” takes as input a Protein Data Bank file and then converts to and writes out a Cartesian coordinates file and, for biopolymers, a sequence file
PIALTER Subroutine
“pialter” first modifies bond lengths and force constants according to the standard bond slope parameters and the bond order values stored in “pnpl”; also alters some 2-fold torsional parameters based on the bond-order * beta matrix
PIMOVE Subroutine
“pimove” rotates the vector between atoms “list(1)” and “list(2)” so that atom 1 is at the origin and atom 2 along the x-axis; the atoms defining the respective planes are also moved and their bond lengths normalized
PIPLANE Subroutine
“piplane” selects the three atoms which specify the plane perpendicular to each p-orbital; the current version will fail in certain situations, including ketenes, allenes, and isolated or adjacent triple bonds
PISCF Subroutine
“piscf” performs an scf molecular orbital calculation for the pisystem using a modified Pariser-Parr-Pople method
PITILT Subroutine
“pitilt” calculates for each pibond the ratio of the actual p-orbital overlap integral to the ideal overlap if the same orbitals were perfectly parallel
PLACE Subroutine
“place” finds the probe sites by putting the probe sphere tangent to each triple of neighboring atoms
POLARGRP Subroutine
“polargrp” generates members of the polarization group of each atom and separate lists of the 1-2, 1-3 and 1-4 group connectivities
POLARIZE Program
“polarize” computes the molecular polarizability by applying an external field along each axis followed by diagonalization of the resulting polarizability tensor
POLYMER Subroutine
“polymer” tests for the presence of an infinite polymer extending across periodic boundaries
POLYP Subroutine
“polyp” is a polynomial product routine that multiplies two algebraic forms
POTNRG Function
POTOFF Subroutine
“potoff” clears the forcefield definition by turning off the use of each of the potential energy Function**s
POWER Subroutine
“power” uses the power method with deflation to compute the few largest eigenvalues and eigenvectors of a symmetric matrix
PRECISE Function
“precise” finds a machine precision value as selected by the input argument: (1) the smallest positive floating point value, (2) the smallest relative floating point spacing, (3) the largest relative floating point spacing
PRECOND Subroutine
“precond” solves a simplified version of the Newton equations Ms = r, and uses the result to precondition linear conjugate gradient iterations on the full Newton equations in “tnsolve”
PRESSURE Subroutine
“pressure” uses the internal virial to find the pressure in a periodic box and maintains a constant desired pressure by scaling the coordinates via coupling to an external constant pressure bath
PRMKEY Subroutine
“field” parses a text string to extract keywords related to force field potential energy Function**al forms and constants
PROCHAIN Subroutine
“prochain” builds up the internal coordinates for an amino acid sequence from the phi, psi, omega and chi values
PROJCT Subroutine
PROMO Subroutine
“promo” writes a short message containing information about the Tinker version number and the copyright notice
PROPERTY Function
“property” takes two input snapshot frames and computes the value of the property for which the correlation Function** is being accumulated
PROPYZE Subroutine
“propyze” finds and prints the total charge, dipole moment components, radius of gyration and moments of inertia
PROSIDE Subroutine
“proside” builds the side chain for a single amino acid residue in terms of internal coordinates
PROTEIN Program
“protein” builds the internal and Cartesian coordinates of a polypeptide from amino acid sequence and torsional angle values for the peptide backbone and side chains
PRTARC Subroutine
“prtarc” writes out a set of Cartesian coordinates for all active atoms in the Tinker XYZ archive format
PRTCAR Subroutine
“prtcar” writes out a set of Cartesian coordinates for all active atoms in the Accelerys InsightII .car format
PRTDYN Subroutine
“prtdyn” writes out the information needed to restart a molecular dynamics trajectory to an external disk file
PRTERR Subroutine
“prterr” writes out a set of coordinates to a disk file prior to aborting on a serious error
PRTINT Subroutine
“prtint” writes out a set of Z-matrix internal coordinates to an external disk file
PRTMOL2 Program
“prtmol2” writes out a set of coordinates in Sybyl MOL2 format to an external disk file
PRTPDB Subroutine
“prtpdb” writes out a set of Protein Data Bank coordinates to an external disk file
PRTPRM Subroutine
“prtprm” writes out a formatted listing of the default set of potential energy parameters for a force field
PRTSEQ Subroutine
“prtseq” writes out a biopolymer sequence to an external disk file with 15 residues per line and distinct chains separated by blank lines
PRTXMOL Subroutine
“prtxmol” writes out a set of Cartesian coordinates for all active atoms in a simple, generic XYZ format originally used by the XMOL Program**
PRTXYZ Subroutine
“prtxyz” writes out a set of Cartesian coordinates to an external disk file
PSS Program
“pss” implements the potential smoothing plus search method for global optimization in Cartesian coordinate space with local searches performed in Cartesian or torsional space
PSS1 Function
“pss1” is a service routine that computes the energy and gradient during PSS global optimization in Cartesian coordinate space
PSS2 Subroutine
“pss2” is a service routine that computes the sparse matrix Hessian elements during PSS global optimization in Cartesian coordinate space
PSSRGD1 Function
“pssrgd1” is a service routine that computes the energy and gradient during PSS global optimization over rigid bodies
PSSRIGID Program
“pssrigid” implements the potential smoothing plus search method for global optimization for a set of rigid bodies
PSSROT Program
“pssrot” implements the potential smoothing plus search method for global optimization in torsional space
PSSROT1 Function
“pssrot1” is a service routine that computes the energy and gradient during PSS global optimization in torsional space
PSSWRITE Subroutine
PTINCY Function
PZEXTR Subroutine
“pzextr” is a polynomial extrapolation routine used during Bulirsch-Stoer integration of ordinary differential equations
QRFACT Subroutine
“qrfact” performs Householder transformations with column pivoting (optional) to compute a QR factorization of the m by n matrix a; the routine determines an orthogonal matrix q, a permutation matrix p, and an upper trapezoidal matrix r with diagonal elements of nonincreasing magnitude, such that a*p = q*r; the Householder transformation for column k, k = 1,2,…,min(m,n), is of the form
QRSOLVE Subroutine
“qrsolve” solves a*x=b and d*x=0 in the least squares sense; normally used in combination with routine “qrfact” to solve least squares problems
QUATFIT Subroutine
“quatfit” uses a quaternion-based method to achieve the best fit superposition of two sets of coordinates
RADIAL Program
“radial” finds the radial distribution Function** for a specified pair of atom types via analysis of a set of coordinate frames
RANDOM Function
“random” generates a random number on [0,1] via a long period generator due to L’Ecuyer with Bays-Durham shuffle
RANVEC Subroutine
“ranvec” generates a unit vector in 3-dimensional space with uniformly distributed random orientation
RATTLE Subroutine
“rattle” implements the first portion of the rattle algorithm by correcting atomic positions and half-step velocities to maintain interatomic distance and absolute spatial constraints
RATTLE2 Subroutine
“rattle2” implements the second portion of the rattle algorithm by correcting the full-step velocities in order to maintain interatomic distance constraints
READBLK Subroutine
“readblk” reads in a set of snapshot frames and transfers the values to internal arrays for use in the computation of time correlation Function**s
READDYN Subroutine
“readdyn” get the positions, velocities and accelerations for a molecular dynamics restart from an external disk file
READINT Subroutine
“readint” gets a set of Z-matrix internal coordinates from an external file
READMOL2 Subroutine
“readmol2” gets a set of Sybyl MOL2 coordinates from an external disk file
READPDB Subroutine
“readpdb” gets a set of Protein Data Bank coordinates from an external disk file
READPRM Subroutine
“readprm” processes the potential energy parameter file in order to define the default force field parameters
READSEQ Subroutine
“readseq” gets a biopolymer sequence containing one or more separate chains from an external file; all lines containing sequence must begin with the starting sequence number, the actual sequence is read from subsequent nonblank characters
READXYZ Subroutine
“readxyz” gets a set of Cartesian coordinates from an external disk file
REFINE Subroutine
“refine” performs minimization of the atomic coordinates of an initial crude embedded distance geometry structure versus the bound, chirality, planarity and torsional error Function**s
RELEASEMONITOR Subroutine
REPLICA Subroutine
“replica” decides between images and replicates for generation of periodic boundary conditions, and sets the cell replicate list if the replicates method is to be used
RFINDEX Subroutine
“rfindex” finds indices for each multipole site for use in computing reaction field energetics
RGDSRCH Subroutine
RGDSTEP Subroutine
“rgdstep” performs a single molecular dynamics time step for a rigid body calculation
RIBOSOME Subroutine
“ribosome” translates a polypeptide structure in Protein Data Bank format to a Cartesian coordinate file and sequence file
RIGIDXYZ Subroutine
“rigidxyz” computes Cartesian coordinates for a rigid body group via rotation and translation of reference coordinates
RINGS Subroutine
“rings” searches the structure for small rings and stores their constituent atoms
RMSERROR Subroutine
“rmserror” computes the maximum absolute deviation and the rms deviation from the distance bounds, and the number and rms value of the distance restraint violations
RMSFIT Function
“rmsfit” computes the rms fit of two coordinate sets
ROTANG Function
ROTCHECK Function
“rotcheck” tests a specified candidate rotatable bond for the disallowed case where inactive atoms are found on both sides of the candidate bond
ROTEULER Subroutine
“roteuler” computes a set of Euler angle values consistent with an input rotation matrix
ROTLIST Subroutine
“rotlist” generates the minimum list of all the atoms lying to one side of a pair of directly bonded atoms; optionally finds the minimal list by choosing the side with fewer atoms
ROTMAT Subroutine
“rotmat” finds the rotation matrix that converts from the local coordinate system to the global frame at a multipole site
ROTPOLE Subroutine
“rotpole” constructs the set of atomic multipoles in the global frame by applying the correct rotation matrix for each site
ROTRGD Subroutine
“rotrgd” finds the rotation matrix for a rigid body due to a single step of dynamics
ROTSITE Subroutine
“rotsite” computes the atomic multipoles at a specified site in the global coordinate frame by applying a rotation matrix
SADDLE Program
“saddle” finds a transition state between two conformational minima using a combination of ideas from the synchronous transit (Halgren-Lipscomb) and quadratic path (Bell-Crighton) methods
SADDLE1 Function
“saddle1” is a service routine that computes the energy and gradient for transition state optimization
SADDLES Subroutine
“saddles” constructs circles, convex edges and saddle faces
SCAN Program
“scan” attempts to find all the local minima on a potential energy surface via an iterative series of local searches
SCAN1 Function
“scan1” is a service routine that computes the energy and gradient during exploration of a potential energy surface via iterative local search
SCAN2 Subroutine
“scan2” is a service routine that computes the sparse matrix Hessian elements during exploration of a potential energy surface via iterative local search
SDAREA Subroutine
“sdarea” optionally scales the atomic friction coefficient of each atom based on its accessible surface area
SDSTEP Subroutine
“sdstep” performs a single stochastic dynamics time step via a velocity Verlet integration algorithm
SDTERM Subroutine
“sdterm” gets frictional and random force terms needed to update positions and velocities via stochastic dynamics
SEARCH Subroutine
“search” is a unidimensional line search based upon parabolic extrapolation and cubic interpolation using both Function** and gradient values; if forced to search in an uphill direction, return is after the initial step
SETACCELERATION Subroutine
SETATOMIC Subroutine
SETATOMTYPES Subroutine
SETCHARGE Subroutine
SETCONNECTIVITY Subroutine
SETCOORDINATES Subroutine
SETENERGY Subroutine
SETFILE Subroutine
SETFORCEFIELD Subroutine
SETGRADIENTS Subroutine
SETIME Subroutine
“setime” initializes the elapsed interval CPU timer
SETINDUCED Subroutine
SETKEYWORD Subroutine
SETMASS Subroutine
SETNAME Subroutine
SETSTEP Subroutine
SETSTORY Subroutine
SETTIME Subroutine
SETUPDATED Subroutine
SETVELOCITY Subroutine
SHAKEUP Subroutine
“shakeup” initializes any holonomic constraints for use with the rattle algorithm during molecular dynamics
SIGMOID Function
“sigmoid” implements a normalized sigmoidal Function** on the interval [0,1]; the curves connect (0,0) to (1,1) and have a cooperativity controlled by beta, they approach a straight line as beta -> 0 and get more nonlinear as beta increases
SKTDYN Subroutine
“sktdyn” sends the current dynamics info via a socket
SKTINIT Subroutine
“sktinit” sets up socket communication with the graphical user interface by starting a Java virtual machine, initiating a server, and loading an object with system information
SKTKILL Subroutine
“sktkill” closes the server and Java virtual machine
SKTOPT Subroutine
“sktopt” sends the current optimization info via a socket
SLATER Subroutine
“slater” is a general routine for computing the overlap integrals between two Slater-type orbitals
SMOOTH Subroutine
“smooth” sets the type of smoothing method and the extent of surface deformation for use with potential energy smoothing
SNIFFER Program
“sniffer” performs a global energy minimization using a discrete version of Griewank’s global search trajectory
SNIFFER1 Function
“sniffer1” is a service routine that computes the energy and gradient for the Sniffer global optimization method
SOAK Subroutine
“soak” takes a currently defined solute system and places it into a solvent box, with removal of any solvent molecules that overlap the solute
SORT Subroutine
“sort” takes an input list of integers and sorts it into ascending order using the Heapsort algorithm
SORT10 Subroutine
“sort10” takes an input list of character strings and sorts it into alphabetical order using the Heapsort algorithm, duplicate values are removed from the final sorted list
SORT2 Subroutine
“sort2” takes an input list of reals and sorts it into ascending order using the Heapsort algorithm; it also returns a key into the original ordering
SORT3 Subroutine
“sort3” takes an input list of integers and sorts it into ascending order using the Heapsort algorithm; it also returns a key into the original ordering
SORT4 Subroutine
“sort4” takes an input list of integers and sorts it into ascending absolute value using the Heapsort algorithm
SORT5 Subroutine
“sort5” takes an input list of integers and sorts it into ascending order based on each value modulo “m”
SORT6 Subroutine
“sort6” takes an input list of character strings and sorts it into alphabetical order using the Heapsort algorithm
SORT7 Subroutine
“sort7” takes an input list of character strings and sorts it into alphabetical order using the Heapsort algorithm; it also returns a key into the original ordering
SORT8 Subroutine
“sort8” takes an input list of integers and sorts it into ascending order using the Heapsort algorithm, duplicate values are removed from the final sorted list
SORT9 Subroutine
“sort9” takes an input list of reals and sorts it into ascending order using the Heapsort algorithm, duplicate values are removed from the final sorted list
SPACEFILL Program
“spacefill” computes the surface area and volume of a structure; the van der Waals, accessible-excluded, and contact-reentrant definitions are available
SPECTRUM Program
“spectrum” computes a power spectrum over a wavelength range from the velocity autocorrelation as a Function** of time
SQUARE Subroutine
“square” is a nonlinear least squares routine derived from the IMSL routine BCLSF and More’s Minpack routine LMDER; the Jacobian is estimated by finite differences and bounds can be specified for the variables to be refined
SUFFIX Subroutine
“suffix” checks a filename for the presence of an extension, and appends an extension if none is found
SUPERPOSE Program
“superpose” takes pairs of structures and superimposes them in the optimal least squares sense; it will attempt to match all atom pairs or only those specified by the user
SURFACE Subroutine
“surface” performs an analytical computation of the weighted solvent accessible surface area of each atom and the first derivatives of the area with respect to Cartesian coordinates
SURFATOM Subroutine
“surfatom” performs an analytical computation of the surface area of a specified atom; a simplified version of “surface”
SWITCH Subroutine
“switch” sets the coeffcients used by the fifth and seventh order polynomial switching Function**s for spherical cutoffs
SYBYLXYZ Program
“sybylxyz” takes as input a Sybyl MOL2 coordinates file, converts to and then writes out Cartesian coordinates
SYMMETRY Subroutine
“symmetry” applies symmetry operators to the fractional coordinates of the asymmetric unit in order to generate the symmetry related atoms of the full unit cell
TANGENT Subroutine
“tangent” finds the projected gradient on the synchronous transit path for a point along the transit pathway
TEMPER Subroutine
“temper” applies a velocity correction at the half time step as needed for the Nose-Hoover extended system thermostat
TEMPER2 Subroutine
“temper2” computes the instantaneous temperature and applies a thermostat via Berendsen velocity scaling, Andersen stochastic collisions, Langevin piston or Nose-Hoover extended systems
TESTGRAD Program
“testgrad” computes and compares the analytical and numerical gradient vectors of the potential energy Function** with respect to Cartesian coordinates
TESTHESS Program
“testhess” computes and compares the analytical and numerical Hessian matrices of the potential energy Function** with respect to Cartesian coordinates
TESTLIGHT Program
“testlight” performs a set of timing tests to compare the evaluation of potential energy and energy/gradient using the method of lights with a double loop over all atom pairs
TESTROT Program
“testrot” computes and compares the analytical and numerical gradient vectors of the potential energy Function** with respect to rotatable torsional angles
TIMER Program
“timer” measures the CPU time required for file reading and parameter assignment, potential energy computation, energy and gradient computation, and Hessian matrix evaluation
TIMEROT Program
“timerot” measures the CPU time required for file reading and parameter assignment, potential energy computation, energy and gradient over torsions, and torsional angle Hessian matrix evaluation
TNCG Subroutine
“tncg” implements a truncated Newton optimization algorithm in which a preconditioned linear conjugate gradient method is used to approximately solve Newton’s equations; special features include use of an explicit sparse Hessian or finite-difference gradient-Hessian products within the PCG iteration; the exact Newton search directions can be used optionally; by default the algorithm checks for negative curvature to prevent convergence to a stationary point having negative eigenvalues; if a saddle point is desired this test can be removed by disabling “negtest”
TNSOLVE Subroutine
“tnsolve” uses a linear conjugate gradient method to find an approximate solution to the set of linear equations represented in matrix form by Hp = -g (Newton’s equations)
TORPHASE Subroutine
“torphase” sets the n-fold amplitude and phase values for each torsion via sorting of the input parameters
TORQUE Subroutine
“torque” takes the torque values on sites defined by local coordinate frames and distributes thme to convert to forces on the original sites and sites specifying the local frames
TORQUE1 Subroutine
“torque1” takes the torque value on a site defined by a local coordinate frame and distributes it to convert to forces on the original site and sites specifying the local frame
TORSER Function
“torser” computes the torsional error Function** and its first derivatives with respect to the atomic Cartesian coordinates based on the deviation of specified torsional angles from desired values, the contained bond angles are also restrained to avoid a numerical instability
TORSIONS Subroutine
“torsions” finds the total number of dihedral angles and the numbers of the four atoms defining each dihedral angle
TORUS Subroutine
“torus” sets a list of all of the temporary torus positions by testing for a torus between each atom and its neighbors
TOTERR Function
“toterr” is the error Function** and derivatives for a distance geometry embedding; it includes components from the distance bounds, hard sphere contacts, local geometry, chirality and torsional restraint errors
TRANSIT Function
“transit” evaluates the synchronous transit Function** and gradient; linear and quadratic transit paths are available
TRIANGLE Subroutine
“triangle” smooths the upper and lower distance bounds via the triangle inequality using a full-matrix variant of the Floyd-Warshall shortest path algorithm; this routine is usually much slower than the sparse matrix shortest path methods in “geodesic” and “trifix”, and should be used only for comparison with answers generated by those routines
TRIFIX Subroutine
“trifix” rebuilds both the upper and lower distance bound matrices following tightening of one or both of the bounds between a specified pair of atoms, “p” and “q”, using a modification of Murchland’s shortest path update algorithm
TRIMTEXT Function
“trimtext” finds and returns the location of the last non-blank character before the first null character in an input text string; the Function** returns zero if no such character is found
TRIPLE Function
“triple” finds the triple product of three vectors; used as a service routine by the Connolly surface area and volume computation
TRUST Subroutine
“trust” updates the model trust region for a nonlinear least squares calculation; this version is based on the ideas found in NL2SOL and in Dennis and Schnabel’s book
UDIRECT1 Subroutine
“udirect1” computes the reciprocal space contribution of the permanent atomic multipole moments to the electrostatic field for use in finding the direct induced dipole moments via a regular Ewald summation
UDIRECT2 Subroutine
“udirect2” computes the real space contribution of the permanent atomic multipole moments to the electrostatic field for use in finding the direct induced dipole moments via a regular Ewald summation
UFIELD Subroutine
“ufield” finds the field at each polarizable site due to the induced dipoles at the other sites using Thole’s method to damp the field at close range
UMUTUAL1 Subroutine
“umutual1” computes the reciprocal space contribution of the induced atomic dipole moments to the electrostatic field for use in iterative calculation of induced dipole moments via a regular Ewald summation
UMUTUAL2 Subroutine
“umutual2” computes the real space contribution of the induced atomic dipole moments to the electrostatic field for use in iterative calculation of induced dipole moments via a regular Ewald summation
UNITCELL Subroutine
“unitcell” gets the periodic boundary box size and related values from an external keyword file
UPCASE Subroutine
“upcase” converts a text string to all upper case letters
VAM Subroutine
“vam” takes the analytical molecular surface defined as a collection of spherical and toroidal polygons and uses it to compute the volume and surface area
VCROSS Subroutine
“vcross” finds the cross product of two vectors
VDWERR Function
“vdwerr” is the hard sphere van der Waals bound error Function** and derivatives that penalizes close nonbonded contacts, pairwise neighbors are generated via the method of lights
VECANG Function
“vecang” finds the angle between two vectors handed with respect to a coordinate axis; returns an angle in the range [0,2*pi]
VERLET Subroutine
“verlet” performs a single molecular dynamics time step by means of the velocity Verlet multistep recursion formula
VERSION Subroutine
“version” checks the name of a file about to be opened; if if “old” status is passed, the name of the highest current version is returned; if “new” status is passed the filename of the next available unused version is generated
VIBRATE Program
“vibrate” performs a vibrational normal mode analysis; the Hessian matrix of second derivatives is determined and then diagonalized both directly and after mass weighting; output consists of the eigenvalues of the force constant matrix as well as the vibrational frequencies and displacements
VIBRIGID Program
“vibrigid” computes the eigenvalues and eigenvectors of the Hessian matrix over rigid body degrees of freedom
VIBROT Program
“vibrot” computes the eigenvalues and eigenvectors of the torsional Hessian matrix
VNORM Subroutine
“vnorm” normalizes a vector to unit length; used as a service routine by the Connolly surface area and volume computation
VOLUME Subroutine
“volume” calculates the excluded volume via the Connolly analytical volume and surface area algorithm
VOLUME1 Subroutine
“volume1” calculates first derivatives of the total excluded volume with respect to the Cartesian coordinates of each atom
VOLUME2 Subroutine
“volume2” calculates second derivatives of the total excluded volume with respect to the Cartesian coordinates of the atoms
WATSON Subroutine
“watson” uses a rigid body optimization to approximately align the paired strands of a nucleic acid double helix
WATSON1 Function
“watson1” is a service routine that computes the energy and gradient for optimally conditioned variable metric optimization of rigid bodies
XTALERR Subroutine
“xtalerr” computes an error Function** value derived from derivatives with respect to lattice parameters, lattice energy and monomer dipole moments
XTALFIT Program
“xtalfit” computes an optimized set of potential energy parameters for user specified van der Waals and electrostatic interactions by fitting to crystal structure, lattice energy and monomer dipole moment data
XTALLAT1 Function
“xtalmol1” is a service routine that computes the energy and numerical gradient with respect to the six lattice lengths and angles for a crystal energy minimization
XTALMIN Program
“xtalmin” performs a full crystal energy minimization by alternating cycles of truncated Newton optimization over atomic coordinates with variable metric optimization over the six lattice dimensions and angles
XTALMOL1 Function
“xtalmol1” is a service routine that computes the energy and gradient with respect to the atomic Cartesian coordinates for a crystal energy minimization
XTALMOL2 Subroutine
“xtalmol2” is a service routine that computes the sparse matrix Hessian elements with respect to the atomic Cartesian coordinates for a crystal energy minimization
XTALMOVE Subroutine
“xtalmove” converts fractional to Cartesian coordinates for rigid molecules during fitting of force field parameters to crystal structure data
XTALPRM Subroutine
“xtalprm” stores or retrieves a crystal structure; used to make a previously stored structure the currently active structure, or to store a structure for later use; only provides for the intermolecular energy terms
XTALWRT Subroutine
“xtalwrt” is a utility that prints intermediate results during fitting of force field parameters to crystal data
XYZATM Subroutine
“xyzatm” computes the Cartesian coordinates of a single atom from its defining internal coordinate values
XYZEDIT Program
“xyzedit” provides for modification and manipulation of the contents of a Cartesian coordinates file
XYZINT Program
“xyzint” takes as input a Cartesian coordinates file, then converts to and writes out an internal coordinates file
XYZPDB Program
“xyzpdb” takes as input a Cartesian coordinates file, then converts to and writes out a Protein Data Bank file
XYZRIGID Subroutine
“xyzrigid” computes the center of mass and Euler angle rigid body coordinates for each atom group in the system
XYZSYBYL Program
“xyzsybyl” takes as input a Cartesian coordinates file, converts to and then writes out a Sybyl MOL2 file
ZATOM Subroutine
“zatom” adds an atom to the end of the current Z-matrix and then increments the atom counter; atom type, defining atoms and internal coordinates are passed as arguments
ZHELP Subroutine
“zhelp” prints the general information and instructions for the Z-matrix editing Program**
ZVALUE Subroutine
“zvalue” gets user supplied values for selected coordinates as needed by the internal coordinate editing Program**