# Routines & Functions¶

The distribution version of the Tinker package contains over 1000 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

**ADDIONS Subroutine**

“addions” takes a currently defined solvated system and places ions, with removal of solvent molecules

**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

**ADJUST Subroutine**

“adjust” modifies site bounds on the PME grid and returns an offset into the B-spline coefficient arrays

**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

**ALTELEC Subroutine**

“altelec” constructs mutated electrostatic parameters based on the lambda mutation parameter “elambda”

**ALTERCHG Subroutine**

“alterchg” calculates the change in atomic partial charge or monopole values due to bond and angle charge flux coupling

**ALTERPOL Subroutine**

“alterpol” finds an output set of atomic multipole parameters which when used with an intergroup polarization model will give the same electrostatic potential around the molecule as the input set of multipole parameters with all atoms in one polarization group

**ALTTORS Subroutine**

“alttors” constructs mutated torsional parameters based on the lambda mutation parameter “tlambda”

**AMBERYZE Subroutine**

“amberyze” prints the force field parameters in a format needed by the Amber setup protocol for using AMOEBA within Amber

**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

**ANALYZE Program**

“analyze” computes and displays the total potential energy; options are provided to display system and force field info, partition the energy by atom or by potential function type, show force field parameters by atom; output the large energy interactions and find electrostatic and inertial properties

**ANGCHG Subroutine**

“angchg” computes modifications to atomic partial charges or monopoles due to angle bending using a charge flux formulation

**ANGGUESS Function**

“angguess” sets approximate angle bend force constants based on atom type and connected atoms

**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

**APBSEMPOLE Subroutine**

**APBSFINAL Subroutine**

**APBSINDUCE Subroutine**

**APBSINITIAL Subroutine**

**APBSNLINDUCE Subroutine**

**ARCHIVE Program**

“archive” is a utility program for coordinate files which concatenates multiple coordinate sets into a new archive or performs any of several manipulations on an existing archive

**ASET Subroutine**

“aset” computes by recursion the A functions 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)

**AUXINIT Subroutine**

“auxinit” initializes auxiliary variables and settings for inertial extended Lagrangian induced dipole prediction

**AVGPOLE Subroutine**

“avgpole” condenses the number of multipole atom types based upon atoms with equivalent attachments and additional user specified sets of equivalent atoms

**BAOAB Subroutine**

“baoab” implements a constrained stochastic dynamics time step using the geodesic BAOAB scheme

**BAR Program**

“bar” computes the free energy, enthalpy and entropy difference between two states via Zwanzig free energy perturbation (FEP) and Bennett acceptance ratio (BAR) methods

**BARCALC Subroutine**

**BASEFILE Subroutine**

“basefile” extracts from an input filename the portion consisting of any directory name and the base filename; also reads any keyfile and sets information level values

**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 Hessian along the directions of a 2D spline grid

**BEEMAN Subroutine**

“beeman” performs a single molecular dynamics time step via the Beeman multistep recursion formula; uses original coefficients or Bernie 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 unit cell as a block of repeated units

**BIOSORT Subroutine**

“biosort” renumbers and formats biotype parameters used to convert biomolecular structure into force field atom types

**BITORS Subroutine**

“bitors” finds the total number of bitorsions as pairs of adjacent torsional angles, and the numbers of the five atoms defining each bitorsion

**BMAX Function**

“bmax” computes the maximum order of the B functions needed for evaluation of Slater-type (STO) overlap integrals

**BNDCHG Subroutine**

“bndchg” computes modifications to atomic partial charges or monopoles due to bond stretch using a charge flux formulation

**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

**BNDGUESS Function**

“bndguess” sets approximate bond stretch force constants based on atom type and connected atoms

**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 implicit 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

**BOXMIN Subroutine**

“boxmin” uses minimization of valence and vdw potential energy to expand and refine a collection of solvent molecules in a periodic box

**BOXMIN1 Function**

“boxmin1” is a service routine that computes the energy and gradient during refinement of a periodic box

**BSET Subroutine**

“bset” computes by downward recursion the B functions used in the evaluation of Slater-type (STO) overlap integrals

**BSPLGEN Subroutine**

“bsplgen” gets B-spline coefficients and derivatives for a single PME atomic site along a particular direction

**BSPLINE Subroutine**

“bspline” calculates the coefficients for an n-th order B-spline approximation

**BSPLINE_FILL Subroutine**

“bspline_fill” finds B-spline coefficients and derivatives for PME atomic sites along the fractional coordinate axes

**BSSTEP Subroutine**

“bsstep” takes a single Bulirsch-Stoer step with monitoring of local truncation error to ensure accuracy

**BUSSI Subroutine**

“bussi” performs a single molecular dynamics time step via the Bussi-Parrinello isothermal-isobaric algorithm

**CALENDAR Subroutine**

“calendar” returns the current time as a set of integer values representing the year, month, day, hour, minute and second

**CART_TO_FRAC Subroutine**

“cart_to_frac” computes a transformation matrix to convert a multipole object in Cartesian coordinates to fractional

**CBUILD Subroutine**

“cbuild” performs a complete rebuild of the partial charge electrostatic neighbor list for all sites

**CELLANG Subroutine**

“cellang” computes atomic coordinates and unit cell parameters from fractional coordinates and lattice vectors

**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 arrays used in both forward and backward transforms; “ifac” is the prime factorization of “n”, and “wsave” contains a tabulation of trigonometric functions

**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

**CHKANGLE Subroutine**

“chkangle” tests angles to be constrained for their presence in small rings and removes constraints that are redundant

**CHKAROM Function**

“chkatom” tests for the presence of a specified atom as a member of an aromatic ring

**CHKPOLE Subroutine**

“chkpole” inverts atomic multipole moments as necessary at sites with chiral local reference frame definitions

**CHKRING Subroutine**

“chkring” tests an atom or a set of connected atoms for their presence within a single 3- to 6-membered ring

**CHKSIZE Subroutine**

“chksize” computes a measure of overall global structural expansion or compaction from the number of excess upper or lower bounds matrix violations

**CHKSOCKET Subroutine**

**CHKTREE Subroutine**

“chktree” tests a minimum energy structure to see if it belongs to the correct progenitor in the existing map

**CHKTTOR Subroutine**

“chkttor” tests the attached atoms at a torsion-torsion central site and inverts the angle values if the site is chiral

**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 a real symmetric positive definite matrix with its upper triangle (including the diagonal) stored by rows

**CIRPLN Subroutine**

“cirpln” determines the points of intersection between a specified circle and plane

**CJKM Function**

“cjkm” computes the coefficients of spherical harmonics expressed in prolate spheroidal coordinates

**CLIGHT Subroutine**

“clight” performs a complete rebuild of the partial charge pair neighbor list for all sites using the method of lights

**CLIMBER Subroutine**

**CLIMBRGD Subroutine**

**CLIMBROT Subroutine**

**CLIMBTOR Subroutine**

**CLIMBXYZ Subroutine**

**CLIST Subroutine**

“clist” performs an update or a complete rebuild of the nonbonded neighbor lists for partial charges

**CLUSTER Subroutine**

“cluster” gets the partitioning of the system into groups and stores a list of the group to which each atom belongs

**CMP_TO_FMP Subroutine**

“cmp_to_fmp” transforms the atomic multipoles from Cartesian to fractional coordinates

**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 programs 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

**CONNYZE Subroutine**

“connyze” prints information onconnected atoms as lists of all atom pairs that are 1-2 through 1-5 interactions

**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 which converts between fractional and Cartesian coordinates, and can generate full unit cells from asymmetric units

**CSPLINE Subroutine**

“cspline” computes the coefficients for a periodic interpolating cubic spline

**CUTOFFS Subroutine**

“cutoffs” initializes and stores spherical energy cutoff distance windows, Hessian element and Ewald sum cutoffs, and allocates pairwise neighbor lists

**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

**DAMPDIR Subroutine**

“dampdir” generates coefficients for the direct field damping function for powers of the interatomic distance

**DAMPEWALD Subroutine**

“dampewald” generates coefficients for Ewald error function damping for powers of the interatomic distance

**DAMPMUT Subroutine**

“dampmut” generates coefficients for the mutual field damping function for powers of the interatomic distance

**DAMPPOLAR Subroutine**

“damppolar” generates coefficients for the charge penetration damping function used for polarization interactions

**DAMPPOLE Subroutine**

“damppole” generates coefficients for the charge penetration damping function for powers of the interatomic distance

**DAMPPOT Subroutine**

“damppot” generates coefficients for the charge penetration damping function used for the electrostatic potential

**DAMPREP Subroutine**

“damprep” generates coefficients for the Pauli repulsion damping function for powers of the interatomic distance

**DAMPTHOLE Subroutine**

“dampthole” generates coefficients for the Thole damping function for powers of the interatomic distance

**DBUILD Subroutine**

“dbuild” performs a complete rebuild of the damped dispersion neighbor list for all sites

**DCFLUX Subroutine**

“dcflux” takes as input the electrostatic potential at each atomic site and calculates gradient chain rule corrections due to charge flux coupled with bond stretching and angle bending

**DEFLATE Subroutine**

“deflate” uses the power method with deflation to compute the few largest eigenvalues and eigenvectors of a symmetric matrix

**DELETE Subroutine**

“delete” removes a specified atom from the Cartesian coordinates list and shifts the remaining atoms

**DEPTH Function**

**DESTROYJVM Subroutine**

**DESTROYSERVER Subroutine**

**DFIELD0A Subroutine**

“dfield0a” computes the direct electrostatic field due to permanent multipole moments via a double loop

**DFIELD0B Subroutine**

“dfield0b” computes the direct electrostatic field due to permanent multipole moments via a pair list

**DFIELD0C Subroutine**

“dfield0c” computes the mutual electrostatic field due to permanent multipole moments via Ewald summation

**DFIELD0D Subroutine**

“dfield0d” computes the direct electrostatic field due to permanent multipole moments for use with with generalized Kirkwood implicit solvation

**DFIELD0E Subroutine**

“dfield0e” computes the direct electrostatic field due to permanent multipole moments for use with in Poisson-Boltzmann

**DFIELDI Subroutine**

“dfieldi” computes the electrostatic field due to permanent multipole moments

**DFTMOD Subroutine**

“dftmod” computes the modulus of the discrete Fourier transform of “bsarray” and stores it in “bsmod”

**DIAGBLK Subroutine**

“diagblk” performs diagonalization of the Hessian for a block of atoms within a larger system

**DIAGQ Subroutine**

“diagq” is a matrix diagonalization routine which is derived from the classical given, housec, and eigen algorithms with several modifications to increase 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

**DLIGHT Subroutine**

“dlight” performs a complete rebuild of the damped dispersion pair neighbor list for all sites using the method of lights

**DLIST Subroutine**

“dlist” performs an update or a complete rebuild of the nonbonded neighbor lists for damped dispersion sites

**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 routines and modules, an index of routines called by each source file, a list of all valid keywords, a list of include file dependencies as needed by a Unix-style Makefile, or a formatted force field parameter 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 or stochastic dynamics trajectory in one of the standard statistical mechanical ensembles and using any of several possible integration methods

**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, special linear 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, special linear 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, special linear 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, spceial linear or Fourier angle bending terms are optionally used

**EANGTOR Subroutine**

“eangtor” calculates the angle-torsion potential energy

**EANGTOR1 Subroutine**

“eangtor1” calculates the angle-torsion energy and first derivatives with respect to Cartesian coordinates

**EANGTOR2 Subroutine**

“eangtor2” calculates the angle-torsion potential energy second derivatives with respect to Cartesian coordinates

**EANGTOR3 Subroutine**

“eangtor3” calculates the angle-torsion potential energy; also partitions the energy terms among the atoms

**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

**EBUCK0C Subroutine**

“ebuck0c” calculates the Buckingham exp-6 van der Waals energy using a pairwise neighbor list

**EBUCK0D Subroutine**

“ebuck0d” 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

**EBUCK1C Subroutine**

“ebuck1c” calculates the Buckingham exp-6 van der Waals energy and its first derivatives using a pairwise neighbor list

**EBUCK1D Subroutine**

“ebuck1d” 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

**EBUCK3C Subroutine**

“ebuck3c” calculates the Buckingham exp-6 van der Waals energy and also partitions the energy among the atoms using a pairwise neighbor list

**EBUCK3D Subroutine**

“ebuck3d” 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

**ECHARGE0C Subroutine**

“echarge0c” calculates the charge-charge interaction energy using a pairwise neighbor list

**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

**ECHARGE0F Subroutine**

“echarge0f” calculates the charge-charge interaction energy using a particle mesh Ewald summation and a neighbor list

**ECHARGE0G Subroutine**

“echarge0g” calculates the charge-charge interaction energy for use with potential smoothing methods

**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

**ECHARGE1C Subroutine**

“echarge1c” calculates the charge-charge interaction energy and first derivatives with respect to Cartesian coordinates using a pairwise neighbor list

**ECHARGE1D Subroutine**

“echarge1d” calculates the charge-charge interaction energy and first derivatives with respect to Cartesian coordinates using a particle mesh Ewald summation

**ECHARGE1E Subroutine**

“echarge1e” calculates the charge-charge interaction energy and first derivatives with respect to Cartesian coordinates using a particle mesh Ewald summation and the method of lights

**ECHARGE1F Subroutine**

“echarge1f” calculates the charge-charge interaction energy and first derivatives with respect to Cartesian coordinates using a particle mesh Ewald summation and a neighbor list

**ECHARGE1G Subroutine**

“echarge1g” calculates the charge-charge interaction energy and first derivatives with respect to Cartesian coordinates for use with potential smoothing methods

**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 loop

**ECHARGE2B Subroutine**

“echarge2b” calculates second derivatives of the charge-charge interaction energy for a single atom using a neighbor list

**ECHARGE2C Subroutine**

“echarge2c” calculates second derivatives of the reciprocal space charge-charge interaction energy for a single atom using a particle mesh Ewald summation via numerical differentiation

**ECHARGE2D Subroutine**

“echarge2d” calculates second derivatives of the real space charge-charge interaction energy for a single atom using a pairwise loop

**ECHARGE2E Subroutine**

“echarge2e” calculates second derivatives of the real space charge-charge interaction energy for a single atom using a pairwise neighbor list

**ECHARGE2F Subroutine**

“echarge2f” calculates second derivatives of the charge-charge interaction energy for a single atom for use with potential smoothing methods

**ECHARGE2R Subroutine**

“echarge2r” computes reciprocal space charge-charge first derivatives; used to get finite difference second derivatives

**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

**ECHARGE3C Subroutine**

“echarge3c” calculates the charge-charge interaction energy and partitions the energy among the atoms using a pairwise neighbor list

**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

**ECHARGE3F Subroutine**

“echarge3f” calculates the charge-charge interaction energy and partitions the energy among the atoms using a particle mesh Ewald summation and a pairwise neighbor list

**ECHARGE3G Subroutine**

“echarge3g” calculates the charge-charge interaction energy and partitions the energy among the atoms for use with potential smoothing methods

**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

**ECHGTRN Subroutine**

“echgtrn” calculates the charge transfer potential energy

**ECHGTRN0A Subroutine**

“echgtrn0a” calculates the charge transfer interaction energy using a double loop

**ECHGTRN0B Subroutine**

“echgtrn0b” calculates the charge transfer interaction energy using the method of lights

**ECHGTRN0C Subroutine**

“echgtrn0c” calculates the charge transfer interaction energy using a neighbor list

**ECHGTRN1 Subroutine**

“echgtrn1” calculates the charge transfer energy and first derivatives with respect to Cartesian coordinates

**ECHGTRN1A Subroutine**

“echgtrn1a” calculates the charge transfer interaction energy and first derivatives using a double loop

**ECHGTRN1B Subroutine**

“echgtrn1b” calculates the charge transfer energy and first derivatives using a pairwise neighbor list

**ECHGTRN2 Subroutine**

“echgtrn2” calculates the second derivatives of the charge transfer energy using a double loop over relevant atom pairs

**ECHGTRN3 Subroutine**

“echgtrn3” calculates the charge transfer energy; also partitions the energy among the atoms

**ECHGTRN3A Subroutine**

“echgtrn3a” calculates the charge transfer interaction energy and also partitions the energy among the atoms using a pairwise double loop

**ECHGTRN3B Subroutine**

“echgtrn3b” calculates the charge transfer interaction energy and also partitions the energy among the atoms using the method of lights

**ECHGTRN3C Subroutine**

“echgtrn3c” calculates the charge transfer interaction energy and also partitions the energy among the atoms using a pairwise neighbor list

**ECRECIP Subroutine**

“ecrecip” evaluates the reciprocal space portion of the particle mesh Ewald energy due to partial charges

**ECRECIP1 Subroutine**

“ecrecip1” evaluates the reciprocal space portion of the particle mesh Ewald summation energy and gradient due to partial charges

**EDIFF Subroutine**

“ediff” calculates the energy of polarizing the vacuum induced dipoles to their SCRF polarized values

**EDIFF1A Subroutine**

“ediff1a” calculates the energy and derivatives of polarizing the vacuum induced dipoles to their SCRF polarized values using a double loop

**EDIFF1B Subroutine**

“ediff1b” calculates the energy and derivatives of polarizing the vacuum induced dipoles to their SCRF polarized values using a neighbor list

**EDIFF3 Subroutine**

“ediff3” calculates the energy of polarizing the vacuum induced dipoles to their generalized Kirkwood values with energy analysis

**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

**EDISP Subroutine**

“edisp” calculates the damped dispersion potential energy

**EDISP0A Subroutine**

“edisp0a” calculates the damped dispersion potential energy using a pairwise double loop

**EDISP0B Subroutine**

“edisp0b” calculates the damped dispersion potential energy using a pairwise neighbor list

**EDISP0C Subroutine**

“edisp0c” calculates the dispersion interaction energy using particle mesh Ewald summation and a double loop

**EDISP0D Subroutine**

“edisp0d” calculates the dispersion interaction energy using particle mesh Ewald summation and a neighbor list

**EDISP1 Subroutine**

“edisp1” calculates the damped dispersion energy and first derivatives with respect to Cartesian coordinates

**EDISP1A Subroutine**

“edisp1a” calculates the damped dispersion energy and derivatives with respect to Cartesian coordinates using a pairwise double loop

**EDISP1B Subroutine**

“edisp1b” calculates the damped dispersion energy and derivatives with respect to Cartesian coordinates using a pairwise neighbor list

**EDISP1C Subroutine**

“edisp1c” calculates the damped dispersion energy and derivatives with respect to Cartesian coordinates using particle mesh Ewald summation and a double loop

**EDISP1D Subroutine**

“edisp1d” calculates the damped dispersion energy and derivatives with respect to Cartesian coordinates using particle mesh Ewald summation and a neighbor list

**EDISP2 Subroutine**

“edisp2” calculates the damped dispersion second derivatives for a single atom at a time

**EDISP3 Subroutine**

“edisp3” calculates the dispersion energy; also partitions the energy among the atoms

**EDISP3A Subroutine**

“edisp3a” calculates the dispersion potential energy and also partitions the energy among the atoms using a pairwise double loop

**EDISP3B Subroutine**

“edisp3b” calculates the damped dispersion potential energy and also partitions the energy among the atomsusing a pairwise neighbor list

**EDISP3C Subroutine**

“edisp3c” calculates the dispersion interaction energy using particle mesh Ewald summation and a double loop

**EDISP3D Subroutine**

“edisp3d” calculates the damped dispersion energy and analysis using particle mesh Ewald summation and a neighbor list

**EDREAL0C Subroutine**

“edreal0c” calculates the damped dispersion potential energy using a particle mesh Ewald sum and pairwise double loop

**EDREAL0D Subroutine**

“edreal0d” evaluated the real space portion of the damped dispersion energy using a neighbor list

**EDREAL1C Subroutine**

“edreal1c” evaluates the real space portion of the Ewald summation energy and gradient due to damped dispersion interactions via a double loop

**EDREAL1D Subroutine**

“edreal1d” evaluates the real space portion of the Ewald summation energy and gradient due to damped dispersion interactions via a neighbor list

**EDREAL3C Subroutine**

“edreal3c” calculates the real space portion of the damped dispersion energy and analysis using Ewald and a double loop

**EDREAL3D Subroutine**

“edreal3d” evaluated the real space portion of the damped dispersion energy and analysis using Ewald and a neighbor list

**EDRECIP Subroutine**

“edrecip” evaluates the reciprocal space portion of the particle mesh Ewald energy due to damped dispersion

**EDRECIP1 Subroutine**

“edrecip1” evaluates the reciprocal space portion of particle mesh Ewald energy and gradient due to damped dispersion

**EGAUSS Subroutine**

“egauss” calculates the Gaussian expansion van der Waals energy

**EGAUSS0A Subroutine**

“egauss0a” calculates the Gaussian expansion van der Waals energy using a pairwise double loop

**EGAUSS0B Subroutine**

“egauss0b” calculates the Gaussian expansion van der Waals energy using the method of lights

**EGAUSS0C Subroutine**

“egauss0c” calculates the Gaussian expansion van der Waals energy using a pairwise neighbor list

**EGAUSS0D Subroutine**

“egauss0d” calculates the Gaussian expansion van der Waals 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 energy and its first derivatives with respect to Cartesian coordinates using the method of lights

**EGAUSS1C Subroutine**

“egauss1c” calculates the Gaussian expansion van der Waals energy and its first derivatives with respect to Cartesian coordinates using a pairwise neighbor list

**EGAUSS1D Subroutine**

“egauss1d” calculates the Gaussian expansion van der Waals interaction energy and its first derivatives for use with 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 use with 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 energy and partitions the energy among the atoms using a pairwise double loop

**EGAUSS3B Subroutine**

“egauss3b” calculates the Gaussian expansion van der Waals energy and partitions the energy among the atoms using the method of lights

**EGAUSS3C Subroutine**

“egauss3c” calculates the Gaussian expansion van der Waals energy and partitions the energy among the atoms using a pairwise neighbor list

**EGAUSS3D Subroutine**

“egauss3d” calculates the Gaussian expansion van der Waals interaction energy and partitions the energy among the atoms for use with potential energy smoothing

**EGB0A Subroutine**

“egb0a” calculates the generalized Born polarization energy for the GB/SA solvation models using a pairwise double loop

**EGB0B Subroutine**

“egb0b” calculates the generalized Born polarization energy for the GB/SA solvation models using a pairwise neighbor list

**EGB0C Subroutine**

“egb0c” 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

**EGB1A Subroutine**

“egb1a” calculates the generalized Born electrostatic energy and first derivatives of the GB/SA solvation models using a double loop

**EGB1B Subroutine**

“egb1b” calculates the generalized Born electrostatic energy and first derivatives of the GB/SA solvation models using a neighbor list

**EGB1C Subroutine**

“egb1c” calculates the generalized Born energy and first derivatives of the GB/SA solvation models for use with potential smoothing methods

**EGB2A Subroutine**

“egb2a” calculates second derivatives of the generalized Born energy term for the GB/SA solvation models

**EGB2B Subroutine**

“egb2b” calculates second derivatives of the generalized Born energy term for the GB/SA solvation models for use with potential smoothing methods

**EGB3A Subroutine**

“egb3a” calculates the generalized Born electrostatic energy for GB/SA solvation models using a pairwise double loop; also partitions the energy among the atoms

**EGB3B Subroutine**

“egb3b” calculates the generalized Born electrostatic energy for GB/SA solvation models using a pairwise neighbor list; also partitions the energy among the atoms

**EGB3C Subroutine**

“egb3c” calculates the generalized Born electrostatic energy for 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

**EGK Subroutine**

“egk” calculates the generalized Kirkwood electrostatic solvation free energy for the GK/NP implicit solvation model

**EGK0A Subroutine**

“egk0a” calculates the electrostatic portion of the implicit solvation energy via the generalized Kirkwood model

**EGK1 Subroutine**

“egk1” calculates the implicit solvation energy and derivatives via the generalized Kirkwood plus nonpolar implicit solvation

**EGK1A Subroutine**

“egk1a” calculates the electrostatic portion of the implicit solvation energy and derivatives via the generalized Kirkwood model

**EGK3 Subroutine**

“egk3” calculates the generalized Kirkwood electrostatic energy for GK/NP solvation models; also partitions the energy among the atoms

**EGK3A Subroutine**

“egk3a” calculates the electrostatic portion of the implicit solvation energy via the generalized Kirkwood model; also partitions the 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**

“ehal0b” calculates the buffered 14-7 van der Waals energy using the method of lights

**EHAL0C Subroutine**

“ehal0c” calculates the buffered 14-7 van der Waals energy using a pairwise neighbor list

**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

**EHAL1C Subroutine**

“ehal1c” calculates the buffered 14-7 van der Waals energy and its first derivatives with respect to Cartesian coordinates using a pairwise neighbor list

**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

**EHAL3C Subroutine**

“ehal3c” calculates the buffered 14-7 van der Waals energy and also partitions the energy among the atoms using a pairwise neighbor list

**EHPMF Subroutine**

“ehpmf” calculates the hydrophobic potential of mean force energy using a pairwise double loop

**EHPMF1 Subroutine**

“ehpmf1” calculates the hydrophobic potential of mean force energy and first derivatives using a pairwise double loop

**EHPMF3 Subroutine**

“ehpmf3” calculates the hydrophobic potential of mean force nonpolar energy; also partitions the energy among the 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

**ELJ0C Subroutine**

“elj0c” calculates the Lennard-Jones 6-12 van der Waals energy using a pairwise neighbor list

**ELJ0D Subroutine**

“elj0d” calculates the Lennard-Jones 6-12 van der Waals energy via a Gaussian approximation for potential energy smoothing

**ELJ0E Subroutine**

“elj0e” 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

**ELJ1C Subroutine**

“elj1c” calculates the Lennard-Jones 12-6 van der Waals energy and its first derivatives using a pairwise neighbor list

**ELJ1D Subroutine**

- “elj1d” calculates the Lennard-Jones 6-12 van der Waals energy
and its first derivatives via a Gaussian approximation for potential energy smoothing

**ELJ1E Subroutine**

“elj1e” 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

**ELJ3C Subroutine**

“elj3c” calculates the Lennard-Jones van der Waals energy and also partitions the energy among the atoms using a pairwise neighbor list

**ELJ3D Subroutine**

“elj3d” 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

**ELJ3E Subroutine**

“elj3e” 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

**EMM3HB0C Subroutine**

“emm3hb0c” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen bonding energy using a pairwise neighbor list

**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

**EMM3HB1C Subroutine**

“emm3hb1c” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen bonding energy with respect to Cartesian coordinates using a pairwise neighbor list

**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

**EMM3HB3C Subroutine**

“emm3hb3c” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen bonding energy using a pairwise neighbor list

**EMPOLE Subroutine**

“empole” calculates the electrostatic energy due to atomic multipole interactions

**EMPOLE0A Subroutine**

“empole0a” calculates the atomic multipole interaction energy using a double loop

**EMPOLE0B Subroutine**

“empole0b” calculates the atomic multipole interaction energy using a neighbor list

**EMPOLE0C Subroutine**

“empole0c” calculates the atomic multipole interaction energy using particle mesh Ewald summation and a double loop

**EMPOLE0D Subroutine**

“empole0d” calculates the atomic multipole interaction energy using particle mesh Ewald summation and a neighbor list

**EMPOLE1 Subroutine**

“empole1” calculates the atomic multipole energy and first derivatives with respect to Cartesian coordinates

**EMPOLE1A Subroutine**

“empole1a” calculates the multipole energy and derivatives with respect to Cartesian coordinates using a pairwise double loop

**EMPOLE1B Subroutine**

“empole1b” calculates the multipole energy and derivatives with respect to Cartesian coordinates using a neighbor list

**EMPOLE1C Subroutine**

“empole1c” calculates the multipole energy and derivatives with respect to Cartesian coordinates using particle mesh Ewald summation and a double loop

**EMPOLE1D Subroutine**

“empole1d” calculates the multipole energy and derivatives with respect to Cartesian coordinates using particle mesh Ewald summation and a neighbor list

**EMPOLE2 Subroutine**

“empole2” calculates second derivatives of the multipole energy for a single atom at a time

**EMPOLE2A Subroutine**

“empole2a” computes multipole first derivatives for a single atom; used to get finite difference second derivatives

**EMPOLE3 Subroutine**

“empole3” calculates the electrostatic energy due to atomic multipole interactions, and partitions the energy among atoms

**EMPOLE3A Subroutine**

“empole3a” calculates the atomic multipole interaction energy using a double loop, and partitions the energy among atoms

**EMPOLE3B Subroutine**

“empole3b” calculates the atomic multipole interaction energy using a neighbor list, and partitions the energy among the atoms

**EMPOLE3C Subroutine**

“empole3c” calculates the atomic multipole interaction energy using a particle mesh Ewald summation and double loop, and partitions the energy among the atoms

**EMPOLE3D Subroutine**

“empole3d” calculates the atomic multipole interaction energy using particle mesh Ewald summation and a neighbor list, and partitions the energy among the atoms

**EMREAL0C Subroutine**

“emreal0c” evaluates the real space portion of the Ewald sum energy due to atomic multipoles using a double loop

**EMREAL0D Subroutine**

“emreal0d” evaluates the real space portion of the Ewald sum energy due to atomic multipoles using a neighbor list

**EMREAL1C Subroutine**

“emreal1c” evaluates the real space portion of the Ewald summation energy and gradient due to multipole interactions via a double loop

**EMREAL1D Subroutine**

“emreal1d” evaluates the real space portion of the Ewald summation energy and gradient due to multipole interactions via a neighbor list

**EMREAL3C Subroutine**

“emreal3c” evaluates the real space portion of the Ewald sum energy due to atomic multipole interactions and partitions the energy among the atoms

**EMREAL3D Subroutine**

“emreal3d” evaluates the real space portion of the Ewald sum energy due to atomic multipole interactions, and partitions the energy among the atoms using a pairwise neighbor list

**EMRECIP Subroutine**

“emrecip” evaluates the reciprocal space portion of the particle mesh Ewald energy due to atomic multipole interactions

**EMRECIP1 Subroutine**

“emrecip1” evaluates the reciprocal space portion of particle mesh Ewald summation energy and gradient due to multipoles

**ENERGY Function**

“energy” calls the subroutines to calculate the potential energy terms and sums up to form the total energy

**ENP Subroutine**

“enp” calculates the nonpolar implicit solvation energy as a sum of cavity and dispersion terms

**ENP1 Subroutine**

“enp1” calculates the nonpolar implicit solvation energy and derivatives as a sum of cavity and dispersion terms

**ENP3 Subroutine**

“enp3” calculates the nonpolar implicit solvation energy as a sum of cavity and dispersion terms; also partitions the energy among the atoms

**ENRGYZE Subroutine**

“enrgyze” 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 or Allinger angle

**EOPBEND1 Subroutine**

“eopbend1” computes the out-of-plane bend potential energy and first derivatives at trigonal centers via a Wilson-Decius-Cross or Allinger angle

**EOPBEND2 Subroutine**

“eopbend2” calculates second derivatives of the out-of-plane bend energy via a Wilson-Decius-Cross or Allinger angle for a single atom using finite difference methods

**EOPBEND2A Subroutine**

“eopbend2a” calculates out-of-plane bend first derivatives at a trigonal center via a Wilson-Decius-Cross or Allinger angle; 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 or Allinger angle; 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

**EPB Subroutine**

“epb” calculates the implicit solvation energy via the Poisson-Boltzmann plus nonpolar implicit solvation

**EPB1 Subroutine**

“epb1” calculates the implicit solvation energy and derivatives via the Poisson-Boltzmann plus nonpolar implicit solvation

**EPB1A Subroutine**

“epb1a” calculates the solvation energy and gradients for the PB/NP solvation model

**EPB3 Subroutine**

“epb3” calculates the implicit solvation energy via the Poisson-Boltzmann model; also partitions the energy among the atoms

**EPITORS Subroutine**

“epitors” calculates the pi-system torsion potential energy

**EPITORS1 Subroutine**

“epitors1” calculates the pi-system torsion potential energy and first derivatives with respect to Cartesian coordinates

**EPITORS2 Subroutine**

“epitors2” calculates the second derivatives of the pi-system torsion energy for a single atom using finite difference methods

**EPITORS2A Subroutine**

“epitors2a” calculates the pi-system torsion first derivatives; used in computation of finite difference second derivatives

**EPITORS3 Subroutine**

“epitors3” calculates the pi-system torsion potential energy; also partitions the energy terms among the atoms

**EPOLAR Subroutine**

“epolar” calculates the polarization energy due to induced dipole interactions

**EPOLAR0A Subroutine**

“epolar0a” calculates the induced dipole polarization energy using a double loop, and partitions the energy among atoms

**EPOLAR0B Subroutine**

“epolar0b” calculates the induced dipole polarization energy using a neighbor list

**EPOLAR0C Subroutine**

“epolar0c” calculates the dipole polarization energy with respect to Cartesian coordinates using particle mesh Ewald summation and a double loop

**EPOLAR0D Subroutine**

“epolar0d” calculates the dipole polarization energy with respect to Cartesian coordinates using particle mesh Ewald summation and a neighbor list

**EPOLAR0E Subroutine**

“epolar0e” calculates the dipole polarizability interaction from the induced dipoles times the electric field

**EPOLAR1 Subroutine**

“epolar1” calculates the induced dipole polarization energy and first derivatives with respect to Cartesian coordinates

**EPOLAR1A Subroutine**

“epolar1a” calculates the dipole polarization energy and derivatives with respect to Cartesian coordinates using a pairwise double loop

**EPOLAR1B Subroutine**

“epolar1b” calculates the dipole polarization energy and derivatives with respect to Cartesian coordinates using a neighbor list

**EPOLAR1C Subroutine**

“epolar1c” calculates the dipole polarization energy and derivatives with respect to Cartesian coordinates using particle mesh Ewald summation and a double loop

**EPOLAR1D Subroutine**

“epolar1d” calculates the dipole polarization energy and derivatives with respect to Cartesian coordinates using particle mesh Ewald summation and a neighbor list

**EPOLAR1E Subroutine**

“epolar1e” calculates the dipole polarizability interaction from the induced dipoles times the electric field

**EPOLAR2 Subroutine**

“epolar2” calculates second derivatives of the dipole polarization energy for a single atom at a time

**EPOLAR2A Subroutine**

“epolar2a” computes polarization first derivatives for a single atom with respect to Cartesian coordinates; used to get finite difference second derivatives

**EPOLAR3 Subroutine**

“epolar3” calculates the induced dipole polarization energy, and partitions the energy among atoms

**EPOLAR3A Subroutine**

“epolar3a” calculates the induced dipole polarization energy using a double loop, and partitions the energy among atoms

**EPOLAR3B Subroutine**

“epolar3b” calculates the induced dipole polarization energy using a neighbor list, and partitions the energy among atoms

**EPOLAR3C Subroutine**

“epolar3c” calculates the polarization energy and analysis with respect to Cartesian coordinates using particle mesh Ewald and a double loop

**EPOLAR3D Subroutine**

“epolar3d” calculates the polarization energy and analysis with respect to Cartesian coordinates using particle mesh Ewald and a neighbor list

**EPOLAR3E Subroutine**

“epolar3e” calculates the dipole polarizability interaction from the induced dipoles times the electric field

**EPREAL0C Subroutine**

“epreal0c” calculates the induced dipole polarization energy using particle mesh Ewald summation and a double loop

**EPREAL0D Subroutine**

“epreal0d” calculates the induced dipole polarization energy using particle mesh Ewald summation and a neighbor list

**EPREAL1C Subroutine**

“epreal1c” evaluates the real space portion of the Ewald summation energy and gradient due to dipole polarization via a double loop

**EPREAL1D Subroutine**

“epreal1d” evaluates the real space portion of the Ewald summation energy and gradient due to dipole polarization via a neighbor list

**EPREAL3C Subroutine**

“epreal3c” calculates the induced dipole polarization energy and analysis using particle mesh Ewald summation and a double loop

**EPREAL3D Subroutine**

“epreal3d” calculates the induced dipole polarization energy and analysis using particle mesh Ewald and a neighbor list

**EPRECIP Subroutine**

“eprecip” evaluates the reciprocal space portion of particle mesh Ewald summation energy due to dipole polarization

**EPRECIP1 Subroutine**

“eprecip1” evaluates the reciprocal space portion of the particle mesh Ewald summation energy and gradient due to dipole polarization

**EQUCLC Subroutine**

**EREPEL Subroutine**

“erepel” calculates the Pauli exchange repulsion energy

**EREPEL0A Subroutine**

“erepel0a” calculates the Pauli repulsion interaction energy using a double loop

**EREPEL0B Subroutine**

“erepel0b” calculates the Pauli repulsion interaction energy using a pairwise neighbor list

**EREPEL1 Subroutine**

“erepel1” calculates the Pauli repulsion energy and first derivatives with respect to Cartesian coordinates

**EREPEL1A Subroutine**

“erepel1a” calculates the Pauli repulsion energy and first derivatives with respect to Cartesian coordinates using a pairwise double loop

**EREPEL1B Subroutine**

“erepel1b” calculates the Pauli repulsion energy and first derivatives with respect to Cartesian coordinates using a pariwise neighbor list

**EREPEL2 Subroutine**

“erepel2” calculates the second derivatives of the Pauli repulsion energy

**EREPEL2A Subroutine**

“erepel2a” computes Pauli repulsion first derivatives for a single atom via a double loop; used to get finite difference second derivatives

**EREPEL3 Subroutine**

“erepel3” calculates the Pauli repulsion energy and partitions the energy among the atoms

**EREPEL3A Subroutine**

“erepel3a” calculates the Pauli repulsion energy and also partitions the energy among the atoms using a double loop

**EREPEL3B Subroutine**

“erepel3b” calculates the Pauli repulsion energy and also partitions the energy among the atoms using a neighbor list

**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 functions 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 for an 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 implicit solvation energy for surface area, generalized Born, generalized Kirkwood and Poisson-Boltzmann solvation models

**ESOLV1 Subroutine**

“esolv1” calculates the implicit solvation energy and first derivatives with respect to Cartesian coordinates for surface area, generalized Born, generalized Kirkwood and Poisson-Boltzmann solvation models

**ESOLV2 Subroutine**

“esolv2” calculates second derivatives of the implicit solvation energy for surface area, generalized Born, generalized Kirkwood and Poisson-Boltzmann solvation models

**ESOLV2A Subroutine**

“esolv2a” calculates second derivatives of the implicit solvation potential energy by finite differences

**ESOLV2B Subroutine**

“esolv2b” finds implicit solvation gradients needed for calculation of the Hessian matrix by finite differences

**ESOLV3 Subroutine**

“esolv3” calculates the implicit solvation energy for surface area, generalized Born, generalized Kirkwood and Poisson-Boltzmann solvation models; 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

**EVCORR Subroutine**

“evcorr” computes the long range van der Waals correction to the energy via numerical integration

**EVCORR1 Subroutine**

“evcorr1” computes the long range van der Waals correction to the energy and virial via numerical integration

**EWALDCOF Subroutine**

“ewaldcof” finds an Ewald coefficient such that all terms beyond the specified cutoff distance will have a value less than a specified tolerance

**EWCA Subroutine**

“ewca” find the Weeks-Chandler-Andersen dispersion energy of a solute using an HCT-like method

**EWCA1 Subroutine**

“ewca1” finds the Weeks-Chandler-Anderson dispersion energy and derivatives of a solute

**EWCA3 Subroutine**

“ewca3” find the Weeks-Chandler-Andersen dispersion energy of a solute; also partitions the energy among the atoms

**EWCA3X Subroutine**

“ewca3x” finds the Weeks-Chandler-Anderson dispersion energy of a solute using a numerical “onion shell” method; also partitions the energy among the atoms

**EWCAX Subroutine**

“ewcax” finds the Weeks-Chandler-Anderson dispersion energy of a solute using a numerical “onion shell” method

**EXPLORE Subroutine**

“explore” uses simulated annealing on an initial crude embedded distance geoemtry structure to refine versus the bound, chirality, planarity and torsional error functions

**EXTENT Subroutine**

“extent” finds the largest interatomic distance in a system

**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**

“fftback” performs a 3-D FFT backward transform via a single 3-D transform or three separate 1-D transforms

**FFTCLOSE Subroutine**

“fftclose” does cleanup after performing a 3-D FFT by destroying the FFTW plans for the forward and backward transforms

**FFTFRONT Subroutine**

“fftfront” performs a 3-D FFT forward transform via a single 3-D transform or three separate 1-D transforms

**FFTSETUP Subroutine**

“fftsetup” does initialization for a 3-D FFT to be computed via either the FFTPACK or FFTW libraries

**FIELD Subroutine**

“field” sets the force field potential energy functions from a parameter file and modifications specified in a keyfile

**FINAL Subroutine**

“final” performs any final program actions such as deallocation of global memory, 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

**FITRSD Subroutine**

“fitrsd” computes residuals for electrostatic potential fitting including total charge restraints, dipole and quadrupole moment targets, and restraints to initial parameter values

**FITTORS Subroutine**

“fittors” refines torsion parameters based on a quantum mechanical optimized energy surface

**FIXFRAME Subroutine**

“fixframe” is a service routine that alters the local frame definition for specified atoms

**FIXPDB Subroutine**

“fixpdb” corrects problems with PDB files by converting residue and atom names to the standard forms used by Tinker

**FIXPOLE Subroutine**

“fixpole” performs unit conversion of the multipole components, rounds moments to desired precision, and enforces integer net charge and traceless quadrupoles

**FLATTEN Subroutine**

“flatten” sets the type of smoothing method and the extent of surface deformation for use with potential energy smoothing

**FPHI_MPOLE Subroutine**

“fphi_mpole” extracts the permanent multipole potential from the particle mesh Ewald grid

**FPHI_TO_CPHI Subroutine**

“fphi_to_cphi” transforms the reciprocal space potential from fractional to Cartesian coordinates

**FPHI_UIND Subroutine**

“fphi_uind” extracts the induced dipole potential from the particle mesh Ewald grid

**FRACDIST Subroutine**

“fracdist” computes a normalized distribution of the pairwise fractional distances between the smoothed upper and lower bounds

**FRAC_TO_CART Subroutine**

“frac_to_cart” computes a transformation matrix to convert a multipole object in fraction coordinates to Cartesian

**FRAME13 Subroutine**

“frame13” finds local coordinate frame defining atoms in cases where the use of 1-3 connected atoms is required

**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]

**GAUSSJORDAN Subroutine**

“gaussjordan” solves a system of linear equations by using the method of Gaussian elimination with partial pivoting

**GDA Program**

“gda” implements Gaussian Density Annealing (GDA) algorithm for global optimization via simulated annealing

**GDA1 Subroutine**

**GDA2 Function**

**GDA3 Subroutine**

**GDASTAT Subroutine**

for a GDA integration step; also saves the coordinates

**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

**GETARC Subroutine**

“getarc” asks for a coordinate archive or trajectory file name, then reads in the initial set of coordinates

**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

**GETCHUNK Subroutine**

“getchunk” determines the number of grid point “chunks” used along each axis of the PME grid for parallelization

**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

**GETMOL Subroutine**

“getmol” asks for a MDL MOL molecule file name, then reads the coordinates from the file

**GETMOL2 Subroutine**

“getmol2” asks for a Tripos 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” searches 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” searches for a quoted text string within an input character string; the region between the first and second double quote is returned as the “text”; if the actual text is too long, only the first part is returned

**GETTEXT Subroutine**

“gettext” searches an input string for the first string of non-blank characters; the region from a non-blank character to the first space or tab is returned as “text”; if the actual text is too long, only the first part is returned

**GETTIME Subroutine**

“gettime” finds the elapsed wall clock and CPU times in seconds since the last call to “settime”

**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” searches 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 separator 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

**GHMCSTEP Subroutine**

“ghmcstep” performs a single stochastic dynamics time step via the generalized hybrid Monte Carlo (GHMC) algorithm to ensure exact sampling from the Boltzmann density

**GHMCTERM Subroutine**

“ghmcterm” finds the friction and fluctuation terms needed to update velocities during GHMC stochastic dynamics

**GRADFAST Subroutine**

“gradfast” calculates the potential energy and first derivatives for the fast-evolving local valence potential energy terms

**GRADIENT Subroutine**

“gradient” calls subroutines to calculate the potential energy and first derivatives with respect to Cartesian coordinates

**GRADRGD Subroutine**

“gradrgd” calls subroutines to calculate the potential energy and first derivatives with respect to rigid body coordinates

**GRADROT Subroutine**

“gradrot” calls subroutines to calculate the potential energy and its torsional first derivatives

**GRADSLOW Subroutine**

“gradslow” calculates the potential energy and first derivatives for the slow-evolving nonbonded potential energy terms

**GRAFIC Subroutine**

“grafic” outputs the upper & lower triangles and diagonal of a square matrix in a schematic form for visual inspection

**GRID_DISP Subroutine**

“grid_disp” places the damped dispersion coefficients onto the particle mesh Ewald grid

**GRID_MPOLE Subroutine**

“grid_mpole” places the fractional atomic multipoles onto the particle mesh Ewald grid

**GRID_PCHG Subroutine**

“grid_pchg” places the fractional atomic partial charges onto the particle mesh Ewald grid

**GRID_UIND Subroutine**

“grid_uind” places the fractional induced dipoles onto the particle mesh Ewald grid

**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

**GSORT Subroutine**

“gsort” uses the Gram-Schmidt algorithm to build orthogonal vectors for sliding block interative matrix diagonalization

**GYRATE Subroutine**

“gyrate” computes the radius of gyration of a molecular system from its atomic coordinates; only active atoms are included

**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

**HESSBLK Subroutine**

“hessblk” calls subroutines to calculate the Hessian elements for each atom in turn with respect to Cartesian coordinates

**HESSIAN Subroutine**

“hessian” calls subroutines 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 numerical Hessian elements with respect to torsional angles; either the diagonal or the full matrix can be calculated; the full matrix needs nomega+1 gradient evaluations while the diagonal needs just two evaluations

**HETATOM Subroutine**

“hetatom” translates water molecules and ions in Protein Data Bank format to a Cartesian coordinate file and sequence file

**HIMPTOR Subroutine**

“himptor” constructs hybrid improper torsional parameters given an initial state, final state and “lambda” value

**HOOVER Subroutine**

“hoover” applies a combined thermostat and barostat via a Nose-Hoover chain algorithm

**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 a periodic box and converts to the components of the minimum image distance

**IMAGEN Subroutine**

“imagen” takes the components of pairwise distance between two points and converts to the components of the minimum image distance

**IMAGER Subroutine**

“imager” 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”

**INDTCGA Subroutine**

“indtcga” computes the induced dipoles and intermediates used in polarization force calculation for the TCG method with dp cross terms = true, initial guess mu0 = 0 and using a diagonal preconditioner

**INDTCGB Subroutine**

“indtcgb” computes the induced dipoles and intermediates used in polarization force calculation for the TCG method with dp cross terms = true, initial guess mu0 = direct and using diagonal preconditioner

**INDUCE Subroutine**

“induce” computes the induced dipole moments at polarizable sites due to direct or mutual polarization

**INDUCE0A Subroutine**

“induce0a” computes the induced dipole moments at polarizable sites using a preconditioned conjugate gradient solver

**INDUCE0B Subroutine**

“induce0b” computes and stores the induced dipoles via the truncated conjugate gradient (TCG) method

**INDUCE0C Subroutine**

“induce0c” computes the induced dipole moments at polarizable sites for generalized Kirkwood SCRF and vacuum environments

**INDUCE0D Subroutine**

“induce0d” computes the induced dipole moments at polarizable sites for Poisson-Boltzmann SCRF and vacuum environments

**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

**INITATOM Subroutine**

“initatom” sets the atomic symbol, standard atomic weight, van der Waals radius and covalent radius for each element in the periodic table

**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

**INITMMFF Subroutine**

“initmmff” initializes some parameter values for the Merck Molecular force field

**INITPRM Subroutine**

“initprm” completely initializes a force field by setting all parameters to zero and using defaults for control values

**INITRES Subroutine**

“initres” sets biopolymer residue names and biotype codes 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; optionally makes atoms inactive when they are not moved by any torsional rotation

**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

**INTERPOL Subroutine**

“interpol” computes intergroup induced dipole moments for use during removal of intergroup polarization

**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

**JACOBI Subroutine**

“jacobi” performs a matrix diagonalization of a real symmetric matrix by the method of Jacobi rotations

**JUSTIFY Subroutine**

“justify” converts a text string to right justified format with leading blank spaces

**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

**KANGLEM Subroutine**

“kanglem” assigns the force constants and ideal angles for bond angles according to the Merck Molecular Force Field (MMFF)

**KANGTOR Subroutine**

“kangtor” assigns parameters for angle-torsion interactions and processes new or changed parameter values

**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

**KBONDM Subroutine**

“kbondm” assigns a force constant and ideal bond length to each bond according to the Merck Molecular Force Field (MMFF)

**KCHARGE Subroutine**

“kcharge” assigns partial charges to the atoms within the structure and processes any new or changed values

**KCHARGEM Subroutine**

“kchargem” assigns partial charges to the atoms according to the Merck Molecular Force Field (MMFF)

**KCHGFLX Subroutine**

“kchgflx” assigns a force constant and ideal bond length to each bond in the structure and processes any new or changed parameter values

**KCHGTRN Subroutine**

“kchgtrn” assigns charge magnitude and damping parameters for charge transfer interactions and processes any new or changed values for these parameters

**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

**KDISP Subroutine**

“kdisp” assigns C6 coefficients and damping parameters for dispersion interactions and processes any new or changed values for these parameters

**KENEG Subroutine**

“keneg” applies primary and secondary electronegativity bond length corrections to applicable bond parameters

**KEWALD Subroutine**

“kewald” assigns particle mesh Ewald parameters and options for a periodic system

**KEXTRA Subroutine**

“kextra” assigns parameters to any additional user defined potential energy contribution

**KGB Subroutine**

“kgb” initializes parameters needed for the generalized Born implicit solvation models

**KGEOM Subroutine**

“kgeom” asisgns parameters for geometric restraint terms to be included in the potential energy calculation

**KGK Subroutine**

“kgk” initializes parameters needed for the generalized Kirkwood implicit solvation model

**KHPMF Subroutine**

“khpmf” initializes parameters needed for the hydrophobic potential of mean force nonpolar implicit solvation model

**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

**KINAUX Subroutine**

“kinaux” computes the total kinetic energy and temperature for auxiliary dipole variables used in iEL polarization

**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

**KNP Subroutine**

“knp” initializes parameters needed for the cavity-plus- dispersion nonpolar implicit solvation model

**KONVEC Subroutine**

“konvec” finds a Hessian-vector product via finite-difference evaluation of the gradient based on atomic displacements

**KOPBEND Subroutine**

“kopbend” assigns the force constants for out-of-plane bends at trigonal centers via Wilson-Decius-Cross or Allinger angles; also processes any new or changed parameter values

**KOPBENDM Subroutine**

“kopbendm” assigns the force constants for out-of-plane bends according to the Merck Molecular Force Field (MMFF)

**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

**KPB Subroutine**

“kpb” assigns parameters needed for the Poisson-Boltzmann implicit solvation model implemented via APBS

**KPITORS Subroutine**

“kpitors” assigns pi-system 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

**KREPEL Subroutine**

“krepel” assigns the size values, exponential parameter and number of valence electrons for Pauli repulsion interactions and processes any new or changed values for these parameters

**KSA Subroutine**

“ksa” initializes parameters needed for surface area-based implicit solvation models including ASP and SASA

**KSOLV Subroutine**

“ksolv” assigns implicit solvation energy parameters for the surface area, generalized Born, generalized Kirkwood, Poisson-Boltzmann, cavity-dispersion and HPMF models

**KSTRBND Subroutine**

“kstrbnd” assigns parameters for stretch-bend interactions and processes new or changed parameter values

**KSTRBNDM Subroutine**

“kstrbndm” assigns parameters for stretch-bend interactions according to the Merck Molecular Force Field (MMFF)

**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

**KTORSM Subroutine**

“ktorsm” assigns torsional parameters to each torsion according to the Merck Molecular Force Field (MMFF)

**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 a Levenberg-Marquardt step during a nonlinear least squares calculation using ideas from the MINPACK LMPAR routine and 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

**MAKEBAR Subroutine**

**MAKEBOX Subroutine**

“makebox” builds a periodic box of a desired size by randomly copying a specified number of monomers into a target box size, followed by optional excluded volume refinement

**MAKEINT Subroutine**

“makeint” converts Cartesian to internal coordinates where selection of internal coordinates is controlled by “mode”

**MAKEPDB Subroutine**

“makepdb” cconstructs a Protein Data Bank file from a set of Cartesian coordinates with special handling for systems consisting of biopolymer 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

**MATCH1 Subroutine**

“match1” finds and stores the first multipole component found on a line of output from Stone’s GDMA program

**MATCH2 Subroutine**

“match2” finds and stores the second multipole component found on a line of output from Stone’s GDMA program

**MATCH3 Subroutine**

“match3” finds and stores the third multipole component found on a line of output from Stone’s GDMA program

**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

**MBUILD Subroutine**

“mbuild” performs a complete rebuild of the atomic multipole electrostatic neighbor list for all sites

**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, force or induced dipole data; 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**

**MEASFQ 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

**MLIGHT Subroutine**

“mlight” performs a complete rebuild of the atomic multipole pair neighbor list for all sites using the method of lights

**MLIST Subroutine**

“mlist” performs an update or a complete rebuild of the nonbonded neighbor lists for atomic multipoles

**MMID Subroutine**

“mmid” implements a modified midpoint method to advance the integration of a set of first order differential equations

**MODECART Subroutine**

**MODERGD Subroutine**

**MODEROT Subroutine**

**MODESRCH Subroutine**

**MODETORS Subroutine**

**MODULI Subroutine**

“moduli” sets the moduli of the inverse discrete Fourier transform of the B-splines

**MOL2XYZ Program**

“mol2xyz” takes as input a Tripos MOL2 coordinates file, converts to and then writes out Cartesian coordinates

**MOLECULE Subroutine**

“molecule” counts the molecules, assigns each atom to its molecule and computes the mass of each molecule

**MOLMERGE Subroutine**

“molmerge” connects fragments and removes duplicate atoms during generation of a unit cell from an asymmetric unit

**MOLSETUP Subroutine**

“molsetup” generates trial parameters needed to perform polarizable multipole calculations on a structure read from distributed multipole analysis output

**MOLUIND Subroutine**

“moluind” computes the molecular induced dipole components in the presence of an external electric field

**MOLXYZ Program**

“molxyz” takes as input a MDL MOL coordinates file, converts to and then writes out Cartesian coordinates

**MOMENTS Subroutine**

“moments” computes the total electric charge, dipole and quadrupole moments for the active atoms as a sum over the partial charges, bond dipoles and atomic multipole moments

**MOMFULL Subroutine**

“momfull” computes the electric moments for the full system as a sum over the partial charges, bond dipoles and atomic multipole moments

**MOMYZE Subroutine**

“momyze” finds and prints the total charge, dipole moment components, radius of gyration and moments of inertia

**MONTE Program**

“monte” performs a Monte Carlo-Minimization conformational search using 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”

**NBLIST Subroutine**

“nblist” builds and maintains nonbonded pair neighbor lists for vdw, dispersion, electrostatic and polarization terms

**NEARBY Subroutine**

“nearby” finds all of the through-space neighbors of each atom for use in surface area and volume calculations

**NEEDUPDATE Subroutine**

**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

**NOSE Subroutine**

“nose” performs a single molecular dynamics time step via a Nose-Hoover extended system isothermal-isobaric algorithm

**NSPLINE Subroutine**

“nspline” computes coefficients for an nonperiodic cubic spline with natural boundary conditions where the first and last second derivatives are already known

**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 one-sided or 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

**OPBGUESS Function**

“opbguess” sets approximate out-of-plane bend force constants based on atom type and connected atoms

**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

**OPREP Subroutine**

“oprep” sets up the frictional and random terms needed to update positions and velocities for the BAOAB integrator

**OPTFIT Function**

**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

**OPTINIT Subroutine**

“optinit” initializes values and keywords used by multiple structure optimization methods

**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 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

**PARTYZE Subroutine**

“partyze” prints the energy component and number of interactions for 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 “tpath”

**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

**PAULING Subroutine**

“pauling” uses a rigid body optimization to approximately pack multiple polypeptide chains

**PAULING1 Function**

“pauling1” is a service routine that computes the energy and gradient for optimally conditioned variable metric optimization of rigid bodies

**PBDIRECTPOLFORCE Subroutine**

**PBEMPOLE Subroutine**

“pbempole” calculates the permanent multipole PB energy, field, forces and torques

**PBMUTUALPOLFORCE Subroutine**

**PDBATOM Subroutine**

“pdbatom” 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” modifies bond lengths and force constants according to the “planar” P-P-P bond order values; also alters 2-fold torsional parameters based on the “nonplanar” bond orders

**PICALC Subroutine**

“picalc” performs a modified Pariser-Parr-Pople molecular orbital calculation for each conjugated pisystem

**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 a pisystem to determine bond orders used in parameter scaling

**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

**PMONTE Subroutine**

“pmonte” implements a Monte Carlo barostat via random trial changes in the periodic box volume and shape

**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

**POLEDIT Program**

“poledit” provides for the modification and manipulation of polarizable atomic multipole electrostatic models

**POLESORT Subroutine**

“polesort” sorts a set of atomic multipole parameters based on the atom types of centers involved

**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

**POTENTIAL Program**

“potential” calculates the electrostatic potential for a molecule at a set of grid points; optionally compares to a target potential or optimizes electrostatic parameters

**POTGRID Subroutine**

“potgrid” generates electrostatic potential grid points in radially distributed shells based on the molecular surface

**POTNRG Function**

**POTOFF Subroutine**

“potoff” clears the forcefield definition by turning off the use of each of the potential energy functions

**POTPOINT Subroutine**

“potpoint” calculates the electrostatic potential at a grid point “i” as the total electrostatic interaction energy of the system with a positive charge located at the grid point

**POTSTAT Subroutine**

“potstat” computes and prints statistics for the electrostatic potential over a set of grid points

**POTWRT Subroutine**

**PRECONBLK Subroutine**

“preconblk” applies a preconditioner to an atom block section of the Hessian matrix

**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 via a barostat method

**PRESSURE2 Subroutine**

“pressure2” applies a box size and velocity correction at the half time step as needed for the Monte Carlo barostat

**PRIORITY Function**

“priority” decides which of a set of connected atoms should have highest priority in construction of a local coordinate frame and returns its atom number; if all atoms are of equal priority then zero is returned

**PRMEDIT Program**

“prmedit” reformats an existing parameter file, and revises type and class numbers based on the “atom” parameter ordering

**PRMFORM Subroutine**

“prmform” formats each individual parameter record to conform to a consistent text layout

**PRMKEY Subroutine**

“prmkey” parses a text string to extract keywords related to force field potential energy functional forms and constants

**PRMORDER Subroutine**

“prmorder” places a list of atom type or class numbers into canonical order for potential energy parameter definitions

**PRMSORT Subroutine**

“prmsort” places a list of atom type or class numbers into canonical order for potential energy parameter definitions

**PRMVAR Subroutine**

“prmvar” determines the optimization values from the corresponding electrostatic potential energy parameters

**PRMVAR Subroutine**

“prmvar” determines the optimization values from the corresponding valence potential energy parameters

**PROCHAIN Subroutine**

“prochain” builds up the internal coordinates for an amino acid sequence from the phi, psi, omega and chi values

**PROJCT Subroutine**

**PROJECT Subroutine**

“project” reads locked vectors from a binary file and projects them out of the components of the set of trial eigenvectors using the relation Y = X - U * U^T * X

**PROJECTK Subroutine**

“projectk” reads locked vectors from a binary file and projects them out of the components of the set of trial eigenvectors using the relation Y = X - U * U^T * X

**PROMO Subroutine**

“promo” writes a banner message containing information about the Tinker version, release date and 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

**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

**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

**PRTFIT Subroutine**

“prtfit” makes a key file containing results from fitting a charge or multipole model to an electrostatic potential grid

**PRTINT Subroutine**

“prtint” writes out a set of Z-matrix internal coordinates to an external disk file

**PRTMOD Subroutine**

“prtmod” writes out a set of modified Cartesian coordinates with an optional atom number offset to an external disk file

**PRTMOL2 Program**

“prtmol2” writes out a set of coordinates in Tripos MOL2 format to an external disk file

**PRTPDB Subroutine**

“prtpdb” writes out a set of Protein Data Bank coordinates to an external disk file

**PRTPOLE Subroutine**

“prtpole” creates a coordinates file, and a key file with atomic multipoles corrected for intergroup polarization

**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

**PRTVAL Subroutine**

“prtval” writes the final valence parameter results to the standard output and appends the values to a key file

**PRTVIB Subroutine**

“prtvib” writes to an external disk file a series of coordinate sets representing motion along a vibrational normal mode

**PRTXYZ Subroutine**

“prtxyz” writes out a set of Cartesian coordinates to an external disk file

**PSCALE Subroutine**

“pscale” implements a Berendsen barostat by scaling the coordinates and box dimensions via coupling to an external constant pressure bath

**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**

**PTEST Subroutine**

“ptest” determines the numerical virial tensor, and compares analytical to numerical values for dE/dV and isotropic pressure

**PTINCY Function**

**PZEXTR Subroutine**

“pzextr” is a polynomial extrapolation routine used during Bulirsch-Stoer integration of ordinary differential equations

**QIROTMAT Subroutine**

“qirotmat” finds a rotation matrix that describes the interatomic vector

**QONVEC Subroutine**

“qonvec” is a vector utility routine used during sliding block iterative matrix diagonalization

**QRFACT Subroutine**

“qrfact” computes the QR factorization of an m by n matrix a via Householder transformations with optional column pivoting; 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; used 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 functions

**READDYN Subroutine**

“readdyn” get the positions, velocities and accelerations for a molecular dynamics restart from an external disk file

**READGARC Subroutine**

“readgarc” reads data from Gaussian archive section; each entry is terminated with a backslash symbol

**READGAU Subroutine**

“readgau” reads an ab initio optimized structure, forces, Hessian and frequencies from a Gaussian 09 output file

**READGDMA Subroutine**

“readgdma” takes the DMA output in spherical harmonics from the GDMA program and converts to Cartesian multipoles in the global coordinate frame

**READINT Subroutine**

“readint” gets a set of Z-matrix internal coordinates from an external file

**READMOL Subroutine**

“readmol” gets a set of MDL MOL coordinates from an external disk file

**READMOL2 Subroutine**

“readmol2” gets a set of Tripos MOL2 coordinates from an external disk file

**READPDB Subroutine**

“readpdb” gets a set of Protein Data Bank coordinates from an external disk file

**READPOT Subroutine**

“readpot” gets a set of grid points and target electrostatic potential values 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 functions

**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

**RESPA Subroutine**

“respa” performs a single multiple time step molecular dynamics step using the reversible reference system propagation algorithm (r-RESPA) via a Verlet core with the potential split into fast- and slow-evolving portions

**RFINDEX Subroutine**

“rfindex” finds indices for each multipole site for use in computing reaction field energetics

**RGDSTEP Subroutine**

“rgdstep” performs a single molecular dynamics time step via a rigid body integration algorithm

**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, and optionally reduces large rings into their component smaller rings

**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

**ROTFRAME Subroutine**

“rotframe” takes the global multipole moments and rotates them into the local coordinate frame defined at each atomic site

**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 rotates the local coordinate system into 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” rotates the local frame atomic multipoles at a specified site into 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

**SAVEYZE Subroutine**

“saveyze” prints the atomic forces and/or the induced dipoles to separate external disk files

**SBGUESS Subroutine**

“sbguess” sets approximate stretch-bend force constants based on atom type and connected atoms

**SCAN Program**

“scan” attempts to find all the local minima on a potential energy surface via an iterative series of local searches along normal mode directions

**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

**SCANPDB Subroutine**

“scanpdb” reads the first model in a Protein Data Bank file and sets chains, alternate sites and insertion records to be used

**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 the velocity Verlet integration algorithm

**SDTERM Subroutine**

“sdterm” finds the frictional and random terms needed to update positions and velocities during stochastic dynamics

**SEARCH Subroutine**

“search” is a unidimensional line search based upon parabolic extrapolation and cubic interpolation using both function and gradient values

**SETACCELERATION Subroutine**

**SETATOMIC Subroutine**

**SETATOMTYPES Subroutine**

**SETCHARGE Subroutine**

**SETCHUNK Subroutine**

“setchunk” marks a chunk in the PME spatial table which is overlapped by the B-splines for a site

**SETCONNECTIVITY Subroutine**

**SETCOORDINATES Subroutine**

**SETELECT Subroutine**

“setelect” assigns partial charge, bond dipole and atomic multipole parameters for the current structure, as needed for computation of the electrostatic potential

**SETENERGY Subroutine**

**SETFILE Subroutine**

**SETFORCEFIELD Subroutine**

**SETFRAME Subroutine**

“setframe” assigns a local coordinate frame at each atomic multipole site using high priority connected atoms along axes

**SETGRADIENTS Subroutine**

**SETINDUCED Subroutine**

**SETKEYWORD Subroutine**

**SETMASS Subroutine**

**SETMDTIME Subroutine**

**SETMOL2 Program**

“setmol2” assigns MOL2 atom names/types/charges and bond types based upon atomic numbers and connectivity

**SETNAME Subroutine**

**SETPAIR Program**

“setpair” is a service routine that assigns flags, sets cutoffs and allocates arrays used by different pairwise neighbor methods

**SETPOLAR Subroutine**

“setpolar” assigns atomic polarizabilities, Thole damping or charge penetration parameters, and polarization groups with user modification of these values

**SETSTEP Subroutine**

**SETSTORY Subroutine**

**SETTIME Subroutine**

“settime” initializes the wall clock and elapsed CPU times

**SETUPDATED Subroutine**

**SETVELOCITY Subroutine**

**SHAKE Subroutine**

“shake” implements the SHAKE algorithm by correcting atomic positions to maintain interatomic distance and absolute spatial constraints

**SHAKE2 Subroutine**

“shake2” modifies the gradient to remove components along any holonomic distance contraints using a variant of SHAKE

**SHAKEUP Subroutine**

“shakeup” initializes any holonomic constraints for use with the SHAKE and RATTLE algorithms

**SHROTMAT Subroutine**

“shrotmat” finds the rotation matrix that converts spherical harmonic quadrupoles from the local to the global frame given the required dipole rotation matrix

**SHROTSITE Subroutine**

“shrotsite” converts spherical harmonic multipoles from the local to the global frame given required rotation matrices

**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

**SIMPLEX Subroutine**

“simplex” is a general multidimensional Nelder-Mead simplex optimization routine requiring only repeated evaluations of the objective function

**SIMPLEX1 Function**

“simplex1” is a service routine used only by the Nelder-Mead simplex optimization method

**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

**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

**SPHERE Subroutine**

“sphere” finds a specified number of uniformly distributed points on a sphere of unit radius centered at the origin

**SQUARE Subroutine**

“square” is a nonlinear least squares routine derived from the IMSL BCLSF routine and the MINPACK LMDER routine; 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 and version 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

**SURFACE1 Subroutine**

“surface1” 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”

**SURFATOM1 Subroutine**

“surfatom1” performs an analytical computation of the surface area and first derivatives with respect to Cartesian coordinates of a specified atom

**SWITCH Subroutine**

“switch” sets the coeffcients used by the fifth and seventh order polynomial switching functions for spherical cutoffs

**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

**SYSTYZE Subroutine**

“systyze” is an auxiliary routine for the analyze program that prints general information about the molecular system and the force field model

**TABLE_FILL Subroutine**

“table_fill” constructs an array which stores the spatial regions of the particle mesh Ewald grid with contributions from each site

**TANGENT Subroutine**

“tangent” finds the projected gradient on the synchronous transit path for a point along the transit pathway

**TCGSWAP Subroutine**

“tcgswap” switches two sets of induced dipole quantities for use with the TCG induced dipole solver

**TCG_ALPHA12 Subroutine**

“tcg_alpha12” computes source1 = alpha*source1 and source2 = alpha*source2

**TCG_ALPHA22 Subroutine**

“tcg_alpha22” computes result1 = alpha*source1 and result2 = alpha*source2

**TCG_ALPHAQUAD Subroutine**

“tcg_alphaquad” computes the quadratic form, <a*alpha*b>, where alpha is the diagonal atomic polarizability matrix

**TCG_DOTPROD Subroutine**

“tcg_dotprod” computes the dot product of two vectors of length n elements

**TCG_RESOURCE Subroutine**

“tcg_resource” sets the number of mutual induced dipole pairs based on the passed argument

**TCG_T0 Subroutine**

“tcg_t0” applies T matrix to ind/p, and returns v3d/p T = 1/alpha + Tu

**TCG_UFIELD Subroutine**

“tcg_ufield” applies -Tu to ind/p and returns v3d/p

**TCG_UPDATE Subroutine**

“tcg_update” computes pvec = alpha*rvec + beta*pvec; if the preconditioner is not used, then alpha = identity

**TEMPER Subroutine**

“temper” computes the instantaneous temperature and applies a thermostat via Berendsen or Bussi-Parrinello velocity scaling, Andersen stochastic collisions or Nose-Hoover chains; also uses Berendsen scaling for any iEL induced dipole variables

**TEMPER2 Subroutine**

“temper2” applies a velocity correction at the half time step as needed for the Nose-Hoover thermostat

**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

**TESTPAIR Program**

“testpair” performs a set of timing tests to compare the evaluation of potential energy and energy/gradient using different methods for finding pairwise neighbors

**TESTPOL Program**

“testpol” compares the induced dipoles from direct polarization, mutual SCF iterations, perturbation theory extrapolation (OPT), and truncated conjugate gradient (TCG) solvers

**TESTROT Program**

“testrot” computes and compares the analytical and numerical gradient vectors of the potential energy function with respect to rotatable torsional angles

**TESTVIR Program**

“testvir” computes the analytical internal virial and compares it to a numerical virial derived from the finite difference derivative of the energy with respect to lattice vectors

**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)

**TORFIT1 Function**

“torfit1” is a service routine that computes the energy and gradient for a low storage BFGS optimization in Cartesian coordinate space

**TORGUESS Subroutine**

“torguess” set approximate torsion amplitude parameters based on atom type and connected atoms

**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 a single site defined by a local coordinate frame and converts to Cartesian forces on the original site and sites specifying the local frame, also gives the x,y,z-force components needed for virial computation

**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

**TORSFIT Program**

“torsfit” refines torsional force field parameters based on a quantum mechanical potential surface and analytical gradient

**TORSIONS Subroutine**

“torsions” finds the total number of torsional angles and the numbers of the four atoms defining each torsional 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

**TRANSFORM Subroutine**

“transform” diagonalizes the current basis vectors to produce trial roots for sliding block iterative matrix diagonalization

**TRANSIT Function**

“transit” evaluates the synchronous transit function and gradient; linear and quadratic transit paths are available

**TRBASIS Subroutine**

“trbasis” forms translation and rotation basis vectors used during vibrational analysis via block iterative diagonalization

**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

**TRIGGER Subroutine**

“trigger” constructs a set of initial trial vectors for use during sliding block iterative matrix diagonalization

**TRIMHEAD Subroutine**

“trimhead” removes blank spaces before the first non-blank character in a text string by shifting the string to the left

**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 based on ideas found in NL2SOL and Dennis and Schnabel’s book

**UBUILD Subroutine**

“ubuild” performs a complete rebuild of the polarization preconditioner neighbor list for all sites

**UDIRECT1 Subroutine**

“udirect1” computes the reciprocal space contribution of the permanent atomic multipole moments to the field

**UDIRECT2A Subroutine**

“udirect2a” computes the real space contribution of the permanent atomic multipole moments to the field via a double loop

**UDIRECT2B Subroutine**

“udirect2b” computes the real space contribution of the permanent atomic multipole moments to the field via a neighbor list

**UFIELD0A Subroutine**

“ufield0a” computes the mutual electrostatic field due to induced dipole moments via a double loop

**UFIELD0B Subroutine**

“ufield0b” computes the mutual electrostatic field due to induced dipole moments via a pair list

**UFIELD0C Subroutine**

“ufield0c” computes the mutual electrostatic field due to induced dipole moments via Ewald summation

**UFIELD0D Subroutine**

“ufield0d” computes the mutual electrostatic field due to induced dipole moments for use with with generalized Kirkwood implicit solvation

**UFIELD0E Subroutine**

“ufield0e” computes the mutual electrostatic field due to induced dipole moments via a Poisson-Boltzmann solver

**UFIELDI Subroutine**

“ufieldi” computes the electrostatic field due to intergroup induced dipole moments

**ULIGHT Subroutine**

“ulight” performs a complete rebuild of the polarization preconditioner pair neighbor list for all sites using the method of lights

**ULIST Subroutine**

“ulist” performs an update or a complete rebuild of the neighbor lists for the polarization preconditioner

**ULSPRED Subroutine**

“ulspred” uses standard extrapolation or a least squares fit to set coefficients of an induced dipole predictor polynomial

**UMUTUAL1 Subroutine**

“umutual1” computes the reciprocal space contribution of the induced atomic dipole moments to the field

**UMUTUAL2A Subroutine**

“umutual2a” computes the real space contribution of the induced atomic dipole moments to the field via a double loop

**UMUTUAL2B Subroutine**

“umutual2b” computes the real space contribution of the induced atomic dipole moments to the field via a neighbor list

**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

**URYGUESS Function**

“uryguess” sets approximate Urey-Bradley force constants based on atom type and connected atoms

**USCALE0A Subroutine**

“uscale0a” builds and applies a preconditioner for the conjugate gradient induced dipole solver using a double loop

**USCALE0B Subroutine**

“uscale0b” builds and applies a preconditioner for the conjugate gradient induced dipole solver using a neighbor pair list

**VALENCE Program**

“valence” refines force field parameters for valence terms based on a quantum mechanical optimized structure and frequencies

**VALFIT1 Function**

“valfit1” is a service routine that computes the RMS error and gradient for valence parameters fit to QM results

**VALGUESS Subroutine**

“valguess” sets approximate valence parameter values based on quantum mechanical structure and frequency data

**VALMIN1 Function**

“valmin1” is a service routine that computes the molecular energy and gradient during valence parameter optimization

**VALRMS Function**

“valrms” evaluates a valence parameter goodness-of-fit error function based on comparison of forces, frequencies, bond lengths and angles to QM results

**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

**VARPRM Subroutine**

“varprm” copies the current optimization values into the corresponding electrostatic potential energy parameters

**VARPRM Subroutine**

“varprm” copies the current optimization values into the corresponding valence potential energy parameters

**VBUILD Subroutine**

“vbuild” performs a complete rebuild of the van der Waals pair neighbor list for all sites

**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

**VDWGUESS Subroutine**

“vdwguess” sets initial VDW parameters based on atom type and connected atoms

**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 via 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

**VIBBIG Program**

“vibbig” performs large-scale vibrational mode analysis using only vector storage and gradient evaluations; preconditioning is via an approximate inverse from a block diagonal Hessian, and a sliding block method is used to converge any number of eigenvectors starting from either lowest or highest frequency

**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

**VIBROT Program**

“vibrot” computes the eigenvalues and eigenvectors of the torsional Hessian matrix

**VIRIYZE Subroutine**

“propyze” finds and prints the internal virial, the dE/dV value and an estimate of the pressure

**VLIGHT Subroutine**

“vlight” performs a complete rebuild of the van der Waals pair neighbor list for all sites using the method of lights

**VLIST Subroutine**

“vlist” performs an update or a complete rebuild of the nonbonded neighbor lists for vdw sites

**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

**WIGGLE Subroutine**

“wiggle” applies a random perturbation to the atomic coordinates to avoid numerical instabilities for various linear, planar and symmetric structures

**XTALERR Subroutine**

“xtalerr” computes an error function value derived from lattice energies, dimer intermolecular energies and the gradient with respect to structural parameters

**XTALFIT Program**

“xtalfit” determines optimized van der Waals and electrostatic parameters by fitting to crystal structures, lattice energies, and dimer structures and interaction energies

**XTALMIN Program**

“xtalmin” performs a full crystal energy minimization by optimizing over fractional atomic coordinates and the six lattice lengths and angles

**XTALMIN1 Function**

“xtalmin1” is a service routine that computes the energy and gradient with respect to fractional coordinates and lattice dimensions for a crystal energy minimization

**XTALMOVE Subroutine**

“xtalmove” converts fractional to Cartesian coordinates for rigid molecules during optimization of force field parameters

**XTALPRM Subroutine**

“xtalprm” stores or retrieves a molecular structure; used to make a previously stored structure the active structure, or to store a structure for later use

**XTALWRT Subroutine**

“xtalwrt” prints intermediate results during fitting of force field parameters to structures and energies

**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 Cartesian coordinates files

**XYZINT Program**

“xyzint” takes as input a Cartesian coordinates file, then converts to and writes out an internal coordinates file

**XYZMOL2 Program**

“xyzmol2” takes as input a Cartesian coordinates file, converts to and then writes out a Tripos MOL2 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

**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