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Computational Chemistry Software

Listed Alphabetically

AbM -
ALCHEMY -
CAChe -
Cerius2 -
Chem3D -
GAMESS -
Gaussian -
HyperChem -
Insight II -
MOPAC -
Nemesis -
PCModel -
SPARTAN -
TurboNMR -
Unichem -
ZINDO


  • AbM - an integrated suite of programs for antibody structure modeling. It combines the benefits of knowledge databases with ab initio methods, permitting you to model the tertiary structure of an antibody starting with its primary sequence. -- Oxford Molecular Group

  • ACD/Labs is a collection of Windows-based structure drawing and analysis tools. Programs available include ACD/ChemSketch, ACD/Tautomers (check and generate predominant tautomeric forms), ACD/LogP, ACD/CNMR and ACD/Dictionary. -- Advanced Chemistry Development Inc.

  • ACES II is an ab initio Molecular Orbital program which uses many-body perturbation theory to derive correlation energy. -- Rodney Bartlett, Quantum Theory Project
    GIAO
  • ACM (Adiabetic Correction Method) replaces part of DFT exchange with exact exchange from HF.

  • ADAPT (Automated Data Analysis using Pattern Recognition Toolkit)

  • ADF (Amsterdam Density Functional) -- Bert te Velde, Vrije Universiyteit

  • AIPHOS (Artificial Intelligence for Planning and Handling Organic Synthesis) Computer Assisted Synthesis -- K. Funatsu

  • ALCHEMY-II is a set of IBM based programs for direct CI and MCSCF on small and medium sized molecules. One-particle density matrices, One-electron properties, natural orbitals, transition density matrices. -- Michael Dupuis, IBM Corporation

  • Alchemy 2000 (3, low end Sybyl relative) is a desktop molecular modeling system for PC (DOS and Windows) and Macintosh computers. Provides structure building, comparison, optimization, and display. Systematic & MC searches., protein builder -- Tripos, Inc., http://www.tripos.com
    Parameters: MM2, MM3, Sybyl
    MP3
    Cons: charge calculations unreproducible
    substitutes for missing parameters
    File Formats:
    Sybyl.mol
    Brookhaven.pdb
    ChemDraw
    HyperChem
    MDL
    SMILES
    SciVision
    Alchemy III.mol
    Dimensions: 3500+ atoms
    Properties:
    IR spectra
    Thermodynamics
    dipole moment
    VdW energy
    steric energy
    distance
    angle
    SciPolymer-polymer property QSPR
    SciQSAR-QSPR spreadsheet tool
    SciProtein-protein structure seq's & DB
    SciLogP-logP QSPR

  • AMBER (Assisted Model Building using Energy Refinement). A suite of programs for molecular mechanics and molecular dynamics simulations. Designed primarily for proteins and nucleic acids.

  • AMPAC (Austin Method PACkage) Computer code that first presented the AM1 method to the world. A semiempirical quantum mechanics program developed by Michael Dewar and co-workers. The program contains the MINDO/3, MNDO and AM1 Hamiltonians. RHF (Restricted Hartree-Fock) and UHF (Unrestricted Hartree-Fock) methods. Extensive CI (Configuration Interactions). Options permit geometry optimization, calculation of transition state geometries and activation energy barriers, calculation of force constants, normal mode analysis, etc. -- QCPE 506

  • AMPAC 6 (8) with graphical user interface
    Z-Matrix editor
    simulated annealing
    symmetry group assignment
    CHAIN
    PATH
    EF
    ESP
    AMSOL
    CODESSA - QSPR tool
    File Formats:
    Mopac Input
    Gaussian
    Hyperchem
    Parameters:
    MINDO/3, MNDO, PM3, AM1
    SAM1
    MNDOC
    Properties:
    IR (Force) Spectra
    ESR
    NLO
    HOMO
    LUMO
    Distance
    Angle
    charges
    molar volume
    molar surface area
    ovality
    dipole moment
    UV (CI)
  • AMSOL AMPAC with explicit solvation effects -- Chris Cramer and Don Truhlar, The University of Minnesota & QCPE
    SM2 Basis:
    AM1
    aqueous
    Atoms:
    H
    C - F
    P - Cl
    Br
    SM5 Basis:
    230 solutes
    90 solvents
    Acc'y: [Delta]G(transfer)+/-0.7 kcal/mol
  • Anaconda - an interactive molecular similarity for visual comparison/alignment of surface properties and pharmacophore discovery. -- Oxford Molecular Group

  • Apex-3D is a rule-based QSAR program. -- BIOSYM/MSI

  • Art of Science is a collection of EPS images prepared especially for the scientific community for import into page layout and word processing and programs including Microsoft Word. -- SoftShell

  • ARITVE is a program for modeling amorphous mean tridimensional structure by a Rietveld-type approach (refining atomic coordinates against neutron or/and X-ray interference functions). It is a freeware. FORTRAN sources are available for DEC-ALPHA-AXP running VMS. -- ftp://aviion.univ-lemans.fr/pub/fluorlab/aritve.html

  • ASP is a fast, automatic similarity assessment program which calculates molecular similarity based on spherical projection of electrostatic, steric, lipophilic or refractive properties. -- Oxford Molecular

  • The Babel file conversion program.

  • BioGraf was formerly available from MSI but has been discontinued as a product line.

  • Bionet - an on-line timesharing system for DNA and protein sequence analysis. -- Oxford Molecular Group

  • BIOPROP is a generalized, programmable neural network simulator for predicting protein structures. Designed for use on mainframe and supercomputers, however, the Fortran 77 code can be modified for use on personal computers. -- Office of Technology Licensing, Berkeley

  • BOSS (Biochemical and Organic Simulation System). Monte Carlo statistical mechanics simulations of organic molecules, complexes and reactions in solution.

  • CACAO (Computer Aided Composition of Atomic Orbitals) is a package of electronic structure programs for the calculation and analysis of molecular orbitals. The package consists of an EHC program (SIMCON), an orbital analysis program (MOAN) and a display program for atomic orbitals (CACAO). The programs require at least a 286 PC with math co-processor. -- Davide M. Proserpio, Universita di Milano

  • CAChe WorkSystem (10, user friendly general purpose modeling) suite of modules covering range of computational chemistry methods. -- Oxford Molecular, http://www.oxmol.com

    - Editor & CAChe Translators

    3-D sketch
    Polymerizer
    Crystal Builder
    12+ search variables
    Sequential search
    Force Field tools
    File Formats:
    MDL .mol
    Tripos .mol
    Brookhaven .pdb
    CCSDB
    Chem3D (original)
    Tribble
    Shelx
    Mopac Input
    ZINDO Input
    - Dynamics: performs molecular dynamics with the augmented MM2 force field.

    - ExtHuckel: Extended Hückel calculations

    Atoms:
    <=150
    H - Lr
    Properties:
    Overlap Matrix
    Total Energy
    Eigenvalues
    Eigenvectors
    Wyberg Bond Index
    Mulliken Atomic Population Array
    Atomic Charges
    Dipole Moment
    - GroupServer: uses SG or RS-6000 as server for CAChe modules

    - Mechanics: molecular mechanics calculations including energy minimization, exhaustive, and sequential search.

    Augmented MM2:
    H
    Li - F
    Na - Cl
    K, Ti - Br
    Rb, Zr - I
    Cs, W - Bi
    Nd, Sm
    U
    Accuracy:
    (M-bonds l+/-7% a+/-9%)
    Properties:
    Energy
    - Steric
    - Strain
    - Van der Waals
    - H-Bond
    Geometry
    - Minimum
    - Cartesian Coordinates
    - Distance
    - Angle
    - Dihedral
    - MOPAC: standard semiempirical calculations (UV, IR, COSMO)
    Dimensions (heavy/light atoms):
    25x40, 66x66
    70x70, 150x150
    Parameters:
    MINDO/3, MNDO, PM3
    AM1 (w/o Li?)
    (w/ Cb, +, ++, -, --)
    Properties:
    Dipole Moment
    Energy
    - Enthalpy
    - Entropy
    - Heat Capacity
    - Heat of Formation
    - Electronic
    - Resonance
    - Total
    - Zero Point
    ESR
    - Spin Density
    Infrared
    - Spectrum
    - Description of Vibrations
    - Frequencies/Vibrational Energy
    - Transition Dipole
    Ionization Potential
    Geometry
    - Minimum
    - Cartesian Coordinates
    - Saddle
    - Transition State
    - Twist Angle
    - 1-Dimensional Polymer
    - Atom distance
    - Van der Waals Surface Area
    Polarizability
    - (Alpha)
    - Finite Field
    - Second Order (Beta)
    - Third Order (Gamma)
    Localized Orbital
    Mulliken Atomic Population
    Partial Atomic Charges
    Valencies
    Bond
    - Angle
    - Length
    - Order
    Ensemble
    - Dynamic Reaction Coordinate, DRC
    - Intrinsic Reaction Coordinate, IRC
    - Potential Energy Profile, Grid
    - Mulliken: accurate, reliable ab initio calculations for large molecules with a powerful graphical interface and optimized performance. Developed by IBM.
    Parameters:
    Dreiding
    MNDO, PM3, AM1, INDO/S
    STO-3G(*),3-21G, 4-31G,
    6-31G...6-311G*, **)
    Dunning-
    D95: H
    Li - Ne
    Al - Cl
    D95*: H
    Li - F
    Al - Cl
    Properties:
    Dipole Moment
    Infrared
    - Spectrum
    - Frequencies/Vibrational Energy
    - Intensity(km/mole)
    Energy
    - Total
    - Orbital
    Polarizability (Alpha)
    Electrostatic Potential
    Geometry
    - Minimum
    - Cartesian Coordinates
    - Distance
    - Angle
    - Dihedral
    Ensembles
    - Intrinsic Reaction Coordinate, IRC
    - Linear Synchronous Transit, LST
    - Monte Carlo
    - Visualizer+: visualizes potential energy surfaces in 3-D, molecular surfaces (electron density, electrostatic potential, superdelocalizabilty), orbitals, IR and UV spectra.

    - ZINDO: Zerners INDO program for semiempirical calculations

    Dimensions (atoms/basis functions):
    60x210, 140x490
    140x490, 200x700
    Parameters:
    INDO/1(+ As, Br, I)
    INDO/S, INDO/2
    CNDO/1 ([Delta]Hfdeg.+/-200, l+/-0.2)
    CNDO/2
    EHT
    PPP
    Properties:
    Dipole Moment
    Electron Affinity
    ESR
    - Spin Density
    Ionization Potential
    UV/Visible
    - Spectrum
    - Lambda Max/Excitation Energy
    - Oscillator Strength
    - Transition Dipole
    - Transition Moment
    Energy
    - Total
    - Solute Polarization
    - Solvent Reorganization
    Geometry
    - Minimum
    - Transition State
    Localized Orbitals
    - Boys
    - Fermi
    - Double Projector
    Orbital
    - Mulliken Populations
    - Natural
    Geometry
    - Atom distance
    - Cartesian Coordinates
    Partial Atomic Charges
    Bond
    - Angle
    - Length
    - Order
    - ProjectLeader: spreadsheet style interface to set up, run, and analyze the results from series of calculations.
    Spreadsheet
    Self Documenting
    QSPR
    - CAChe logP
    DIPPR Database
    Properties:
    Dipole Moment
    - Vacuum
    - Aqueous
    - vector
    Electron Affinity
    Energy
    - Enthalpy
    - Entropy
    - Free energy
    - Heat Capacity
    - Heat of Formation
    - Dielectric
    - Steric
    - Total
    Infrared
    - Spectrum
    - Frequencies/Vibrational Energy
    - Peak Identification
    - Transition Dipole
    Ionization Potential
    log P - octanol-water partition coefficient
    logW - water solubility
    Molar refractivity
    Molecular Formula
    Molecular Weight
    Polymer - Tg
    UV/Visible
    - Spectrum
    - Lambda Max/Excitation Energy
    - Transition Dipole
    - Transition Moment
    Atom Count
    Polarizability
    - (Alpha)
    - Tensor
    Connectivity Index
    - Chi0 (atomic)
    - Chi1 (bond)
    - Chi2 (path)
    - valence Chi0 (atomic)
    - valence Chi1 (bond)
    - valence Chi2 (path)
    Molecular ovality
    Polymer
    - Cohesive Energy
    - solubility parameter, Delta
    - MVol
    Shape Index
    - Kappa, Order1 (cycles)
    - Kappa, Order2 (linearity)
    - Kappa, Order3 (branching)
    Surface Area
    - isosurface
    - Solvent Accessible
    - Van der Waals
    Surface Volume
    - isosurface
    - VdW
    - Frontier Electron Density
    - HOMO Energy
    - LUMO Energy
    - Molecular Orbital Energy
    - Molecular Orbital Occupation
    Superdelocalizability
    - Electrophilic
    - Nucleophilic
    - Radical
    Susceptibility
    - Electrophilic
    - Nucleophilic
    - Radical
    Atom distance
    Partial Charges
    Bond
    - Angle
    - Dihedral angle
    - Length/ Atom Distance
    - Order
    - Strain
  • CAChe Satellite: (for Windows) - a set of powerful desktop modeling tools, many features of CAChe WorkSystem, but CAChe "Experiments" rather than ProjectLeader procedures. -- Oxford Molecular

  • CACTVS: a universal, networked visual chemistry data manager for computation, analysis and visualization of arbitrary chemical information.

  • CADPAC (Cambridge Analytical Derivatives PACkage) is a quantum chemical program designed to calculate geometry, vibrational frequencies and a variety of molecular properties with a variety of correlation methods. -- Roger Amos, University Chemical Laboratory, part of UNICHEM.
    RHF, ROHF, UHF
    MP2, MP3, MP4
    CISD, CEPA, ACPE, CCD, QCISD(T)
    analytical gradients w/ MP2, MP3
    Properties: electronic moment
    polarizability
    hyperpolarizability
    IR spectrum
    Raman spectrum
    vibrational circular dichroism
    magnetizability
    NMR chemical shift
    Mulliken Population Analysis
  • CAMELEON is a set of multiple sequence alignment tools with links to databases of known 3D structural fragments. -- Oxford Molecular
    protein structure from sequence
  • CAMEO (Computer Assisted Mechanistic Evaluation of Organic Reactions) is a forward chaining reaction prediction program. Runs on VAX/VMS computer systems and uses Tektronix graphics. -- William L. Jorgensen, Yale University

  • CAR-PARINELLO (-1) a plane wave DFT code for Molecular Dynamics.
    Pros: electronic MD
    periodic boundary conditions
    B88-P86
    Cons: must recompile to run
  • CAVEAT accomplishes a number of tasks to assist in the structure-based design of molecules

  • CAVITY is a program designed to evaluate the shape of active sites. It has been compiled for and runs on ESV, SGI Iris, and Sun workstations. A paper describing CAVITY can be found in J. Comp.-Aided Mol. Des., 4: 337-354 (1990). -- Garland Marshall, Washington University

  • CCP4 (Collaborative Computational Project). An integrated suite of nearly 100 programs for protein crystallography. Application areas include data processing, scaling, Patterson search and refinement, molecular replacement, structure refinement, phasing and more. -- David Love, Daresburry Laboratory

  • CCP14 (Collaborative Computational Project). An integrated suite of programs for protein crystallography.

  • CEDAR - biopolymer force field

  • Cerius2 - Software environment designed to facilitate the chemical computing needs of R&D organizations: visualize structures, predict the properties and behavior of chemical systems, refine structural models, and integrate in-house computational codes in a commercial software environment. The Cerius2 environment integrates builder modules, development tools, force fields, simulation and visualization tools with tools specifically developed for applications in the life and materials sciences. Several modules. -- MSI/Biosym, http://www.msi.com/
    Dreiding
    UFF: (Rappe & Landis)
    Basis: Organic
    Inorganic
    parms calc'd from basic props
    Pros: full periodic table
    Cons: needs charge equilibration
    2-MeO -THP equatorial
    OFF: H - No
    MM2
    CFF93
    Amber
    - C2*ADF: interface to the Amsterdam Density Functional Codes. Perform electronic structure calculations which compute the structure, energetics, and properties of organic and inorganic molecules, transition metals and heavy-element compounds.

    - C2*Align: aligns sets of molecules for easy comparison during the study of drug candidates using automated or manual alignment methods.

    - C2*Amorphous Builder: used to build models of amorphous polymers and polymer/solvent systems. Combined with simulation and analysis functionality, this offers a powerful way to understand the relationship between amorphous structure and properties.

    - C2*Analog Builder: used to specify combinatorial libraries and select fragments/reagents based on their diversity. Generate sets of congeneric analogs that can be rapidly screened to identify drug candidates.

    - C2*Blends: predicts phase diagrams and interaction parameters for liquid-liquid, polymer-polymer, and polymer-additive mixtures, for studying the structural factors affecting the behavior of blends and formulations.

    - C2*CASTEP: a quantum mechanics module used to simulate the properties of solids, interfaces, and surfaces for a wide range of materials classes including ceramics, semiconductors, and metals. Determine quantities such as geometric structure, energies, band-structures, and charge density.

    - C2*CAVEAT: identifies molecular frameworks from which novel active lead candidates can be designed de novo. Clustering and filtering tools.

    - C2*Conformers: provides conformational search algorithms and associated analysis tools, to characterize molecular conformation and flexibility, and gain insight into geometric and energetic properties.

    - C2*Crystal Builder: builds and visualizse models of inorganic or molecular crystals, to understand crystalline structure and simulate the behavior of solids.

    - C2*Crystal Packer: provides rigid-body energy minimization routines to construct and analyze molecular packing in organic crystals such as pigments and drugs.

    - C2*DBAccess: provides direct access to structural databases (Catalyst and MDL ISIS) for use in modeling experiments. Hits can be browsed in 2D or 3D.

    - C2*Descriptor+: extends the range of QSAR analysis in Cerius2 by supplying a wide range of generic descriptors. The capabilities of C2.QSAR+ and C2.GA can be applied to problems like combinatorial chemistry analysis, optimization of formulations, and the properties of polymers and blends.

    - C2*Diffraction-Amorphous: simulates non-crystalline diffraction, including small angle scattering for comparison with experimental data to determine amorphous structure, polymer chain conformation, copolymer sequence structure, and orientation.

    - C2*Diffraction-Crystal: simulates powder, fiber, and single crystal diffraction from crystalline models, for interpreting experimental data from molecular, inorganic, and polymeric crystalline materials.

    - C2*Diffraction-Faulted: simulates powder diffraction from faulted or layered structures, for characterizing structures such as zeolites and clays.

    - C2*Diversity: analyzes chemical diversity to design and evaluate compound libraries and reagent sets for combinatorial chemistry to sample all potential drug candidates so that a reduced set can be synthesized and screened.

    - C2*DLS: uses geometric refinement to predict the structures of inorganic frameworks, especially zeolites, from a trial model.

    - C2*Dynamics: applies molecular mechanics to study structure relaxation and investigate the behavior of a material over a time period. Properties which can be deduced include: stability, diffusion, radial distribution functions and structure factors, and velocity auto-correlation functions.

    - C2*EXAFS: integrates the EXAFS analysis and refinement techniques of Daresbury's EXCURV92 with Cerius2's modeling tools, radically improving ability to interpret EXAFS data. (Jointly developed with the CCLRC Daresbury Laboratory, UK.)

    - C2*FFE: (Force Field Editor) adapts force fields from the Cerius2 database or create new to apply force fields from the literature and to develop and validate in-house parameterizations.

    - C2*Gaussian: interfaces to the Gaussian code to apply ab initio, semi-empirical, and density functional techniques to study the energetics, structure, and chemistry of molecules and transition states.

    - C2*GA: provides the breakthrough technology of Genetic Algorithms to evolve a family of predictive models. Develop QSAR models from receptor surface and other data, leading to faster screening of drug candidates.

    - C2*HRTEM: simulates High Resolution Transmission Electron Microscope images from crystals, interfaces and defect structures. Set up and interpret EM experiments that investigate technologically important materials.

    - C2*Interface Builder: builds and displays models of the interface between two materials. Visualize complex structural features and provides the basis for further simulation work.

    - C2*LEED/RHEED: interpret Low Energy Electron Diffraction patterns and Reflection High Energy Electron Diffraction from surfaces.

    - C2*Mechanical Properties: predicts a range of ideal elastic modulii for any materials type for designing novel crystalline and amorphous polymers, ceramics, and semiconductors.

    - C2*MFA: permits field-based 3D QSAR and visualization to predict the activities of new molecules based on the geometric properties of existing compounds.

    - C2*Minimizer: predicts low-energy structures using molecular mechanics calculations and the power of Cerius2's Open Force Field. Increase understanding of molecular, macromolecular, amorphous, crystalline, and surface structure and properties.

    - C2*MMFF: provides the Merck Molecular Force Field for accurately studying the structure, energetics, and dynamics of molecular systems in the life sciences. MMFF is broadly parameterized for organic and bio-organic systems and for the intermolecular interactions crucial to enzyme binding.

    - C2*Mopac: interfaces to the popular semi-empirical quantum code MOPAC to study molecular structure and energetics, and compute properties such as molecular orbitals and charges.

    - C2*Morphology: predicts and analyzes the morphology of crystals from their internal crystal structure. Relates morphological features to structure and the likely effects of solvents and growth modifying additives.

    - C2*OFF: (Open Force Field) provides molecular mechanics force fields to support Cerius2's property prediction modules. Extensive database of force fields covering organics, polymers, zeolites, organometallics, and other materials types.

    - C2*Polymer Builder: is used to construct models of polymer chains from monomers that may be user-defined or taken from an extensive fragment library, to understand and characterize polymer structure.

    - C2*Polymer Properties: analyzes models of polymer structure by calculating properties such as the radius of gyration, end-to-end distance, order parameters, distribution of torsional states, free volume, density, and Voronoi volume.

    - C2*Polymorph: predicts the polymorphs of organic crystalline materials such as drugs, pigments, or fine chemicals, from their molecular structure. Predict unsynthesized polymorphs or determine structures in combination with techniques such as Rietveld refinement.

    - C2*Powder: Indexing completes a comprehensive package of software modules for crystal structure determination from powder data. Establish unit cell and symmetry information and assist Rietveld refinement or crystal structure predictions.

    - C2*Protein Active Site Viewer: visualizes the key elements of protein structure and protein-ligand interactions. A Hit-List-Browser is included to review an active site, enabling you to visualize the results of a database search in the context of the protein active site.

    - C2*QSAR+: provides a wide range of regression and analysis technologies integrated in a "chemically aware" molecular spreadsheet. Existing data can be used to predict the activities of novel drug candidates.

    - C2*Receptor: investigates interaction of lead candidates for drug developmentwith a protein receptor site - represented as a 3D surface. Develop predictive QSAR models or rank the results of a database search by volumetric similarity.

    - C2*Rietveld: performs crystal structure refinement and quantitative phase analysis using powder diffraction data and the Rietveld method. Combines refinement programs and advanced modeling tools to determining the structures of both inorganic and molecular crystals.

    - C2*SDK: a software toolkit to integrate and extend applications within the Cerius2 modeling and simulation environment, eliminating the need for writing graphics, windowing, or systems-level code. Extensive library of computational and visualization subroutines.

    - C2*Sorption: predicts the adsorption properties of molecules in microporous solids, such as zeolites, to predict adsorption isotherms, binding sites, adhesion energies, diffusion paths, and molecular selectivity.

    - C2*Surface Builder: builds 2D periodic models to investigate surface chemistry, structure, and interactions.

    - C2*Visualizer: provides a comprehensive modeling environment for building, editing and visualizing models of molecular structure as well as the core requirements for running Cerius2 applications.

    - C2*X-GEN: processes X-ray diffraction data for macromolecular X-ray crystallography. Index and clean up the data from multiple detectors - making it suitable for input to refinement packages such as X-PLOR.

  • CHAIN is a computer graphics program designed to fit atomic coordinates to electron density maps. Features include ability to use multiple coordinate files, regulation of coordinates, a selection of display modes, plotting capabilities and a scripting language. -- Andrew Shraff, Baylor College of Medicine

  • CHARMm (Chemistry at HARvard, Macromolecular mechanics): is a molecular dynamics program which provides molecular mechanics, solvation, electrostatics, crystal packing, vibrational analysis, free energy perturbation, combined quantum mechanics/molecular mechanics, stochastic dynamics, etc. Academic program (CHARMM) -- Martin Karplus, Harvard University; Commercial program (CHARMm) -- BIOSYM/MSI
    Basis: 18 parameter force field
    Pros: biopolymers
    QM-MD
    GAMESS or AMPAC QM
    CHARMm: H
    C - O
    Na - S
    K - Fe
    Rb
    Eu
    Acc'y: [Delta]Hr+/-0.9
  • Chem3D Pro (4, useful but limited) - Molecular

    modeling program gives chemists instant access to the 3rd Dimension. Gain insight into molecular behavior by rotating and visualizing 5000+ atom models in color. Performs real-time animation, energy minimization and molecular dynamic calculations. Build your own models in Chem3D or convert a 2D structure to 3D just copy in a structure from ChemDraw. -- CambridgeSoft

    DLS
    MD
    Geometry Minimization
    Undo
    File Formats:
    MDL .mol
    Tripos .mol
    MSI .mol
    Brookhaven .pdb
    CCSDB
    Alchemy
    Macromodel
    Mopac Input
    Dimensions:
    700+ atoms
    1 search variable
    Parameters:
    MM2 (w/o F, S, Cl, Sr, Te, I):
    MM2+
    Basis: includes [pi] calculation
    multicoordinate centers
    Atoms: H
    Li - F
    Na - Cl
    K - Br
    Rb - I
    Cs - La, Hf - At
    Properties:
    Heat of Formation
    Partial Charges
    Bond Lengths/Distances
    Bond Angles
    Torsional Angles
    Steric Energy
    Gradient Norm
  • chemDIAGRAM is a Windows based program for creating diagrams, graphic illustrations, formulae, equations and professional page layouts. -- Molecular Arts Corporation

  • ChemDraw Pro/Std - The chemistry drawing program which provides specialized tools for drawing structures and reactions. ChemDraw is designed for chemists, so difficult to draw chemical notations are created automatically. -- CambridgeSoft

  • chemEXHIBIT is a Windows based software for creating publication quality illustrations. Includes a complete 2-D diagram drawing tool kit, 3-D structure rendering tools, graphic drawing tools, text editor and more. -- Molecular Arts Corporation

  • ChemFinder Pro - Chemical searching and information integration. The first organizational software for today's chemist. Create electronic lab notebooks, find structure-activity correlations, calculate MW and much more. This chemistry-savvy organizer greatly increases both your productivity and creativity. CS ChemFinder Pro acts as a gateway to chemical information sources and client-server with Beilstein, Oracle, Sybase and Rdb. -- CambridgeSoft

  • ChemIntosh and ChemWindow, chemical structure drawing applications for the Macintosh and Windows platform. Several other application programs are also available including: Entropy, ChemIntosh Lite, C-13 NMR Module, Spell Checker Module, Structure Library, Chemical Engineering Symbols, Laboratory Glassware Collection, Icons of Science, MS Calculator, MS Palette Tool, RxnDriller, GraphPad Prism and SciWords -- SoftShell
    Properties:
    gNMR - spectral simulation
    SymApps - symmetry point groups, character tables
    logP - octanol/water partition
    logH - air/water partition
    MR - molar refractivity
  • ChemModII - molecular mechanics -- Fraser Williams Scientific Systems, Ltd.
    Dimensions: <=2000 atoms
  • ChemOffice Pro - Includes: CS ChemDraw Pro, CS Chem3D Pro and CS ChemFinder Pro. Chemical structure drawing, molecular modeling and information integration. CS has combined its products into one powerful and seamlessly integrated desktop solution for chemists' daily software needs. Convert 2D structures into 3D models; organize and annotate your 2D structures and 3D models. Search and sort compounds by substructure, name, ID, and annotation. Create electronic notebooks and reaction cards that include 3D models and automatically perform chemistry calculations. FREE Net version available from CambridgeSoft's Web site! -- CambridgeSoft

  • Chemistry 4-D Draw is a chemical drawing program which "understands" IUPAC nomenclature.

  • ChemProtect is a new software program designed to help chemists in the selection of protective groups in synthesis.

  • ChemWeb is a free chemistry drawing software for creation and transfer of two-dimensional chemical structures over the World-Wide Web. ChemWeb can be used to output GIF89a formatted files for use in WWW-based documents. -- http://www.softshell.com

  • Chem-X (1, still eccentric) is a full suite of molecular modeling programs for Macintosh, PC (Windows, Windows/95) and UNIX computer systems. Components address systems including small molecular drawing and modeling, biopolymer building and manipulation, polymers, materials, QSAR and chemical database systems. -- Chemical Design, Ltd.
    Undo
    File Formats:
    MDL .mol
    Brookhaven .pdb
    Tribble
    CSSR (CCSDB)
    Smiles
    Gaussian
    GAMESS
    Dimensions:
    8000+ atoms
    150 search variables
    Parameters:
    ChemX FF
    Basis: organics
    inorganics
    peptides
    Acc'y: [Delta]Hr+/-1, [Delta]HÝ+/-2
    AMPAC, Mopac (60x60)
    EHT
    CNDO
  • Chiron is an interactive program for the analysis and perception of stereochemical features in molecules and for the selection of chiral precursors in organic synthesis.

  • COBRA is a "smart" conformational analysis program which utilizes heuristic techniques to automate conformational analysis and 3D structure generation. -- Oxford Molecular
    2D to 3D conversion
    strain relief
    constrained searching
  • COLUMBUS is a modular package of ab initio molecular structure programs including SCF, MCSCF, multi-reference configuration interaction and other correlation methods. Post-SCF procedures based on the graphical unitary group approach (GUGA). Programs run on Cray, IBM mainframes, RS/6000, VAX, Fujitsu VP2000, Alliant, Convex, Stardent, FPS, SGI, SUN and others. -- Isaiah Shavitt, The Ohio State University

  • Composer is a set of routines which assists in the construction of three dimensional homology models for proteins. -- Tripos, Inc.

  • Concord is used to quickly generate 3D structures from 2D or 2.5D connection tables. -- Tripos, Inc.

  • Constrictor is a suite of distance geometry programs for the generation of 3-D structures of small molecules and proteins from distance information. -- Oxford Molecular

  • CORINA is a 2D-to-3D conversion program.

  • CREATOR is an integrated molecular modeling package for nucleic acids, protein engineering and drug design. The system couples molecular modeling, sequence analysis and structural analysis. The knowledge based query and modeling system is used to identify comparative structure-activity relationships for pharmacophore design. -- Thomas Kieber-Emmons, Wistar Institute

  • Crossfire - Computer Assisted Synthesis -- Bielstein Information Systems

  • CSEARCH automates routine interpretation of 13C NMR spectroscopic data and provides spectroscopic data management for archival and retrieval of spectra. Developed by Wolfgang Robien at The University of Vienna. The system comes with a 53,000 assigned spectral database. CSEARCH runs on Sun, SPARC, SGI and Digital VAX computers. -- Joan Kuzmack, Bio-Rad Sadtler Division

  • DARC (Description, Acquisition, Retrieval and Correlation) is a chemical database system for storage, query and reporting on 2-D representations of chemical structures. -- Questel

  • DayMenus is a menu driven program which integrates a large number of chemical information functions including structure specification, display, lookup, crossreferencing, searching, property prediction and data analysis. -- Daylight Chemical Information Systems

  • deMon (DEnsity functional, MONtreal): Density Functional code from Dennis Salahub's group.VWN, BP, PP

  • Desktop Molecular Modeller -- Oxford University Press.

  • DGEOM is a distance geometry program developed by Blaney, Crippen, Dearing and Dixon for building molecular models and receptor models. Utilizes the algorithms developed by Kuntz, Havel and Crippen. DGEOM runs on a wide variety of computer systems. -- QCPE 590

  • Discover is a molecular mechanics and dynamics program for simulation of a variety of organic, biopolymer, polymer and material molecular assemblies. -- BIOSYM/MSI
    periodic
    - NVE
    - NVT
    - NPT
    - NST
    conformational analysis
    Ewald sum w/ surface correction
    Parameters:
    CFF91/93 (Consistent Force Field)
    CVFF (Consistent Valence ForceField)
    - general purpose
    Basis:
    Morse function stretch term
    nondiagonal force field
    crossterms
    empirical parameterization
    GENFF (generalized CVFF)
    ESFF (Extensible & Systematic Force Field)
    Basis:
    diagonal valence
    rule based:
    - electronegativity
    - atomic radii
    - hardness
    - scaling
    - d-p [pi] bonding
    - organics, inorganic, organometallic & biomolecules
    Atoms:
    H - Rn
    Pros: any element
    organometallic complexes
    Cons: accuracy
    Amber
    Properties:
    radial distribution function
    self-diffusion coefficient
    H-bonds
    Energies
    - interaction
    - strain
    - entropy
    - enthalpy
    IR
    - modes
    - intensity
  • DMol is a density functional theory (DFT) based program for quantum mechanical calculations. -- BIOSYM/MSI
    Dimensions:
    <=~100 atoms
    Parameters:
    DNP (~6-31G**):
    numeric basis set
    - Atoms: H, He
    Li - Ne
    Na - Ar
    K - Kr
    Rb - Xe?
    - Acc'y: l+/-3%
    gradient corrections
    VWN
    BVWN
    BP
    BLYP
    Properties:
    IR frequencies
    Dipole moments
    optical polarizability
    EA
    IP
    Mulliken & Hirshfeld Populations
    charge density
    spin density
    electrostatic potential
    equilibrium geometry
  • DOCK is a suite of programs used to produce a negative image of a biomacromolecular surface. This image is matched to positive images of putative ligands of known 3-D structure. Molecules which fit the receptor are scored and saved in PDB format. The program has been used to propose novel compounds of pharmaceutical interest. Graphical user interface must be supplied from external programs. -- I.D. Kuntz, University of California San Francisco

  • ECEPP (Empirical Conformational Energy Program for Peptides) is a molecular mechanics based conformational searching program for proteins and peptides. -- Harold Scheraga, Cornell University,

  • EROS (Elaboration of Reactions for Organic Synthesis) is a computer assisted synthesis program developed by Gasteiger et.al. which uses a set of rules to propose synthetic routes. -- Dr. Johann Gasteiger, Erlangen University

  • EuGene and SAm is a menus based DNA and protein sequence analysis package. The program efficiently manages data during DNA sequencing projects. The system can simulate genetic engineering experiments, search databases of DNA and protein sequences, compare multiple sequences for similarities and provide detailed structural information of sequences. Runs on Sun workstations. -- Christine B. Powaser, Lark Sequencing Technologies

  • Explorer EyeChem

  • FLIMSY is a molecular graphics and analysis program. -- Nigel Richards, University of Florida

  • FRODO is a molecular graphics program for crystallography applications. -- Florante Quiocho, Baylor College of Medicine

  • FUNGUS Born model molecular dynamics with periodic boundary conditions for large complex, heterogeneous/amorphous systems. NVE ensemble, minimum image convention, empirical potentials for short range, Ewald summation for coulombic. -- J. R. Walker, G. Mills
    Parameters:
    Born Model
  • Galaxy is a combination macromolecular modeling and drug design program for SGI and IBM RS/6000 computer systems.

  • GAMESS (General Atomic and Molecular Electronic Structure System) ab initio package. Assembled from HONDO and others. -- Mike Schmidt, Iowa State University
    RHF, UHF, ROHF, GVB
    MCSCF, CI, MP2
    Analytical Gradients
    Saddle
    Parameters:
    MNDO, AM1, PM3
    ECPs -
    - SBK, -31G splits:
    Li - Ne
    Na - Ar
    K - Kr
    Rb - Xe
    Cs - Ba, Hf - Rn
    La, Ce
    - HW, -21 splits:
    H, He
    Li - Ne
    Na - Ar
    K - Kr
    Rb - Ag
    Cs - Ba, Hf - Au
    STO-nG(*), n-21G(*,+):
    MINI/MIDI:
    H, He
    Li - Ne
    Na - Ar
    K - Kr
    Rb - Xe
    n-31G(*,**,+,++)
    DZV -
    - DH:
    H
    Li - Ne
    Al - Ar
    BC:
    Ga - Kr
    TZV -
    Li - Ne
    Na - Ar
    K - Zn
    Properties:
    Energy Hessian
    Normal Modes
    Vibrational Frequencies
    IR Intensities
    Intrinsic Reaction Path
    Dynamic Reaction Coordinate
    Radiative Transition Probabilities
    Spin Orbit Coupling
    Linear Polarizability
    First & Second Order Polarizability
    NLO Polarizability
    Localized Orbitals
    Self Consistent Reaction Field
    Dipole, quadrupole, & octupole moments
    Electrostatic Potential
    Electric Field
    Electric Field Gradients
    Electron Density
    Spin Density
    Distributed Multipole Analysis
    Output Sections:
    MOMENTS OF INERTIA
    INTERNUCLEAR DISTANCES
    NUCLEAR REPULSION ENERGY
    FINAL ENERGY
    E CHANGE
    DENSITY CHANGE
    SPIN SZ
    S-SQUARED
    EIGENVECTORS
    TOTAL ENERGY
    ENERGY COMPONENTS
    ONE ELECTRON ENERGY
    TWO ELECTRON ENERGY
    POTENTIAL ENERGY
    KINETIC ENERGY
    VIRIAL RATIO
    PI ENERGY ANALYSIS
    FOCK ENERGY
    BARE H ENERGY
    ELECTRONIC ENERGY
    SIGMA PART
    PI PART
    MULLIKEN ATOMIC POPULATION
    (MULLIKEN) ATOMIC SPIN POPULATION
    (LOWDIN) ATOMIC SPIN POPULATION
    MULLIKEN ATOMIC OVERLAP POPULATIONS
    MULL.POP. CHARGE
    LOW.POP. CHARGE
    BOND ORDER AND VALENCE
    ATOMIC SPIN DENSITY AT THE NUCLEUS
    ELECTROSTATIC MOMENTS
  • Gaussian One of the most popular ab initio programs. The program originated in the research group of Pople at Carnegie-Melon. The program is now developed and supported by GAUSSIAN, Inc. The name is usually seen followed by a double digit number indicating the year the version was released. The most recent version is GAUSSIAN-92, sometimes abbreviated as G92. An ab initio electronic structure program used to calculate structures, reaction transition states and a wide range of molecular properties. The package contains programs for the calculation of 1- and 2-electron integrals over s,p,d,f contracted GAUSSIAN functions, self-consistent field for restricted or unrestricted Hartree-Fock wave functions, correlation energy using Moller-Plesset perturbation theory, configuration interaction method and coupled-cluster theory. The program runs on Cray, DEC-RISC, Fujitsu, Kubota, IBM RS/6000, Multiflow, Silicon Graphics, Sun and VAX/VMS computer systems. -- Gaussian, Inc. e-mail at info@gaussian.com.
    BLYP
    SCRF
    GIAO
    Output Sections:
    Symbolic Z-matrix:
    SCF DONE:
    MOLECULAR ORBITAL COEFFICIENTS
    DENSITY MATRIX.
    Mulliken population analysis:
    Total atomic charges:
    Dipole moment
    Quadrupole moment
    Octapole moment
    Hexadecapole moment
  • GEMM (Generate, Edit and Manipulate Molecules) is an interactive molecular graphics program used at NIH. It can be used to construct, view, modify and manipulate 3-D molecular structures. GEMM runs on SGI and supports the GL library. -- Dr. B. K. Lee, NIH

  • GENESEQ - a database of protein and nucleic acid sequences extracted from world-wide patent documents. -- Oxford Molecular Group

  • GeneWorks - an integrated sequence analysis and database searching on the Macintosh. -- Oxford Molecular Group

  • GERM (Genetically Evolved Receptor Models) is used to develop three-dimensional atom-based models of previously uncharacterized receptor sites starting from a small structure-activity model of active and inactive compounds.

  • getpdb a ksh script which automates incremental mirroring of the Protein Data Bank.

  • GIAO (Gauge Invariant Atomic Orbitals -> Gauge Including AOs) usual AO's are multiplied by a "gauge vector" to provide "gauge-invariant" magnetic properties.
    Acc'y: ([sigma] in PPM w 6-311G** perturbed HF)
    P+/-32
    C+6
    H+6.1%
  • GMMX is available as part of PCModel, a structure building, manipulation and minimization program. -- Serena Software

  • GRADSCF is an ab initio quantum chemistry program which has been designed for the Cray environment. Its major function is to provide energies and properties for a variety of molecules of chemical interest. Gradscf runs under the Unicos operating system. -- Dr. Andrew Komornicki, Polyatomics Research Institute

  • GRID is a computational procedure for detecting energetically favorable binding sites on molecules of known structure. It may be used to study arrays of molecules in membranes and crystals or macromolecules such as proteins. The energies are calculated as the electrostatic, hydrogen-bond and Lennard Jones interactions of a specific probe group with the target structure. GRID can distinguish between selective binding sites for different probes. Input for GRIN is prepared and checked by GRID. Display of results is through output files produced by GRID. The programs are written in Fortran 77 and run on all computer systems. -- Peter Goodford, Molecular Discovery Ltd.

  • GROMOS (GROningen MOlecular Simulation package) is a molecular mechanics and dynamics program developed by W. F. van Gunsteren and co-workers at The University of Groningen. -- Biomos B. V., University of Groningen
    Molecular & Stochastic Dynamics
    Perturbation Thermodynamics
    GROMOS FF Basis:
    proteins
    nucleotides
    sugars
  • GroupServer - a suite of computational tools for molecular modeling, networked to the CAChe WorkSystem. -- Oxford Molecular Group

  • GULP (General Utility Lattice Program) general lattice simulation with periodic boundary conditions and Ewald sums for electrostatics. Calculates properties, or inverse operation to fit potentials to structure, properties, QM potential surfaces. Minimize energy with P, V and optical constraints. Locate phase transition states. (Phase diagrams, charge defect correction.) -- Julian Gale, Imperial College
    Properties:
    Crystal lattice energy
    Entropy
    Free Energy
    Heat capacity
    Elastic constants
    Dielectric constants
    Phonon frequencies
    IR activities
    Electric field gradients
  • GVB (Generalized Valence Bond) - Bill Goddards "laid back southern California wavefunctions." Equivalent to MCSCF correlation treatment: 2 configurations used to represent each e- pair and solved for 2 associated orthogonal functions.

  • Hingefind is a new algorithm to determine and visualize protein domain movements by comparing two structures.

  • HINT (Hydrophobic INTeractions) a program for calculating and visualizing hydrophobic and hydrophobic interactions of biomolecular specie. -- eduSoft.

  • HMO-Plus1.5
    Atoms:
    B - F
    Si - Cl
    Properties:
    Secular Determinant
    Eigenvalues
    Total energy
    delocalization energy
    Polarographic half-wave reduction potential
    Eigenvectors
    Charge densities
    [pi]-dipole moment
    Bond lengths
    Electron density - bond order matrix
    Atom-atom polarizabilities
    Superdelocalizabilities
    - Electrophilic
    - Radical
    - Nucleophilic
    Free valences
  • HONDO7 is a semiempirical molecular orbital program with single configuration SCF (closed shell RHF, spin restricted UHF, restricted open shell ROHF), generalized valance bond (GVB) and general multiconfiguration SCF MCSCF wavefunctions as well as configuration interaction (CI) wavefunctions. Written by Dupuis, Watts, Villar and Hurst. -- QCPE 544

  • HyperChem 4.5 (3, general modeling system with potential) is a building, optimization, manipulation and display program for PC and SGI. -- HyperCube Inc. Originally code for parallel computing serialized to PC product.
    solvent box
    MD
    ab initio SCF
    MP2
    File Formats:
    MDL .mol
    Tripos .mol
    Brookhaven .pdb
    Mopac Input
    CCSDB
    Dimensions:
    20,000+ atoms
    Parameters:
    MM2
    Amber
    BIO+
    OPPLS
    Basis: liquids
    solutions
    ab initio calc'ns on 100 organics
    EHT
    MNDO (w/o Cr, Zn, Br, Sn, Hg, Pb?)
    MINDO/3
    AM1 (w/o Hg?)
    PM3 (w/o Hg, Tl, Pb, Bi?)
    CNDO
    INDO/1 (w/o As, Br, I?)
    INDO/S
    Properties: Dipole moment
    IP
    IR (Force)
    UV (CI)
    - Chem Plus
    Crystal builder
    renderings
    MC search
    biomolecules
    logP
    scripts
    - HyperChem Lite - HyperNMR
    SCF-MO
    magnetic shielding (shifts)
    nuclear coupling
  • ICON8 and FORTICON8 provide Extended Hückel calculations for molecules containing 50 (or fewer) atoms which contain S, S and P and S,P and D electrons. Written by Howell, Rossi, Wallace, Haraki and Hoffmann. -- QCPE 344

  • Iditis - This package provides instant access to protein motifs, substructures and interactions buried in the Brookhaven databank, 500 descriptors. -- Oxford Molecular Group
    corrected PDB database
    500 descriptors
  • Iditis Architect - suite of programs that lets you create protein structure data for inclusion in the Iditis database. -- Oxford Molecular Group

  • IG Suite - these tools allow you to do DNA and protein sequence analysis using Sun and VAX workstations. -- Oxford Molecular Group

  • IMSL Libraries IMSL supplies two libraries of subroutines for graphics, Mathematics and Statistics. IMSL/IDL is an array oriented interactive command language complete with graphics and a robust set of mathematical, statistical, image processing and signal processing functions which allow visual exploration of numerical data. Exponent Graphics is a library of graphical subroutines that alleviates the task of coding low-level graphics primitives. The IMSL Libraries is an extensive set of 900 Fortran subroutines for applications in general applied mathematics, special functions and for analyzing and presenting statistical data. Libraries are also available for C programming needs. All of the IMSL software runs on a wide variety of platforms. -- IMSL, Inc.

  • Insight II (6, specialized modeling on workstations) is a 3D graphical environment for the creation, modification, manipulation, display and analysis of molecular systems and related data. User interface integrates array of builder modules, development tools, force fields, simulation and visualization tools with tools specifically developed for applications in the life and materials sciences. -- BIOSYM/MSI, http://www.msi.com/
    transparency
    spreadsheet
    "Open Interface"
    - Affinity: automated docking of ligands to receptors in the structure-based drug design process. Calculations include an implicit solvation term, and the component effects of this term, and of other energetic partitions, can be viewed graphically.

    - Amorphous Cell: constructs and analyzes models of bulk amorphous systems such as polymers and glasses. Investigate properties such as cohesive energy, chain dimensions, chain packing, and local dynamical behavior.

    atomistic
    glassy or melt
    IR
    cohesive energy density
    self diffusion
    elasticity
    correlation function
    solubility parameter
    - Apex-3D: identifies pharmacophores and active conformations from a set of biologically active and inactive compounds to predict the activity of new compounds.

    - Biopolymer: constructs models of peptides, proteins, carbohydrates, and nucleic acids for visualizing complex macromolecular structures and for use in further simulation work.

    - CFF95: advanced Class II force field used to optimize DNA, RNA, carbohydrates, lipids, proteins, peptides, and small-molecule models, giving a high confidence level for calculations in drug discovery, protein design, genomic theraputics, NMR spectroscopy, and X-ray crystallography.

    - Characterize: simulates, displays, and interprets a wide variety of analytical data: HRTEM, NMR, diffraction, IR Raman, EXAFS, and Morphology data.

    XRD, ND, ED
    29Si NMR
    EXAFS
    Crystal morphology
    IR, Raman
    Pore characterization
    - Consensus: builds a 3D model of a protein from its amino acid sequence and the known structures of related proteins using distance constraints derived from the reference protein structures.

    - Converter: builds 3D models from 2D structural database output.

    - Crystal Cell: study and characterize crystal structure, stability, and mechanical properties.

    minimize packing energy w/ MM
    vibrational dispersion curve
    entropy
    heat capacity
    mechanical properties
    - DBAccess: uses a hypothesis that may include binding features, structural and property constraints, as a search query against databases containing hundreds of thousands of molecules to select molecules for trial or to the guide synthesis of new compounds. Includes the Maybridge catalog and the NCI database.

    - DeCipher: powerful and flexible program for high-level analysis of molecular structure and the results of molecular dynamics simulations.

    - DelPhi: calculates electrostatic potentials and solvation energies of both large and small molecules, including nucleic acids. Examine the effects of charge distribution, ionic strength, and dielectric constant on the electrostatic potentials of macromolecules.

    - Discover: simulation program available within Insight II. It incorporates a range of well validated forcefields for dynamics simulations, minimization, and conformational searches to predict the structure, energetics and properties of organic, inorganic, organometallic, and biological systems. Implements IPC (Inter Process Communications), which allows users to instruct Discover to turn processing control over to external programs, and retrieve the results of those external processes, incorporating them into the continuing Discover computations.

    - DMol: quantum mechanics module for fast, reliable, quantitative predictions of molecular structure, energetics and properties for ground and transition states. Employs advanced density functional theory. COSMO is a continuum dielectric solvation model implemented in DMol to accurately compute the structure and properties of molecules in a solvent environment using quantum mechanics.

    - DSolid: provides accurate simulation of molecules, molecular crystals, and surfaces. An adaptation of the DMol program to compute structural and vibrational properties as well as electron densities and molecular orbitals for periodic solids.

    - ESOCS: (Electronic Structure Of Closed-packed Solids) calculates the electronic and magnetic properties of solids, including electronic structure of defects, optical absorption and reflection spectra, and magnetic properties of materials. Applicable to metals and alloys, the pigment industry, and for optimizating and designing magnetic materials.

    all purpose
    periodic electronic structure
    - Fast Structure: determines equilibrium geometries of crystals, interfaces, surfaces and molecules using fast first-principles density functional methods in conjunction with molecular dynamics, simulated annealing and minimization techniques. Used in the electronics, chemicals, petrochemicals, and glass industries.

    - Flexiblend: estimates polymer miscibility. Approximate but fast to screen polymer blend candidates.

    miscibility w/ specific interactions
    - Homology: builds a 3D model of a protein from its amino acid sequence and the known structure of related proteins. Standard techniques of backbone building, loop modeling, structural overlay and statistical analysis of the resulting models.

    - Insight II: creates, modifies, manipulates, displays, and analyzes molecular systems and related data and provides the core requirements for all Insight II software modules.

    - Interphases: calculates the conformational properties of polymers in the vicinity of an interface.

    graph theory model
    monolayers & bilayers
    - Ludi: tool for de novo+rational drug design. Fits molecules into the active site of a receptor by identifying and matching complementary polar and hydrophobic groups.

    - Ludi/ACD: links the design tools of Ludi to MDL's Available Chemicals Directory with access to over 65,000 commercially available structures to search for drug candidates.

    - MADSYS: provides phasing of multi-wavelength anomalous dispersion (MAD) data collected at synchrotron radiation X-ray sources.

    - Miscibility: navigational aid for predicting liquid-liquid phase diagrams of polymer solutions or blends by unifying MSI*s tools for phase diagram prediction and leading through appropriate simulation strategies.

    - Modeler: automatically generates a refined homology model of a protein, given only the sequence alignment to a known 3D protein structure. Excellent structural models given as little as 30% homology to known structures.

    - Networks: simulates cross-linking or cure reactions to understand properties of gels, elastomers, adhesives, and coatings.

    statistical & kinetic models
    elasticity
    gel point
    - NMR Refine/Advanced: expands the refinement capabilities found in NMR Refine/DG-II to include simulated annealing and restrained molecular mechanics and dynamics (MD Schedule), refinement of NOE intensities using hybrid-matrix approaches (IRMA), direct refinement of NOE volumes (NOE-MD), an interface to back-calculating 2D NOESY crosspeak intensities (NOE Simulate), and a spreadsheet method of analyzing NMR-related structural and dynamical molecular parameters (Query).

    - NMR Refine/DG-II: entry-level option into NMR refinement software with capabilities for generating structures from NMR-derived distance and dihedral restraints. Restraint Analysis, NMR Database and ProStat pulldown tools for generating, analyzing and verifying high resolution structures.

    - Phase Diagram: calculates liquid-liquid phase diagrams for polymer solutions and blends, to optimize the properties of formulations.

    binary & ternary
    calculate from Chi
    fit Chi to experiment
    - Pilot: solution oriented self-help tool for Insight II. Interactive training sessions for practical modeling of solutions.

    - Plane Wave: quantum mechanics module for the materials sciences to simulate solids, interfaces, and surfaces for a wide range of materials classes including ceramics and semiconductors, determining properties such as geometric structure, energies, band-structures, and charge density.

    full periodic table
    pseudopotentials
    - Polymerizer: builds 3D models of linear and branched homopolymers and copolymers,u to visualize and simulate polymer structure and behavior.

    - PolyNMR: helps you to interpret NMR spectra for homo- and copolymers.

    C-13 from RIS w/ tables
    - PRISM: predicts polymer blend miscibility and related properties based on the chemical composition of the chains in the blend.
    omega functions
    phase equilibria
    - Profiles-3D: "environmental classification" of protein residues to

    assess whether a primary sequence is compatible with the current 3D structural model. Searches a structural-motif database with a new sequence, looking for compatibility; a sequence database with an example stucture, seeking similarity; or verifies the agreement between the sequence and current model of a protein sequence/structure under study.

    - QSPR: estimates the properties of a wide range of thermoplastic materials using group additivity methods.

    Synthia
    Van Krevelan
    - QuanteMM: combines quantum mechanical and force field methods, to use accurate first-principles methods to study cluster models while taking the surrounding environment fully into account to study large and complex systems.

    QM embedded in MM

    - Reaction Patterns: visualizes, interprets and analyzes chemical reactivity and reactions. It combines kinetic models and the analysis of quantum mechanical energy surfaces to give insight into fundamental chemical processes.

    chemical kinetics
    vibrations
    - RIS: (Rotational Isomeric States) calculates the conformational properties of polymer chains, which to relate these to their chemical structure.
    statistical properties of single chain
    - Search/Compare: generates and compares the conformers of different molecules.

    - Sketcher: draws molecules in 2D and automatically convert them to 3D models.

    - Solids Adjustment: edits crystal or cluster structures, to explore new or derivative materials.

    symmetry display & modifications
    find cell
    - Solids Builder: constructs models of inorganic and organic crystals, metals, layers, and interfaces, to develop and validate models of solids and surfaces.
    crystal, metal, glass
    solid, surface, sheet
    modify space group
    - Solids Docking and Sorption: probes the interactions of single molecules or groups of molecules with a host matrix, to model adsorption mechanisms and predict key thermodynamic data for gas adsorption in zeolites or polymer membranes.
    Monte Carlo docking
    heat of sorption
    preferred binding
    diffusion strategy
    - Solids Simulation: performs optimizations of bulk and surface structures and crystal dynamics, to investigate the structure and behavior of ionic solids.
    METAPOCS
    FUNGUS
    minimization w/ symmetry
    dynamics w/ symmetry
    - Structure Image: simulates electron diffraction patterns for interpreting EM data from crystals, interfaces, and defect structures.
    lattice images
    HRTEM
    - Structure Refine: uses powder or single crystal diffraction data and the Rietveld method to determine and refine crystal structures.
    Visual interface to GSAS
    - Structure Solve: provides a range of novel computational techniques for predicting the crystal structures of molecular crystals, zeolites, and metal oxides.
    generic ionic models
    fit xtal structures to experiment
    - Synthia: estimates polymer properties using statistically-derived correlations to predict properties quickly from existing data for a broader range of polymers than a strictly interpolative QSPR.

    - Turbomole: calculates molecular structure, energetics, and transition states. It predicts properties including electrostatic potentials, ESP charges, molecular moments, polarizabilities, IR spectra, and NMR chemical shifts. Computations use traditional Hartree-Fock and MP2 quantum mechanics methods as well as density functional theory. TurboNMR is a component of Turbomole which uses ab initio quantum mechanical methods to predict NMR chemical shifts, to interpret solid-state NMR and magnetic relaxation experiments.

    - Viscoelasticity: estimates the dynamic mechanical response of dilute polymer solutions, to relate these to polymer structure and chemistry.

    dilute solutions
    - X-PLOR/Refine: an X-ray structure determination program that integrates crystallographic diffraction data with molecular mechanics, dynamics and energy minimization for the solution of three-dimensional structures.

    - Xsight: integrates all of the major computational techniques for macromolecular crystallography: analyze and interpret X-ray data, build models of protein structures and relate them to electron density, refine structure against X-ray data, analyze structures for symmetry, and visualize and validate structure.

    - ZINDO: semi-empirical molecular-orbital program for studying the spectroscopic properties of molecules and complexes. Applicable to a wide range of compounds, including organic and inorganic molecules, polymers, and organometallic complexes.

  • INTERCHEM is a molecular modeling system designed for use on Silicon Graphics workstations. It includes facilities for handling and display of small molecules and large biomolecules. Building new structures is made easy by a library of 380 pre-optimized (MOPAC) fragments. It incorporates a molecular mechanics program PIFF (written by Armin Widmer, Sandoz A.G.), which provides rapid optimization of structures. Structure files may be read into the program in SYBYL, BIOSYM, Cambridge Crystallographic Database XR and native INTERCHEM formats. The Proteins Package provides selective editing, display and highlighting of special features, investigation of homology, prediction of protein secondary structure, prediction of important sites, etc. The Crystal Structure package allows reading of files in Cambridge XR format, display of unit cells, the replication of the asymmetric unit necessary to fill a 3X3X3 nest of unit cells. -- Peter Bladon, The University of Strathclyde

  • ISIS Draw is available for downloading to your Mac or PC.

  • KGNMOL provides ab initio electronic structure calculations for large molecules. Single configuration SCF (RHF and ROHF). Second order Moeller-Plesset correction. Density functional and sum of pair correlation methods for correlation energy estimation. Program runs on IBM 3090 computer systems. Distributed as a part of MOTECC. -- Michael Dupuis, IBM Corporation

  • Latticepatch is an interactive graphics program used by crystallographers to evaluate data collection strategies for area detector X-ray diffraction studies. Using Latticepatch, a crystallographer can visualize how rotation of the crystal will spread reflected X-radiation across the surface of an area detector. Using the crystal's symmetry characteristics, its orientation in the lab frame and the crystal-to- detector distance, Latticepatch helps the crystallographer to collect the unique data most efficiently. The program runs on Silicon Graphics 4D series workstations. -- Alexandra Klinger, Health Sciences Center, Charlottesville

  • LHASA (Logic and Heuristics Applied to Synthetic Analysis) is a backward chaining synthesis planning program which uses a database of specially coded chemical reactions and definitions for strategic bonds to analyze potential synthetic pathways for a molecule. The target molecule is analyzed according to the number of rules and likely synthetic pathways are produced for examination. -- Alan Long, Harvard University

  • LiqCryst a database of Liquid Crystalline

    Compounds for Personal Computers

  • Ludi provides a tool which can quickly generate a series of potential binding compounds for a given ligand binding site on a protein. The knowledge-based system chooses fragments from a library based on their ability to bind to portions of the binding site through hydrogen bonding and lipophilic interactions. -- BIOSYM/MSI

  • MACCS (Molecular ACCess System)is a chemical information management system which runs on a variety of computers. -- MDL Information Systems

  • MACCS-3D a 3D searching system for structures stored in a fixed conformation. -- MDL Information Systems

  • MacMimic -- InStar Software AB
    <=32,000 atoms
    MM2
  • MacroModel is a molecular mechanics/dynamics program for calculating energies, conformational properties for organic molecules, biopolymers using force fields modeled after AMBER, MM2, MM3 and OPLS. -- W. Clark Still, Columbia University
    Monte Carlo
    Molecular Dynamics
    Grid search
    Saddle point
    Transition states
    Normal mode
    SHAKE annealing
    Free Energy Perturbation
    Continuum solvent
    Basis:
    generalized force field shell
    point charges instead of dipoles
    no [pi] calculations
    Parameters:
    AMBER*
    - Acc'y: [Delta]HÝ+/-1, [Delta]Hr+/-0.9
    MM2*
    - Acc'y: [Delta]HÝ+/-0.4, [Delta]Hr+/-0.5
    MM3*
    - Acc'y: [Delta]HÝ+/-1, [Delta]Hr+/-0.5
    OPLS
    - protein/DNA
  • MD-Display is designed to allow creation of colored, animated displays of the data produced by a molecular dynamics program. Rotation, clipping, translation, coloring and scaling are controlled through the mouse and keyboard. Additional display features include stereo, half-bond coloring, control of animation speed and direction. Allows user to monitor distances, bond angles, dihedrals and hydrogen bonds during animation. Other display options include solvent accessible surfaces (static), Ramachandran plots, frequency filtering of trajectories in real time, generation of PostScript files. NM Display is available for visualization of normal mode displacements. The programs were developed by T. Callahan, E. Swanson and T.P. Lybrand. -- QCPE 623

  • MARVIN (Minimisation And Relaxation of Vacancies and Interstitial Near Surfaces Program) simulates surfaces with 2-D periodicity: one region is surface, other region retains bulk solid geometry. Docking w/ Buckingham, Lennard-Jones, Morse, Coulomb subtraction, and Harmonic potentials; BFGS/Newton optimizers.
    Properties:
    Docking
    Surface Energy/Morphology
  • Merlin provides the ability to perform extremely fast searches on selected data in Thor chemical information databases. Merlin operates on sets of structures and is ideal for exploratory data analysis. -- Daylight Chemical Information Systems

  • METAPOCS energy minimization for solids.
    Parameters:
    Born Model
  • MicroChem -- ChemLab, Inc. (no longer available)
    organic
    inorganic
    polymer
    Craig Plots
  • MidasPlus is a molecular modeling and drug design support system developed by the Computer Graphics Laboratory at UCSF. The program allows real-time display of color, line and surface displays of several interacting molecules, while qualitatively monitoring the stereo chemistry. The complete model of the molecules is generated, however it is possible to view any sub-segment in isolation for clarification. Various display options are available. MidasPlus runs on SGI, DECstation 5000 (with PXG 3D graphics option) and NeXT workstations. -- Norma Belfer, UCSF

  • MM2, MM3 are molecular mechanics programs used to optimize geometry, determine thermodynamic values and IR spectral data. -- Tripos, Inc.

  • MM3(92) Macintosh implementation of MM3.
    - BDNR minimizer
    - transition state optimization
    - entropy by vibrational analysis
    - [pi] calculation
  • MOBY -- Springer-Verlag Inc., New York
    Geometries
    Dynamics
    AMBER
    MNDO
    AM1
    <=150 atoms
    - ARGOS
    connection -> 2D
    - Autonom
    nomenclature
    - MOLKIK
    DB queries
  • MOIL-View is a program for SGI and IBM RS/6000 workstations designed to allow the user to view and analyze molecular structures and dynamics.

  • Mol2Mol is a file conversion program for many of the widely used molecular data formats used in chemistry.

  • MolDraw

  • MOLDY is a molecular dynamics simulation program for solids and liquids. It will handle atoms, ions and rigid molecules, but is currently limited to pairwise central forces. The program can be obtained from the Web server.

  • MOLDYN is an interactive general-purpose program for calculation and evaluation of data from molecular dynamics. Written by Kumar, Craik and Levy. -- QCPE 489

  • Molecular Presentation Graphics is a Windows based chemical structure drawing program. It includes automatic bond propagation, chain drawing, ring attachment, etc. -- ACS Software

  • MOLGEN is used to construct all isomers corresponding to a given brutto formula and further side conditions. -- J. Eric Slone Consulting Services
    MM
    2D -> 3D
    logP database
  • MOMEC a new program for modeling transition metal complexes. MOMEC was developed by Drs. Peter Comba and Trevor Hamley. -- Heinz Hofmann

  • MOPAC (Molecular Orbital PACkage) is a general purpose semiempirical molecular orbital package developed by J.J.P. Stewart and co-workers. The computer code that first presented the MNDO method to the world. The program contains the MNDO, MINDO/3, AM1 and PM3 Hamiltonians. It is used to calculate molecular geometries and electronic properties. The program runs on a wide variety of platforms. -- QCPE
    OVGF

    Output Sections:
    FINAL HEAT OF FORMATION
    TOTAL ENERGY
    ELECTRONIC ENERGY
    CORE-CORE REPULSION
    DIELECTRIC ENERGY
    VAN DER WAALS AREA
    GRADIENT NORM
    IONIZATION POTENTIAL
    DERIVATIVES
    INTERNAL COORDINATE DERIVATIVES
    FORCE MATRIX
    ZERO POINT ENERGY
    NORMAL COORDINATE ANALYSIS
    MASS-WEIGHTED COORDINATE ANALYSIS
    DESCRIPTION OF VIBRATIONS
    FREQ.
    T-DIPOLE
    ENERGY CONTRIBUTION
    PARTITION FUNCTION
    H.O.F.
    ENTHALPY
    HEAT CAPACITY
    ENTROPY
    BOND LENGTH, BOND ANGLE, TWIST ANGLE
    INTERATOMIC DISTANCES
    EIGENVECTORS
    ATOMIC CHARGES
    DIPOLE
    CARTESIAN COORDINATES
    FOCK MATRIX
    DENSITY MATRIX
    SIGMA-PI BOND-ORDER MATRIX
    BONDING CONTRIBUTION
    BOND ORDERS
    VALENCIES
    COMPOSITION OF ORBITALS
    LOCALIZED ORBITALS
    ENERGY PARTITIONING
    RESONANCE ENERGY
    EXCHANGE ENERGY
    COULOMBIC INTERACTION
    SPIN DENSITIES
    MULLIKEN POPULATION ANALYSIS
    FINITE-FIELD POLARIZABILITIES
    MOMENTS OF INERTIA
    DIPOLE
    POLARIZABILITY (ALPHA)
    SECOND-ORDER (BETA)
    THIRD-ORDER (GAMMA)
  • MOZYME -- James J. P. Stewart
    Basis:
    Lewis bond input
    hybrid coordinates
    Pros:
    avoids diagonalization
    Parameters:
    same as MOPAC
    Dimensions:
    4000 atoms
  • MOTECC (MOdern TEchniques in Computational Chemistry) contains a broad range of programs that span atomic calculations, molecular structure determination, molecular simulations, dynamics of fluid flows, molecular graphics, etc. The suite of programs is available for IBM (VM, CMS and AIX operating systems). -- Omar G. Stradella, Sviluppo e Studi Superiori in Sardegna

  • MPA/MPG (Molecular Packing Analysis/Molecular Packing Graphics) This software package finds intermolecular energy minima of molecular clusters (including molecular docking) or molecular crystals (including polymorph and space group prediction). The program contains a library of intermolecular

    force fields (e.g., WH86, MM85, Biosym, Charmm, etc.), or the user can supply the force field. The program selects energy minimization by OREM (off-ridge eigenvector minimization), SD (steepest descents), or the NR (Newton-Raphson) method. Simulated annealing is included to aid in locating global, rather than subsidiary, energy minima. The mpg module provides fast and convenient graphical visualization of the results. -- Donald E. Williams.

  • MPSRCH - this program permits rapid searches of DNA and protein sequence data banks using the full Smith-Waterman algorithm for the most rigorous searching available. -- Oxford Molecular Group

  • MS calculates coordinates of points on the solvent-accessible surface of a molecule. These points can be used to display a variety of properties. Written by Michael Connolly. -- QCPE

  • MSEQ is a user-friendly program which combines novel graphics and integration of predictive parameters from several sources for the prediction and display of protein secondary structures. A full description of the software can be found in Analytical Biochemistry, 193, 72-82, 1991. The software runs under DOS on IBM and compatibles. -- Colleen Healy, University of Michigan Software

  • MSP (Molecular Surface Package) computes molecular surfaces, areas and volumes. Five programs provide robust, highly accurate areas and volumes and identify internal cavities. The programs are written in machine independent C. Source code is included with the license.

  • NAB was designed to construct models of helical and non-helical nucleic acids from a few dozen to a few hundred nucleotides in size. The program uses a combination of rigid body transformations and distance geometry to create candidate structures that match input criteria.

  • namd is a new package for high performance parallel molecular dynamics simulations.

  • NAOMI is a program system for studying proteins at the atomic level including automatic structure analysis and manipulation, and interfaces to graphics programs. -- http://www.ocms.ox.ac.uk/~smb/Software/N_details/naomi.html

  • NBO (Natural Bond Orbitals) the 1- and 2-center set of orthogonal orbitals which takes account of the greatest amount of the electron density in a maximum occupancy set.

  • Nemesis (6, inexpensive but limited) - an interactive molecular modeling for IBM PCs, PS/2s, and compatibles running Windows 3.1, and Apple Macintosh II. -- Oxford Molecular Group
    building
    VDW minimization
    MM optimization
    conformational analysis
    MOPAC Interface
    File Formats:
    MDL .mol
    Brookhaven .pdb
    CCSDB
    ChemDraw
    Mopac Input, Archive
    Dimensions:
    <=125 atoms
    5 search variables
    Parameters:
    COSMIC:
    H
    C - F
    P - Cl
    Br
    I
    Properties:
    partial charge
    Dipole moment
    distance
    angle
  • O is a molecular graphics program for protein crystallographers. -- T. Alwyn Jones, Dalby

  • Open Molecule is a Sun SPARCstation based graphics server for molecular modeling. The program is a menu based front end for computational chemistry codes which do not have graphics capabilities, a distributed 3-D graphics system used to visualize the results of complex computations generated on a supercomputer or other high-end system and a supplemental graphics facility for commercial programs. OpenMolecule can display up to nine molecules (up to 10,000 atoms each), each with their own local graphics transformation. The program runs on OpenWindows and utilizes the XGL graphics library. -- Andataco, UCSD

  • ORAC - (Organic Reaction Accessed by Computer) Computer Assisted Synthesis -- Pergamon

  • PAP is a suite of programs to analyze protein structures. Modules are available to compute and display as a function of sequence Ramachandran and linear phi-psi plots, distance diagonal plots and temperature factors. Modules are also available to compute and plot RMS structure differences for two proteins. Proteins with sequence insertions or deletions can be handled. Priestle's RIBBON program has been converted to run as an interactive stand-alone program of SGI 4D series workstations. All programs accept Brookhaven PDB format for input and all programs have options to generate HP and PostScript output files. The programs run on Silicon Graphics 4D GT, GTX, Personal Iris and Indigo workstations. The programs were developed by T. Callahan, W.B. Gleason and T.P. Lybrand. -- QCPE 594

  • PC/GENE - package permits you to do DNA and protein sequence analysis using the IBM-PC. -- Oxford Molecular Group

  • PCModel (5, original PC based system) is a structure building, manipulation and display program which uses molecular mechanics and semiempirical quantum mechanics to optimize geometry. Energy routines available include MMX (an extension of MM2 and MM1) and MOPAC. Available on PC (DOS and Windows), Macintosh, SGI, Sun and IBM/RS computers. -- Kevin Gilbert, Serena Software
    MC simulated annealing
    solvent dynamics
    Dimensions:
    <=500 atoms
    50 search variables
    Parameters:
    MMX: - extended MM2
    - includes transition states
    - [pi] calculation
    Acc'y: [Delta]Hr+/-0.4
    AM1
    PM3
    EHT
    MNDO
    Properties:
    distance
    angle
    charges
    dipole moment
    IR (Force)
  • PDM93: Electric Potential Derived Monopoles and Multipoles. This program finds net atomic charges or multipoles in any combination to fit the molecular electrostatic potential. Charge dependency conditions (equal charges, neutral groups,s, ion charges, etc.) are handled transparently. Bond dipoles and lone pair sites can be included. A complete error analysis is made. -- Donald E. Williams, University of Louisville

  • PERCH a PC-based, integrated NMR Software package for processing and analyzing 1D NMR spectra

  • Personal CAChe - a powerful 3-D visualization of molecules, including complex derived data, with an intuitive Macintosh interface. -- Oxford Molecular Group

  • PIMMS -- Oxford Molecular (no longer supported)

  • PlotData is a software package consisting of a plotter with data analysis capability. Data can be plotted on the screen, viewed, edited, analyzed, differentiated, integrated, calculated and reproduced graphically. Many sets of data can be overlapped to solve systems of equations graphically. The three versions of PlotD11A.ZIP are available (listserv@vm1.nodak.edu). -- Dr. Weiguang HUANG, University of New South Wales

  • pmd (Parallel Molecular Dynamics) is an advanced parallel molecular dynamics program which allows the efficient inclusion of long-range Coulomb interactions using a fast multipole algorithm.

  • Polar simulates 16 types of voltammograms with charge current and random noise.

  • PROCHECK is a program which conducts knowledge-based analysis of protein structures.

  • Pro-Explore - 3D protein & peptides from 1D sequence. -- Oxford Molecular (no longer supported)
    SWISSPROT, NBRF, PDB databases
    - Pro-Simulate
    GROMOS
    Amber
    BOSS
    - ES CALC
    electrostatics
    - N-DEG
    NMR analysis
    - PC-PROT+
    sequence analysis
    - PC-TAMMO+
    protein-lipid
  • Pro-Quantum -- Oxford Molecular (no longer supported)

  • Pro-Simulate -- Oxford Molecular (no longer supported)
    Parameters:
    GROMOS
  • Protein Adviser visualization, analysis and drawing program for biomolecular structures

  • PS - A Macintosh based graphics program for molecular analysis and modeling. It is designed to display, analyze, manipulate and redesign protein structures. It is applicable to proteins, DNA, RNA and small molecules. -- Office of Technology Licensing, Berkeley

  • QUEST a data analysis and retrieval system for the Cambridge Structural Database of small molecule organics and organometallics. -- Frank Allen, Cambridge Crystallographic Data Centre

  • RasMol

  • RASTER3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles and cylinders with specular highlighting and shadowing. Ancillary programs process atomic coordinates from Brookhaven PDB files into rendering descriptions for pictures composed of mixtures of ribbons, space-filling atoms, bonds, ball&stick, etc. Programs for previewing and figure composition are written for Iris workstations (GL graphics). Output modules are available for generating raster files compatible with AVS, ImageMagick, Sun and Iris display programs. Source is available free of charge from anonymous ftp: stanzi.bchem.washington.edu. -- Ethan Merritt, University of Washington

  • REACCS - (REaction ACCess System) Computer Assisted Synthesis -- MDL

  • React is a program to calculate reaction kinetics equations. The program is available in compiled form for the Macintosh, DOS, and OS/2 platforms.

  • Ribbons is designed to display molecular models as rendered images. The data required consist of atomic coordinates in PDB format and files of color coding information. Ribbons runs on SGI and Evans & Sutherland ESV workstations. -- Dr. Mike Carson, University of Alabama at Birmingham

  • SCARECROW: A program for the display of molecular structures and the analysis of molecular dynamics trajectories is available at URL http://www.csc.fi/lul/chem/scarecrow/jmg_scare.html. -- Leif Laaksonen, Center for Scientific Computing

  • SEA is a program which aligns molecular structures based on maximizing the overlap of electrostatic potential and steric fields. -- QCPE 567

  • SEAL (Steric and Electrostatic ALignment) fortran program to automatically align one molecule w/ another maximizing steric similarities & electrostatic fields. -- QCPE 634

  • SECS (Simulation and Evaluation of Chemical Synthesis) is a retro-synthesis analysis program in much the same mold as LHASA and SYNCHEM. The target molecule is analyzed according to strategic reactions using a database of known reactions as a guide for predicting single step transformations to simplified compounds. Several iterations of the procedure are required to develop a synthesis plan. -- W. Todd Wipke, University of California, Santa Cruz

  • Selectivity can be used for the calculation of the selectivity - expressed as the Enantiomeric Ratio E - of a kinetic resolution of enantiomers for irreversible reactions.

  • SMILES Toolkit A programming library which provides basic functions needed for chemical information processing. The Toolkit is the basis for all other Daylight Toolkits. -- Daylight Chemical Information Systems

  • SPARTAN (Changes Submitted by Sean Ohlinge from Wavefunction, Inc., on Oct 27, 2003)

    SPARTAN'04 and SPARTAN'04 ESSENTIAL for Windows are the latest molecular modeling applications from Wavefunction supporting Windows 98 or higher. These new versions add to user interface features including builders for organic and inorganic molecules, peptides and nucleotides, with an internal database of over 60,000 molecules pre-calculated at up to 5 quantum mechanical theory levels. Offering substantial ease-of-use with internal spreadsheets and plotting tools for organizing your data, custom clipboards, and file import/export features including: SYBYL MOL and MOL2 , PDB, MacroModel, SDF, TGF, MOL files (2D), Spartan Exchange and Collection files and graphical export of BitMap, JPEG and AVI graphics files.


    Spartan for Windows will determine equilibrium and transition state geometries; identify lowest energy conformers and generate conformational and Boltzmann distributions (with optional use of NOE data); align molecules and scan geometrical coordinates; generate reaction sequences and generate and follow intrinsic reaction coordinates; calculate reaction and activation energies; calculate and plot IR, NMR, and UV/vis spectra; and search the Spartan Molecular Database and the Cambridge Structural Database. These tasks elucidate a host of numerical and graphical data and properties including:


    Mulliken, electrostatic-fit and natural-bond-orbital (NBO) charges

    Dipole moments and higher moments

    Polarizabilities and Hyperpolarizabilities

    Ovality

    Electronegativity and hardness

    Enthalpies, entropies and free energies

    Highest Occupied and Lowest Unoccupied Molecular Orbital Energies (and homo/lumo gaps)

    Aqueous solvation energies

    LogP

    NMR Chemical shifts (Hartree-Fock only)

    UV/vis excitation energies from CIS and TDDFT models

    Display of molecular orbitals, electron densities, contour displays

    Display spin densities and electrostatic potentials as isosurfaces

    Display ionization potentials

    Composite surface maps

    Ribbon displays for biopolymers

    Display of hydrogen bonds


    Available computational methods:


    SYBYL and MMFF94 molecular mechanics

    MNDO, MNDO/d, AM1 and PM3 semi-empirical MO including PM3 parameters for transition metals

    Hartree-Fock molecular orbital

    SVWN, BP, BLYP, EDF1 and B3LYP density functional for ground and TDDFT for excited states

    MP2, MP3, MP4 and LMP2

    CCSD, CCSD(T), OD, and OD(T)

    G2, G3 and G3 (MP2)

    QCCD and QCCD(T)

    QCISD and QCISD(T)

    CIS and CIS(D), for excited states

    STO-3G, 3-21G, 6-31G*, 6-311G*, cc-pVDZ, cc-pVTZ and cc-pVQZ all-electron basis sets

    With additional polarization and/or diffuse functions - additional and custom basis sets available

    Pseudopotential basis sets for calculations on molecules with heavy elements




    SPARTAN'02 for Unix / Linux support Unix: SGI IRIX 6.5 or later Linux: RedHat 6.2 or later, Mandrake 7.0 or later, SuSE 6.3 or later, or Generic Linux (Kernel 2.2 Xfree86 3.3, glibc 2.1). These applications are the latest versions of the original Unix Spartan program and contain interface features including builders for organic and inorganic molecules, polypeptides and polynucleotides. Both versions offer internal spreadsheets and plotting tools for organizing data, and file import/export features including: SYBYL MOL and MOL2 , PDB, MacroModel, and Spartan Exchange files, import of FDAT crystal files, and export of JPEG and VRML graphics files.


    Spartan for Unix / Linux will determine equilibrium and transition state geometries, identify lowest energy conformers and generate conformational distributions, align molecules and scan geometrical coordinates, generate reaction sequences, calculate reaction and activation energies, calculate Infrared Spectra frequencies and intensities and search the Cambridge Structural Database. These tasks elucidate a host of numerical and graphical data and properties including:


    Mulliken, electrostatic-fit and natural-bond-orbital (NBO) charges

    Dipole moments and higher moments

    Polarizabilities and Hyperpolarizabilities

    Ovality

    Electronegativity and hardness

    Enthalpies, entropies and free energies

    Highest Occupied and Lowest Unoccupied Molecular Orbital Energies (and homo/lumo gaps)

    Aqueous solvation energies

    LogP

    NMR Chemical shifts (Hartree-Fock only)

    UV/vis excitation energies from CIS and TDDFT models

    Display of molecular orbitals, electron densities, contour displays

    Display spin densities and electrostatic potentials as isosurfaces

    Display ionization potentials

    Composite surface maps


    Available computational methods:


    SYBYL and MMFF94 molecular mechanics

    MNDO, MNDO/d, AM1 and PM3 semi-empirical MO including PM3 parameters for transition metals

    Hartree-Fock molecular orbital

    SVWN, BP, BLYP, EDF1 and B3LYP density functional for ground and excited states

    MP2, MP3, MP4 and LMP2

    CCSD, CCSD(T), OD, and OD(T)

    G2 and G3

    QCCD and QCCD(T)

    QCISD and QCISD(T)

    CIS and CIS(D), for excited states

    STO-3G, 3-21G, 6-31G*, 6-311G*, cc-pVDZ, cc-pVTZ and cc-pVQZ all-electron basis sets

    With additional polarization and/or diffuse functions - additional and custom basis sets available

    Pseudopotential basis sets for calculations on molecules with heavy elements




    SPARTAN'02 and SPARTAN'02 ESSENTIAL for MACINTOSH are the latest molecular modeling applications from Wavefunction, Built for OSX. With a state-of-the-art Open GL interface including builders for organic and inorganic molecules, peptides and nucleotides, these programs place sophisticated molecular mechanics and quantum chemical calculations at your fingertips. Offering substantial ease-of-use with internal spreadsheets and plotting features for organizing your data, custom clipboards, and file import/export features including: SYBYL MOL and MOL2 , PDB, MacroModel and Spartan Exchange and Collection files and graphical export of PICT, PNG, JPEG and QuickTime graphics files.


    Spartan for Macintosh will determine equilibrium and transition state geometries, identify lowest energy conformers and generate conformational distributions, align molecules and scan geometrical coordinates, generate reaction sequences, calculate reaction and activation energies, and calculate IR frequencies and intensities. These tasks elucidate a host of numerical and graphical data and properties including:



    Mulliken, electrostatic-fit and natural-bond-orbital (NBO) charges

    Dipole moments and higher moments

    Polarizabilities and Hyperpolarizabilities

    Ovality

    Electronegativity and hardness

    Enthalpies, entropies and free energies

    Highest Occupied and Lowest Unoccupied Molecular Orbital Energies (and homo/lumo gaps)

    Aqueous solvation energies

    LogP

    Display of molecular orbitals, electron densities, contour displays

    Display spin densities and electrostatic potentials as isosurfaces

    Display ionization potentials

    Composite surface maps

    Ribbon displays for biopolymers


    Available computational methods:


    SYBYL and MMFF94 molecular mechanics

    MNDO, MNDO/d, AM1 and PM3 semi-empirical MO including PM3 parameters for transition metals

    Hartree-Fock molecular orbital

    SVWN, BP, BLYP, EDF1 and B3LYP density functional for ground and excited states

    MP2, MP3, MP4 and LMP2

    CCSD, CCSD(T), OD, and OD(T)

    G2 and G3

    QCCD and QCCD(T)

    QCISD and QCISD(T)

    CIS and CIS(D), for excited states

    STO-3G, 3-21G, 6-31G*, 6-311G*, cc-pVDZ, cc-pVTZ and cc-pVQZ all-electron basis sets

    With additional polarization and/or diffuse functions - additional and custom basis sets available

    Pseudopotential basis sets for calculations on molecules with heavy elements


    Contact:


    Nathan Dacuycuy/Sean Ohlinger

    Wavefunction, Inc.

    18401 Von Karman Ave, Suite 370

    Irvine, CA 92612

    Tel: (949) 955 2120

    Fax: (949) 955 2118

    Email: sales@wavefun.com

    Web: http://www.wavefun.com


  • Sprout is an interactive system that assists chemists in several steps of the structure-based rational drug design process.

  • SwaN-MR is a Macintosh-based NMR data analysis and reporting program.

  • SYBYL is a suite of molecular modeling programs for building, editing and analyzing small molecule organics, biopolymers, polymers and materials. Modules include Base SYBYL, Biopolymer, QSAR, Advanced Comp (for conformation searching and interfaces to QCPE programs). Additional functionality is also available. -- Tripos, Inc.
    Parameters:
    MM(P)2, MM3
    Sybyl- general purpose
    - nonbonded attractions high
    - coordination complexes
  • SYBYL/3DB UNITY is Tripos' 3D-database and chemical information system. -- Tripos, Inc.

  • SymbMath is a computer algebra system that can perform exact numeric, symbolic and graphic computation.

  • SYNLIB (SYNthesis LIBrary) is a chemical reaction retrieval computer program through which laboratory scientists can rapidly search databases of chemical reaction information. A facile sketchpad method is available for building chemical structure diagrams. The searching portion of the program provides unique methods for querying chemical reaction libraries for matches to combinations of both structural and non-structural chemical questions. SYNLIB runs on Silicon Graphics, HP9000/720, NEC EWS4800, VAX/VMS and Macintosh II computer systems. -- W. Clark Still, Columbia University

  • Thor A high performance, full distributed database system designed for the storage and retrieval of chemical information. Data fields have the capability of holding any amount or kind of data. -- Daylight Chemical Information Systems

  • TRIAD (TRIcyclics for Automated Design) is a database of more than 400,000 energy minimized molecular structures representing a comprehensive collection of tricyclic hydrocarbons. The database is available in MacroModel format (TRIAD-M) and CAVEAT vector format (TRIAD-V). -- Office of Technology Licensing, Berkeley

  • Tsar - a fully integrated analysis package for investigation of Quantitative Structure-Activity Relationships (QSARs). -- Oxford Molecular Group
    3D QSAR spreadsheet
    fragment descriptor library
    topological indices
    statistical tools
    neural net
  • TurboDFT -
    BLYP
    VWN
    BP
    ACM
  • TurboNMR - BIOSYM/MSI
    1H, 13C, 31P, etc.
    ab initio shielding tensors
    GIAO (Gauge-Independent Atomic Orbital)
    Acc'y:
    SCF/6-31G -
    [partialdiff][Delta] 1H +/-0.2
    [partialdiff][Delta] 13C +/-4
    SCF/6-31G
    [partialdiff][Delta] 1H +/-0.1
    [partialdiff][Delta] 13C +/-2
  • Turbomole -- BIOSYM/MSI
    Natural Internal Coordinates
    semidirect SCF, MP-2
    Properties:
    optimized geometry
    IR
    - force constants
    - energies
    - intensity
    Dipole - hexadecapole moments
    polarizability
    electrostatic potential
    0th order shielding
    Mulliken Population Analysis
    Roby-Davidson Population Analysis
    Boys orbital localization
    intermolecular interaction energy
    Parameters:
    Gaussian basis sets
    DZVP
    VWN
    BP
    ACM
    BLYP
    Schafer -
    - SV(+P):
    H, He
    Li - Ne
    Na - Ar
    K - Kr
    - DZ(+P):
    H, He
    Li - Ne
    Na - Ar
    K - Kr
    - TZ(+1-2P):
    H, He
    Li - Ne
    Na - Ar
    ECPs: Hurley; K -Kr
    LaJohn; Rb - Xe
    Ross; Cs - La, Hf - Rn
    Cundari; Ce - Lu
    Ermler; Fr - Ac, Th - Pu
    STO-3G, 3-21G, 6-31G( *,**)
  • UCSD MMS (Molecular Modeling System) is an interactive 3-D molecule display program which is used to represent molecules as line drawings, dot surfaces and wire frames electron density contours. Source code is included. -- Steve Dempsey, UCSD

  • Unichem - a suite of modeling software developed by Cray Research to bring together different modeling methods on a super computer, as well as workstations. -- Oxford Molecular, http://www.oxmol.com

    - CADPAC: ab initio Hartree Fock calculations.

    - DGauss 3.0: a molecular DFT program for studying electronic, magnetic, & structural properties of atoms, molecules, & clusters. -- developed by Cray Research

    Pros: analytical gradients
    analytical 2nd Derivatives
    SCRF
    point charge fitting
    f-functions
    relativistic pseudo-potentials
    Cons: no search driver
    "weak" TS optimizer
    Parameters:
    VWN
    BP
    BLYP
    BSPP
    Properties:
    multipole moments
    IR spectra
    Raman frequencies
    polarizability
    NMR chemical shift
    Density of States
    photoelectron spectra
    Population Analysis
    - Mulliken
    - Landis
    - Nazer
    - MNDO96: latest version of Professor Walter Thiel's semiempirical program for studying the electronic and structural properties of molecules. MNDO96 has been implemented with tremendous efficiency on Cray Research's vector/parallel hardware, and is part of Unichem
    SCRF
    Direct MD
    Ground State
    analytical gradients
    Transition State
    CI
    Parameters:
    MNDO
    MNDO/H, MNDOc, MNDO/d
    MINDO/3
    CNDO/2
    AM1
    PM3
    MP2
    BWEN
    Properties:
    multipole moments
    IR spectra
    Raman frequencies
    enthalpy, entropy, heat capacity
    time-correlation function
    Radial Distribution Function
  • USURFA is a program for rapid generation of smooth molecular dot surfaces on macromolecules. -- QCPE 566

  • UXNMR/P is a suite of display and processing programs for data acquired on Bruker NMR spectrometers. The program features selectable regions, digital filtering functions, plotting routines and storage/archival capabilities. Runs on Sun SPARCstation. -- Dr. Charles Thibault, Bruker Instruments, Inc.

  • Vamp - an exceptionally powerful semiempirical molecular orbital package. -- Oxford Molecular Group
    semiempirical QM
    electrostatic potentials
    Natural Atomic Orbital Point Charges
    Clark Solvation Model
    Properties:
    ESR hyperfine coupling
    C13 NMR shifts
  • VMD is a new package for the graphical display and visualization of biomolecular systems

  • VOID (Volume Overlap, Isotopy and Docking) is a program for computing the packing defects and the tunnels that connect them in protein molecules and for attempting to predict protein-protein

    associations. The program examines structures from the perspective of solid geometry rather than physical chemistry. -- QCPE 617

  • VoxBlast is a 3-D volume rendering program designed to create 3D projections from a series of images. It uses an alpha blending algorithm to create transparency effects. In addition, the user can create and apply color palettes, apply a lighting model, make 3D movies, use scripts and much more. VoxBlast can render data from many sources including MR, CAT, microscopes and voxel based molecular models. -- John Kesterson, VayTek, Inc.

  • WHAT IF is an extensive protein modeling, protein structure analysis, database handler, molecular graphics package. It is available for all Evans & Sutherland equipment and Silicon Graphics machines. The program is supplied with source code, databases and documentation. -- G. Vriend, E.M.B.L.

  • The Wisconsin Package (GCG) contains over 100 interrelated software programs for molecular biologists. Enables analysis of DNA and protein sequences by editing, mapping, comparing and aligning them. Other programs facilitate RNA secondary structure prediction and DNA fragment assembly. In addition, the major genetic databases (GenBank, EMBL, PIR, SWISS-PROT) are distributed with the software and are fully accessible with the database searching and manipulation programs. Documented source code is included. The software runs on SGI, VAX/VMS, DECStation, Sun SPARCstation. -- Dina Beers, Genetics Computer Group, Inc.

  • WODCA - Computer Assisted Synthesis -- J. Gasteiger

  • Yeti and Yak molecular mechanics and display programs for receptor modeling with special treatment of h-bonding. -- Angelo Vedani, Swiss Institute for Alternatives to Animal Testing,

  • ZINDO is a semiempirical quantum mechanics program which has been parameterized for transition metals. -- Michael Zerner, Quantum Theory Project
    RHF, UHF, ROHF, UHFA, CI, MP2CI
    Transition Dipoles and Moments
    Natural Orbitals
    Self Consistent Reaction Field
    Localized Orbitals
    - Boys
    - Fermi
    - Double Projector
    Ionization Potentials
    Electron Affinities
    Transition State
    Metal Configuration Mixing
    CI Excitation Indicator
    Transition Dipole
    Transition Energy
    Oscillator Strength
    Geometry optimization cycle
    Change of Energy
    Norm of the gradient
    Max component of the gradient
    Output Sections:
    (Total) ENERGY
    BOND LENGTH MATRIX
    INTERATOMIC DISTANCES
    BOND ANGLES
    ATOMIC BOND INDEX
    OVERLAP MATRIX
    COULOMB MATRIX
    ONE ELECTRON MATRIX
    HAMILTONIAN MATRIX
    SOLUTE POLARIZATION CONTRIBUTION
    SOLVENT REORGANIZATION COST
    EIGENVALUES
    ATOMIC DENSITIES
    EIGENVECTOR MATRIX
    BOND ORDER MATRIX
    TOTAL DENSITY
    SPIN DENSITY
    FOCK MATRIX
    ALPHA SPIN
    ATOMIC BOND INDEX
    (ZDO Basis) CHARGE
    DIPOLE MOMENT
    (Mulliken) ORBITAL POPULATIONS
    EXCITED STATES
    CONFIGURATION INTERACTION
    SINGLETS, TRIPLETS
    GROUND STATE DEPRESSION
    EIGENVALUES
    EIGENVECTORS

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    3/97 Ernie Chamot / Chamot Labs / (630) 637-1559 / echamot@chamotlabs.com
  • Modified: Mon Oct 27 15:49:03 2003 GMT
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