Warning: these listings rapidly become out of date, and this guide is inherently out of date as soon as it is published. It is currently undergoing a major revision, to reflect some of the changes that have taken place this last year, and I expect to have a new guide available in the next month. In the mean time, the old guide, based on information as of 4/99, is still being made available here.

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. Combines knowledge databases with ab initio methods, to model the tertiary structure of an antibody starting with its primary sequence. For modeling variations in sequence for humanization (of antibodies), mutagenesis, and structure-activity studies. -- Oxford Molecular Group.
  

• ACD/Labs is a collection of Windows-based structure drawing and analysis tools. -- Advanced Chemistry Development Inc.
  

• ACD/ChemSketch: structure drawing package
  
• ACD/ISIS 3D Viewer
  
• ACD/Tautomers (check and generate predominant tautomeric forms)
  
• ACD/LogP
  
• ACD/CNMR
  
• ACD/Dictionary
  

• 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 (Adiabatic Correction Method) replaces part of DFT exchange with exact exchange from HF.
  

• ADAPT (Automated Data Analysis using Pattern Recognition Toolkit).
  

• ADF (Amsterdam Density Functional) uses Slater type orbitals as basis functions. -- Bert te Velde, Vrije Universiyteit; Molecular Simulations Inc.
  

• AIMPAC (Atoms In Molecules) Suite of QM software based on Baders scheme for partitioning the total system into a set of bonded spatial regions. Properties of these groups recover the traditional characteristics of atoms and functional groups.
  

• 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 III, 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.
  

Parms:

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

Props:

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. NMR structure refinement. Designed primarily for proteins and nucleic acids -- Kollman, UCSF.
  

• 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. -- MJS Dewar, QCPE 506.
  

• AMPAC 6 (8) with graphical user interface. Latest version of semiempirical program originated in Dewars group. With CODESSA for QSPR. -- A. Holder, Semichem.
  

undo
Z-Matrix editor
simulated annealing
symmetry group assignment
Gaussian interface
Sybyl interface
animate vibrations
CHAIN
PATH
EF
ESP
AMSOL
COSMO
File Formats:

Mopac Input
Gaussian
Hyperchem

Parms:

MINDO/3, MNDO, PM3, AM1
SAM1, SAM1/d
MNDOC
MNDO/d
SM1-AM1, SM2-AM1, SM3-PM3

Props:

IR (Force) Spectra
ESR
NLO
HOMO
LUMO
Distance
Angle
charges
molar volume
molar surface area
ovality
dipole moment
UV (CI)
IP

CODESSA - QSPR tool

• AMSOL AMPAC with explicit solvation effects -- Chris Cramer and Don Truhlar, The University of Minnesota; Oxford Molecular Group.
  

SM2
Basis:

AM1
aqueous

Atoms:

H
C - F
P - Cl
Br

SM5
Basis:

PM3
index of refraction
surface tension
Abraham H-bonding
% aromaticity
halogens
230 solutes
90 solvents

Acc’y:

ΔG(transfer)±0.7 kcal/mol
pKa(aq) ± 1

• Anaconda - an interactive molecular similarity program for visual comparison/alignment of surface properties and pharmacophore discovery and 3D QSAR. Calculates surface properties of molecules by gnomonic projection onto a sphere. -- Oxford Molecular Group.
  

• Apex-3D is a rule-based QSAR program. -- BIOSYM/Molecular Simulations Inc.
  

• 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/Bio-Rad.
  

• ArgusLab 1.0. Multithreaded, Semiempirical QM program for Windows.
  

Energies, geometries
electronic spectra
SCRF
Dipole moments
Mulliken and ZDO charges
Wiberg bond orders
Parms: AM1, PM3, MNDO, EHT, INDO/s
Formats: XYZ, PDB.

• 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.
  

• ASP is a fast shape and electrostatic similarity assessment program. Calculates molecular similarity index based on spherical projection of electrostatic, steric, lipophilic or refractive properties from Anaconda. For SGI. -- Oxford Molecular Group.
  

• Autodock - Suite of programs to predict the bound conformations of a flexible ligand to a macromolecular target of known structure, like an enzyme or nucleic acid. -- Oxford Molecular Group.
  

• The Babel file conversion program -- Pat Walters & Matt Stahl, University of Arizona. Also Open Babel
  

• 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 -- Yale.
  

• 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. -- CAChe/Oxford Molecular Group/Fujitsui/disappeared.
  

• 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.

constant N,V,E

• ExtHuckel: Extended Hückel calculations.
  

Atoms:

≤150
H - Lr

Props:

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
(M-bonds l±7% a±9%)

Props:

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

Parms:

MINDO/3, MNDO, PM3
AM1 (w/o Li?)
(w/ Cb, +, ++, -, --)

Props:

Dipole Moment
Energy
- Enthalpy
- Entropy
- Heat Capacity
- Heat of Formation
- Electronic
- Resonance
- Total
- Zero Point
ESR
- Spin Density
- Spectrum
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 Interface: accurate, reliable ab initio calculations for large molecules with a powerful graphical interface and optimized performance. Developed by IBM.

Parms:

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

Props:

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

DGauss Interface

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

Parms:

INDO/1(+ As, Br, I)
INDO/S, INDO/2
CNDO/1 (ΔHf°±200, l±0.2)
CNDO/2
EHT
PPP

Props:

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
Props:

Dipole Moment
- Vacuum
- Aqueous
- vector
Electron Affinity
Energy
- Enthalpy
- Entropy
- Free energy
- Heat Capacity
- Heat of Formation
- Dielectric
- Steric
- Total
Fukui indices
Frontier density
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 (Keir & Hall)
- Chi0 (atomic)
- Chi1 (bond)
- Chi2 (path)
- valence Chi0 (atomic)
- valence Chi1 (bond)
- valence Chi2 (path)
Molecular ovality
Polymer
- Cohesive Energy
- solubility parameter, Delta
- MVol
- Tg
Shape Index (Keir & Hall)
- 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. -- CAChe/Oxford Molecular Group.
  

• 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; Oxford Molecular Group.
  

RHF, ROHF, UHF
MP2, MP3, MP4
CISD, CEPA, ACPE, CCD, QCISD(T)
analytical gradients w/ MP2, MP3
Props:

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 Group.

protein structure from sequence

• CAMEO (Computer Assisted Mechanistic Evaluation of Organic Reactions) is a forward chaining reaction prediction program. Runs on VAX/VMS, SGI, Mac, and Java. -- William L. Jorgensen, Yale University.
  

Rxns:

carbene
Basic/Nucleophylic
Acidic/Electrophylic
Transition organometallic
Free radical
Heterocyclic
Oxidative/Reductive
Pericyclic
Photocyclic

• CAR-PARRINELLO (-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 -- Berkeley.
  

• 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, CCP14 (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.
  

• 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. -- Molecular Simulations Inc..
  

Dreiding, UFF
OFF: H - No
Amber
MM2
Burchart
MM2 77, 85
CFF91, 93
CVFF
GlassFF
PCFF
COMPASS

• 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.
  

dH, TdS, and dG of mixing

• C2•CASTEP: (CAmbridge Serial Total Energy Package) 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.
  

Pros: metals

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

Library (management, analysis, construction)
DB interface (MDL, Catalyst, Catshape
Receptor model
HIPHOP

• 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 visualizes 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•Discover single point energy, gradient, minimization, dynamics
  
• C2•DLS: uses geometric refinement to predict the structures of inorganic frameworks, especially zeolites, from a trial model.
  
• C2•DMol3: DFT calculations for molecular species and solids
  
• 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•ESOCS:
  
• 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•FastStructure:
  
• 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 moduli for any materials type for designing novel crystalline and amorphous polymers, ceramics, and semiconductors.
  

Elastic Stiffness Constants, Cij
Elastic Compliance constants, Sij
Bulk modulus
Compressibility
Young Modulus (x, y, z)
Poisson Ratios
Velocities of sound (x, y, z)
Lame constants, lamda, mu

• C2•Mesodyn: mesoscale simulation. evolution of thermodynamic properties and morphology
  
• C2•MFA: (Mean Field Analysis) 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 parametrized 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/FFE: (Open Force Field, Force Field Editor) 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.
  

Mean Field Analysis
Genetic Analysis
Mean Shape Analysis

• C2•Reaction Explorer:
  
• C2•Receptor: investigates interaction of lead candidates for drug development with 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•RMMCC
  

End-to-end Distance
Dipole Moment
Radius of Gyration
Persistence Length
Dihedral Distribution

• 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•Synthia: Polymer property QSPR developed by Bicerano at Dow.
  

Props:

VdW volume
Connectivity indices
Tg
Half Decomposition Temp
Coeff. Vol. Therm. Expansion
V(298K)
Molar Volume
Density
Cp (solid, liquid, delta)
Cohesive Energy (Fedors, van Krevelen)
Solubility Parameter (Fedors van Krevelen)
Surface Tension (MolPar, Fedors, van Krevelen)
Thermal Conductivity
Refractive Index, Molar Refraction
Dielectric constant
Volume Resistivity
Diamagnetic Susceptibility
Modulus (Bulk, Shear, Young's)
Poisson's Ratio
Stress (Shear Yield, Brittle Fracture)
Characteristic Ratio
Molar Stiffness Function
Entanglement (MW, length)
Critical MW
Activ En Visc Flow
Permeability (O2, N2, CO2)
Shear Viscosity

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.

C2•Zindo:

• 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) -- Molecular Simulations Inc..
  

• Charge Program for fast partial charge derivation. -- Oxford Molecular Group.
  

• 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 Corp.
  

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

Parms:

MM2 (w/o F, S, Cl, Sr, Te, I):
MM2+
- Basis:
hybrid conjugation term
multicoordinate centers
quartic stretch
-Atoms:
H
Li - F
Na - Cl
K - Br
Rb - I
Cs - La, Hf - At

Props:

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 Corp.
  

• 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 Corp.
  

• 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/Bio-Rad.
  

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 Corp.
  

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

• 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. -- Softshell/Bio-Rad.
  

• 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., (see Oxford Molecular Group.)
  

Undo
File Formats:

MDL .mol
Brookhaven .pdb
Tribble
CSSR (CCSDB)
Smiles
Gaussian
GAMESS

Dimensions:

8000+ atoms
150 search variables

Parms: ChemX

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. -- Steve Hannisan, U. of Montreal.

• CIS - (Chemical Information System) On-line system of over 30 databases covering information related to chemistry and the environment, including toxicology, carcinogenicity, chemical/physical properties/MSDS's, site assessment. -- Oxford Molecular Group.
  

• COBRA is a "smart" conformational analysis program which utilizes heuristic techniques to automate conformational analysis and 3D structure generation. -- Oxford Molecular Group.
  

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 Group. (no longer available).
  

• CORINA - fast 1D/2D to 3D structure conversion program for SGI, including SMILES and SD formats. -- Oxford Molecular Group.
  

• Cosmic - fast structure optimization program. -- Oxford Molecular Group.
  

• 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.
  

• CRYSTAL95 - computes the electronic structure of periodic materials within Hartree Fock, density functional or various hybrid approximations. The Bloch functions of the periodic systems are expanded as linear combinations of atom centered Gaussian functions. Perform consistent studies of the physical, electronic and magnetic structure of molecules, polymers, surfaces, and crystalline solids. -- Torino & Daresbury groups.
  

• 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.
  

• Dalton - ab initio program for optical activity.
  

• 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 program from Salahub's group.
  

VWN, BP, PP

• Desktop Molecular Modeller -- Polyhedron Software?
  

• 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/Molecular Simulations Inc..
  

periodic
- NVE
- NVT
- NPT
- NST
conformational analysis
Ewald sum w/ surface correction
Parms:

CFF91/93
CVFF
GENFF (generalized CVFF)
ESFF
Amber

Props:

radial distribution function
self-diffusion coefficient
H-bonds
Energies
- interaction
- strain
- entropy
- enthalpy
IR
- modes
- intensity

DIVA - Visualization and analysis tool for scientific data. Displays chemical structures and property data in a spreadsheet model. Statistical tools include recursive partitioning. -- Oxford Molecular Group.

• DMol is a density functional theory (DFT) based program for quantum mechanical calculations. -- BIOSYM/Molecular Simulations Inc..
  

Dimensions: ≤~100 atoms
Parms: numeric basis sets

DNP (≊6-31G**):
H, He
Li - Ne
Na - Ar
K - Kr
Rb - Xe?
gradient corrections
VWN
BVWN
BP
BLYP

Props:

IR frequencies
Dipole moments
optical polarizability
EA
IP
Mulliken & Hirshfeld Populations
charge density
spin density
electrostatic potential
equilibrium geometry

Output Sections:

Total Energy
Optimization Cycle:
Energy is
opt==
Charge partitioning by Hirshfeld method:
Dipole moment vectors (au):
dipole magnitude:
Mulliken Population analysis
orbital file:
Energy of Highest Occupied Molecular Orbital
vibrational frequencies, intensities
Frequencies (cm-1) and normal modes
Dipole derivatives wrt normal modes
Zero point vibrational energy:
STANDARD THERMODYNAMIC QUANTITIES AT

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, QCPE 454.
  

• 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.
  

• EyeChem is a set of Explorer modules which support for various areas of molecular modeling. -- Omer Casher, Imperial College.
  

• FlexX is a receptor-ligand docking program. GMD-SCAI. M. Raney.
  

• 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.
  

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. Also GAMESS-UK -- Computing for Science Ltd.
  

RHF, UHF, ROHF, GVB
MCSCF, CI, MP2
Analytical Gradients
Saddle
Parms:

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

Props:

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 Ab initio electronic structure program that originated in the research group of Pople at Carnegie-Melon. Calculate structures, reaction transition states and a wide range of molecular properties. -- Gaussian, Inc., http://www.gaussian.com.
  

1- and 2-electron integrals over s,p,d,f contracted GAUSSIAN functions
Conventional, direct, semi-direct & in-core
fast multipole method (FMM) & sparse matrix
Quadratic Convergence SCF
network, shared distributed memory parallelism
geometries
transition states
mode walking, Newton-Raphson, Synchronous Transit-Guided Quasi-Newton
IRC & IRCMax search
Optimized search
IRC
internal, Cartesian, & redundant internal coordinates
energies, gradients, frequencies, RPA energies
Outer Valence Greens for IP & EA
analytical MP2 second derivatives
Atoms in Molecules
Methods:

SCF, RHF, ROHF,, GVB
MP2, MP3, MP4(SDQ), MP5
CASSCF
CI, QCISD(TQ)
CCD, CCSD, CCSD(T)
G1, G2, G2(MP2), CBS-4, CBS-q,
CBS-QB3, CBS-Q, CBS-APNO
GIAO
ONIOM (2- and 3-layer)
SCF simulated annealing
SCRF: Onsager, PCM, I-PCM, SCI-PCM

Parms:

Amber, DREIDING, UFF
AM1, CNDO/2, INDO, MINDO3, MNDO, & PM3
Slater, Xa, B88, PW91, Gill96
VWN, VWN5, LYP, P81, P86, PW91, B96
B3, B1
MIDI!, SV, SVP, TZV, cc-pVDZ, cc-pVTZ
CEP ECPs, Stuttgart/Dresden ECPs

Props: Frequencies & Normal Modes

Infrared intensities
Raman intensities
NMR shielding tensors/shifts
magnetic susceptibilities
circular dichroism intensities
Multipole moments
Charges (CHelp, CHelpG, Merz-Kollman-Singh, AIM)
Electrostatic energy & potential
electron density & gradient
bond orders (AIM)
Fermi contact
Natural orbital analysis
Natural Bond Orbital (NBO) analysis
Polarizabilities and hyperpolarizabilities
Spin densities
spin orbit coupling

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 >200,000 protein and nucleic acid sequences extracted from world-wide patent documents. Searchable online via Bionet. -- Oxford Molecular Group, http://www.oxmol.com.
  

• GeneWorks - an integrated sequence analysis and database searching on the Macintosh. -- Oxford Molecular Group. (no longer available).
  

• 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: (σ 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. -- CAChe/Oxford Molecular Group, http://www.oxmol.com.

• 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.
  

Crystal lattice energy
Entropy
Free Energy
Heat capacity
Elastic constants
Dielectric constants
Phonon frequencies
IR activities
Electric field gradients

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

• HINT (Hydrophobic INTeractions) D. Haney's program for calculating and visualizing, mapping, & scoring hydrophobic and hydropathic interactions of biomolecular specie. -- eduSoft.
  

logP
ligand/inhibitor docking

• HMO-Plus1.5.
  

Atoms:

B - F
Si - Cl

Props:

Secular Determinant
Eigenvalues
Total energy
delocalization energy
Polarographic half-wave reduction potential
Eigenvectors
Charge densities
π-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
crystal builder
sugar builder
File Formats:

MDL .mol
Tripos .mol
Brookhaven .pdb
Mopac Input
CCSDB

Dimensions: 20,000+ atoms
Parms:

MM2
Amber
BIO+
OPLS
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

Props:

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 - Relational database of 3D protein structures with instant access to protein motifs, substructures and interactions buried in the Brookhaven databank. -- Oxford Molecular Group, http://www.oxmol.com.
  

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, http://www.oxmol.com.
  

• IGOR/RAIN - program for exhaustive bond reordering for synthesis planning. -- Ugi.
  

• IG Suite - these tools allow you to do DNA and protein sequence analysis using Sun and VAX workstations. -- Oxford Molecular Group. (no longer available).
  

• 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/Molecular Simulations Inc, 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 therapeutics, 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 optimizing 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 structure, 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.
  

• Jaguar (Formerly PS-GVB) Fast ab initio electronic structure software package that provides chemical accuracy for realistic systems in reasonable time. Uses combination of pseudospectral methods to calculate two- electron integrals and correlation techniques that are local to allow the HF, DFT, MP2, GVB, and GVB-RCI methods to scale better than N3. Jaguar's solvation modeling enables one to calculate geometries, transition states and properties in a variety of solvents, based upon the standard self-consistent reaction field (SCRF) model, using the actual molecular surfaces for the dielectric boundary. Correlation can be treated locally, applying Local MP2 to a specific region of the molecule, with virtually no basis set superposition error from the MP2 treatment. GVB and GVB-RCI take just a fraction longer than HF calculations, but offer a convenient means to treat spin couplings in metals, dissociate bonds correctly, obtain a very intuitive picture of metal-ligand bonding, or calculate accurate solvation energies. -- Schroedinger, Inc., http://www.psgvb.com.
  

GUI
DFT
Props:

energy
geometry
transition states
forces
frequencies
charges
-ESP
-Mulliken
polarizabilities & hyperpolarizabilities
thermochemistry
solvation free energies
dipole moment/multipole moments

Kekule - Molecular drawing program which can be used with a scanner to create compute-readable electronic models from printed documents. Integration with ISIS, ChemDraw. -- Oxford Molecular Group, http://www.oxmol.com.

• 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.
  

• LabVIEW is a graphical programming development environment based on the G programming language for data acquisition and control, data analysis, and data presentation.
  

• 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/Molecular Simulations Inc., http://www.msi.com.
  

• 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 π calculations

Parms:

AMBER*
-Acc’y: ΔH^†±1, ΔH_r±0.9
MM2*
-Acc’y: ΔH^†±0.4, ΔH_r±0.5
MM3*
-Acc’y: ΔH^†±1, ΔH_r±0.5
OPLS

• MacVector is a Bioinformatics product for DNA and protein sequence analysis with Internet access to Entrez databases. Supports BLAST searches. -- Oxford Molecular Group.
  

• 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.
  

Docking
Surface Energy/Morphology

• MEAD (Macroscopic Electrostatics with Atomic Detail) D. Bashford.
  

• 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.
  

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
π calculation

• MOBY -- Springer-Verlag Inc., New York.
  

Geometries
Dynamics
AMBER
MNDO
AM1
≤150 atoms

• ARGOS – connection -> 2D
  
• Autonom – nomenclature
  
• MOLKIK – DB queries
  

• MOE (Molecular Operating Environment) is not a software package in the usual sense, but an integrated Applications Environment and Methodology Development Platform; that is, a tool for chemical computing software development and deployment. MOE integrates visualization, simulation and application development in one package.The built-in scientific applications of MOE break down into four broad categories: High Throughput Discovery (High Throughput Screening, Combinatorial Chemistry, QSAR), Protein Modeling and 3D Bioinformatics, Molecular Modeling and Simulation (Mechanics, Dynamics, Properties, Diffraction), Methodology Development and Corporate Deployment. -- Chemical Computing Group Inc.
  

• QuaSAR-Cluster: a rapid molecular clustering procedure intended for use on very large collections of compounds in order to select representative subsets of compounds. The algorithm is statistical in nature and can cluster molecules based on physical-property descriptors. Outputs Principal Components Analysis, Cluster Codes, and Importance Weights.
  
• QuaSAR-Binary: a method for the analysis of High Throughput Screening data using Binary QSAR, i.e., activity measures that are binary (active/inactive or pass/fail). A Bayesian statistics technique is used to estimate the probability that a new compound is active.
  
• QuaSAR-Contingency: a statistical procedure that assists in selecting molecular descriptors for use in QSAR studies, based on whether or not a given descriptor is associated with the activity measurement. Both linear and non-linear assessments are performed.
  
• QuaSAR-Descriptor: a collection of programs that calculate (over 200) molecular descriptors for QSAR studies and clustering efforts. Includes: topological indices, physical properties, 3D descriptors, and 2.5D descriptors.
  
• QuaSAR-Reagent: a "pure" combinatorial library design method for use in focused library design applications. Uses a QuaSAR-Binary model of biological activity as focusing agent.
  
• QuaSAR-CombiDesign: is a new Combinatorial Library Design method for selecting diverse subsets from billion or trillion compound virtual libraries, integrating product construction, descriptor calculation, principal components analysis and diverse subset selection into one calculation.
  
• QuaSAR-PLS: build Quantitative Structure Activity Relationships using Partial Least Squares methodology from large data sets.
  
• MOE-CombiGen: enumerate virtual combinatorial libraries. Generates structures from Multiple central groups and up to four R-group.
  
• MOE-Align: performs multiple sequence alignment and simultaneous structure superposition of proteins. Tree-based and Pile-Up build up procedures.
  
• MOE-SearchPDB: a protein family-based homologue search procedure (in contrast to pairwise search procedures like BLAST) based on clustering the Brookhaven Protein Databank into protein families. Incorporates rigorous sequence-to-group alignment, predicted secondary structure, hydrophobic fitness evaluation, and Z-scoring of alignments.
  
• MOE-Consensus: uses a geometric definition of conservation to identify conserved features in a family of structures.
  
• MOE-ContactAnalyzer: searches for stabilizing non-bonded contacts in a single structure or in a family of structures.
  
• MOE-Homology: builds a 3D model of a protein sequence given one or more homologous structures with Segment Match modeling to generate multiple models of the target sequence. Averages structures and refines model with AMBER forcefield.
  
• MOE-ProEval: a statistical procedure to measure the stereochemical quality of a protein structure.
  
• MOE-Dock: a grid-based ligand-receptor docking program with a simulated annealing search procedure to flexibly dock small molecules against protein targets.
  
• Energy Minimization: MOE-OptLib is a comprehensive non-linear optimization library that efficiently calculates local minima of a molecular potential energy surface. Includes the carbohydrate forcefield PEF95SAC and the AMBER'89, AMBER'94 and MMFF94 forcefields. Cascading energy minimization procedure employs three methods in sequence: Steepest Descent, Conjugate Gradient, and Truncated Newton.
  
• Molecular Builders: a suite of molecule builders to build systems in 3D. Includes Carbohydrate, Protein, DNA, Small Molecule, and Crystal Builders.
  
• Molecular Surfaces: multidimensional grid functionality, calculates Gaussian approximations to the Accessible Surface and the Connolly Surface. Can be renderd as dots, lines or solid surfaces colored by properties such as hydrophobicity and partial charge.
  
• MOE-Polymer: predicts over 50 properties of polymers using QSPR methods and models. Properties include amorphous volume, heat capacity, cohesive energies, solubilities, glass transition temperature, refractivity, and mechanical properties.
  
• MOE-Diffraction: suite of programs to simulate X-Ray, Neutron and Electron diffraction experiments. Gas, Amorphous Liquid, Powder, fiber and Single Crystal diffractions are supported. Full support for all crystal symmetry groups and cell parameters.
  
• MOE-Dynamics: generates a trajectory in either the NVE, NVT, NPT or NPH statistical ensembles. The trajectory can be written to a molecular database for subsequent animation and analysis.
  
• MOE-CSearch: a collection of powerful techniques. The collection of algorithms for conformational search and analysis include, Systematic Rotation, Random Pulse Search, 4D Conformational Sampling, Hybrid MC/MD Sampling and Distance Geometry Search.
  
• Scientific Vector Language (SVL): built-in high performance programming language of MOE. CCG applications can be customized by end-users and that entirely new MOE applications can be rapidly prototyped, developed and deployed throughout an organization.
  

• 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 rigid body 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.
  

Ewald sum for periodic
Gaussian thermostat
Noose-Hoover thermostat
constant pressure

• 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. (Basis of MOZYME and of MOPAC2000 by Fujitsui) -- 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)

MOPAC 2000 -- commercial version of MOPAC. -- Futitsu; distributed by Schrodinger, Inc.

MOZYME algorithm
2-D & 3-D periodic boundary conditions
point groups up to order 7
defect solids
MOS-F
COSMO
Tomasi solvation model
intersystem crossing geometry
amino acid residue sequencing
frequency dependent non-linear optics
geometry in electric field
transparent restarts
Parms:

MNDO, MNDO/3
AM1, PM3
AM1-d (for Cu, Ag)
MNDO-d (Al, Si, P, S, Cl, Br, I)

Dimensions: 1000's of atoms
File Formats: pdb
Props:

UV-Visible spectra
Solvent Accessible surface
Dynamic Jahn Teller states
Brillouin Zond band structures
polymer phonon spectra
Young's modulus
tensile strength
band structures
density of states
heat of polymerization

• MOZYME -- (MOpac for enZYMEs) semiempirical method, derived from MOPAC implementing scheme to speed up calculation and allow modeling very large systems -- incorporated into MOPAC2009, James J. P. Stewart
  

Basis:

Lewis bond input
hybrid coordinates

Pros:

avoids diagonalization
linear SCF scaling

Cons:

no UHF or CI
no polarizability or solvation
limited convergers & optimizers

Parms: 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) finds intermolecular energy minima of molecular clusters (including molecular docking) or molecular crystals (including polymorph and space group prediction). Accepts random or nonrandom input trial models for the determination of molecular crystal structures or molecular clusters. Contains a library of intermolecular force fields, or the user can supply the force field. Energy minimization by OREM (off-ridge eigenvector minimization), SD (steepest descents), or the NR (Newton-Raphson) method. Simulated annealing to aid in locating global, rather than subsidiary, energy minima. Mpg displays the input and output structures of mpa -- Donald E. Williams.
  

minimization of nonbonded and hydrogen bonded energy in molecular clusters or crystals
molecular docking
ab initio prediction of space group symmetry
polymorph prediction
simulated annealing
limited molecular flexibility
multiple molecules in asymmetric unit
Parms: WH86, MM85, Biosym, CHARMM

• 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. (no longer available).
  

• 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.
  

• 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. (no longer available).
  

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

Parms:

COSMIC:
H
C - F
P - Cl
Br
I

Props:

partial charge
Dipole moment
distance
angle

NWChem is an ab initio code for massively parallel computers -- Pacific Northwest Labs.

DFT
Periodic w/ symmetry

• O is a molecular graphics program for protein crystallographers. -- T. Alwyn Jones, Dalby.
  

• OMIGA is a Bioinformatics tool for sequence analysis under Windows: multiple alignments, motif scans. -- Oxford Molecular Group.
  

• 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. (no longer available)
  

• 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. Available on PC (DOS and Windows), Macintosh, SGI, Sun and IBM/RS computers. -- Kevin Gilbert, Serena Software.
  

MC simulated annealing
solvent dynamics
Ampac/Mopac interface
Gaussian interface
Jaguar interface
Any Force Fields
File Formats: PDB
Dimensions:

≤500 atoms
50 search variables

Parms:

MMX:

- extended MM2
- includes transition states
- generic metal atom w/ covalent or electrostatic bonds
- π calculation
Acc’y: ΔH_r±0.4

MM3
AM1
PM3
EHT
MNDO

Props:

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. -- CAChe/Oxford Molecular Group.
  

• PIMMS -- Oxford Molecular Group (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 Group (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 Group (no longer supported).
  

• 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.
  

• Q-Chem "Fastest" ab initio implementation of multipole-based methods (Continuous Fast Multipole Method), for linear scaling of calculations. Integration with HyperChem and UniChem. -- Q-Chem, Inc.
  

counterpoise calculations
SCRF
-Poisson-Boltzmann
-DelPhi
symmetry recognition
analytical gradients
Natural Bond Orbital Analysis
CFMM,
RHF, ROHF
MP2,LMP2
CIS, XCIS and CIS(D)
GVB, GVB-RCI, GVB-LMP2, GVB-DFT
Dimensions:

200 atoms
5000 basis functions
50 GVB pairs

Parms:

STO-3G, 3-21G, 4-21G, 6-21G, 4-31G, 6-31G, 6-311G
D95V, D95
Hay-Wadt ECPs
MSV, cc-pVDZ, and cc-pVTZ
Slater, Becke, Gill '96
VWN, PZ81, Wigner, P86, LYP
EDF1, B3LYP, B3P, GGA91

Props:

electrostatic potential charge fitting
multipole moments (through hexadecapole)
polarizability and hyperpolarizability (CPHF)
IR
-frequencies
-intensities
Raman frequencies
thermochemical properties
Mulliken populations
orbital
electron density
NBO analyses

File Formats:

MacroModel
GVB2P5
GAUSSIAN

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 universal program for visualization of molecules, particularly PDB files.
  

• 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.
  

• RS3 Discovery - Information management system based on Oracle 7 relational DB for storing, searching and retrieving chemical structures, chemical and biological properties, experimental data and registration information. -- Oxford Molecular Group.
  

• RS3 Discovery HTS - (High Throughput Screening) RS3 Discovery application for plate management and laboratory automation. -- Oxford Molecular Group.
  

• SAP - Cheminformatics product for plate management. -- Oxford Molecular Group.
  

• SCARECROW: A program for the display of molecular structures and the analysis of molecular dynamics trajectories. -- 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.
  

• SIESTA periodic DFT code with a local-orbital basis set. Forces, optimization, MD. -- P. Ordegon.
  

• 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 (9, easy-to-use, complete set of methods), created by UCI Professor Warren Hehre, is a next-generation molecular modeling/computational chemistry program which embraces high performance computing and state-of-the-art visualization. SPARTAN provides chemists with modern theoretical techniques (molecular mechanics, semiempirical, ab initio, and DFT quantum mechanics) for the description of molecular structure and energetics, investigation of reaction mechanisms and elucidation of product distributions. Capabilities are accessed via an intuitive interface which includes molecule builders and interactive dialogs for input preparation and output analysis. SPARTAN displays structural models, orbitals, electron densities and electrostatic potentials as isosurfaces or slices. Computational components are fully parallelized. Additional SPARTAN features include five methods of conformational analysis, similarity/superpositioning, reaction coordinate simulation, calculation of quantitative structure activity relationship (QSAR) descriptors, and seamless interfaces with Gaussian, Allinger's MM3, IBM's Mulliken, and Schrodinger's PS-GVB software. SPARTAN runs on SGI, IBM, DEC Alpha, HP, and Cray. -- Shawn Butler/Jim Parisi, Wavefunction.
  

cyclic search
genetic search
protein builder
nucleotide builder
spreadsheet
transparency
symmetry identification
File Formats:

MDL .mol
Tripos .mol
Brookhaven .pdb
Mopac Input
Macromodel

Parms:

SYBYL, MM2, MM3
MMFF
MNDO, AM1, PM3(aq,hd)
MNDO/d
SM1, SM1a, SM2,SM3
PM3(tm)
STO-3G, 3-21G, 6-31G, 6-311G(*,**)
LDFT- SVWN

Props:

distance
angle
charges
Dipole moment
IR (Force)
UV (CI)
logP

MacSpartan

Cons:

no search
no DFT
no spectra
11 elements

Dimensions:

ab initio – 50 atoms/500 basis fcns
semiempirical –100 atoms

Parms:

SYBYL
AM1
AM1-SM2
-Atoms:

H
C - F
P - Cl
Br

3-21G(*)
-Atoms:

H
C - F
Si - Cl
Br
I

6-31G*
-Atoms:

H
C - F
Si - Cl

Output Sections:

Point group:
Cycle no:
Mulliken
electro fit
Dipole moments
Time for Properties
Time for Graphics

• 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.
  

MM(P)2, MM3, Sybyl

• SYBYL/3DB UNITY is Tripos' 3D-database and chemical information system. -- Tripos, Inc.
  

partial match 3-D search

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

• SYNGEN -- Jim Henderson, Brandeis University.
  

• 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.
  

• TINKER is a modular, general package for molecular mechanics and dynamics with some special facilities and parameter sets for peptides and proteins. Contains advanced algorithms for energy minimization, distance geometry and global search. Distributed with full source code, a User's Guide, and several examples and test molecule files, for building the package on many Unix variants, Windows 95/NT and Macintosh. Prebuilt executables limited to a maximum of 3000 atoms are also provided for Windows 95/NT and Power Macintosh. -- Jay Ponder.
  

Cons: no GUI
Parms:

TINKER polarizable multipole force field
AMBER-95
CHARMM
MM2, MM3
AMBER/OPLS and OPLS-AA

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 QSARs package to store and analyze structures, properties, and associated data. Based around an intuitive spreadsheet to easily bring together and manipulate both structural and property data. Works as front end to Corina, Charge, Cosmic, Asp, Vamp, Topkat, & RS3 For SGI. -- Oxford Molecular Group.
  

3D QSAR spreadsheet
fragment descriptor library
topological indices
statistical tools
neural net
nonlinear mapping
2D/3D/4D graph plotting
Univariate data analysis
Correlation matrices
Principal components analysis
ReNDeR and forward feed neural networks
cluster (including Ward) and cluster significance analysis
discriminant analysis
multiple regression
partial least squares
FIRM (a recursive partitioning algorithm)
Props:

Molecular mass, surface area and volume
R-group analysis with Verloop calculation
Moments of inertia
Dipole moments
logP and molar refractivity
Rotatable bond count
Kier and Hall (and similar) indices
Autocorrelograms
Atom and ring counting
Hydrogen bond donor/acceptor counting
Substructure counting
Lipinski's rules for screening for "drug-like" compounds

TOPKAT - Toxicology technology to assess various toxic metrics of chemicals and predict toxicity from molecular structure for Windows or SGI, and as server for TSAR. -- Oxford Molecular Group.

• TurboDFT - VWN, BP, ACM, BLYP
  

• TurboNMR - BIOSYM/Molecular Simulations Inc.
  

1H, 13C, 31P, etc.
ab initio shielding tensors
GIAO (Gauge-Independent Atomic Orbital)
Acc’y:

SCF/6-31G -

δΔ 1H ±0.2
δΔ 13C ±4

SCF/6-31G

δΔ 1H ±0.1
δΔ 13C ±2

Turbomole -- Reinhart Ahlrichs, University of Karlsruhe. BIOSYM/Molecular Simulations Inc.

Natural Internal Coordinates
semidirect SCF, MP-2
Props:

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

Parms:

STO-3G, 3-21G, 6-31G( *,**)
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

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 SGI, Cray, and IBM compute servers. Build molecules, predict molecular properties, and view 3D displays of MOs, charge density, and potentials with GUI. -- Oxford Molecular Group.
  

• CADPAC: ab initio Hartree Fock calculations.
  
• DGauss 3.0: a molecular DFT program for studying electronic, magnetic, & structural properties of atoms, molecules, & clusters. Includes metals. Also available for CAChe desktops on NT. -- 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

Parms:

VWN
BP
BLYP
BSPP

Props:

multipole moments
IR spectra
Raman frequencies
polarizability
NMR chemical shift
Density of States
photoelectron spectra
Population Analysis
-Mulliken
-Landis
-Nazer

MNDO96: 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
Parms:

MNDO
MNDO/H, MNDOc, MNDO/d
MINDO/3
CNDO/2
AM1
PM3
MP2
BWEN

Props:

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 - semiempirical molecular orbital package for optimization and property calculations on SGI. Relative of Ampac. -- Oxford Molecular Group.
  

semiempirical QM
electrostatic potentials
Natural Atomic Orbital Point Charges
Clark Solvation Model
Props:

ESR hyperfine coupling
C13 NMR shifts

Viewmol - a graphical front end for computational chemistry programs. Aid in the generation of molecular structures for computations and to visualize their results. Can make use of helper applications. For Linux, AIX, IRIX. file://ftp.osc.edu/pub/chemistry/software/SOURCES/C/viewmol.

Building and editing of molecules
periodic systems
Visualization geometry of a molecule
H-bonds, isosurfaces
Visualize trajectories
Animate normal vibrations or show as arrows
IR, Raman, and inelastic neutron scattering spectra
MO energy level or density of states diagram
basis functions, molecular orbitals, and electron densities
Display of forces acting on each atom
Formats:

TIFF, HPGL, PostScript files
MPEG
Rayshade
Discover, DMol/DSolid/DMol3, CAR
Gaussian 9x
Gulp
Mopac
Turbomole
Viewmol, CAR, MDL, PDB

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., Oxford Molecular Group.
  

• 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 parametrized 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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8/6/10 Ernie Chamot / Chamot Labs / / echamot@chamotlabs.com