Welcome to NetSci's
List of Software for Quantum Mechanics

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The Software Section of NetSci is accessed by hundreds of scientists every week. Our goal is to make this resource as comprehensive as possible. If your software program is not included, please send e-mail with a brief description, the categories under which your program should appear, the platforms supported, and contact information.

For programs currently listed in NetSci, please check the table and description and notify us of any changes or additions.

[ A, B, C ] -- [ D, E, F ] -- [ G, H, I ] -- [ J, K, L ]
[ M, N, O ] -- [ P, Q, R ] -- [ S, T, U ] --
[ V, W ] -- [ X, Y, Z]




--- A, B, C ---





 

ABCRATE is a computer program that calculates rate constants by generalized transition state theory (GTST) for atom-diatom reactions with collinear reaction paths. The program requires a user-supplied subprogram that, given the internal coordinates, can return the potential energy and its gradient at that geometry (sample subprograms for several systems are provided with ABCRATE). The reaction path for dynamics calculations is calculated as the path of steepest descent from the collinear saddle point, which is called the minimum-energy path (MEP). Vibrational modes are treated in curvilinear internal coordinates. The GTST methods include two versions of variational transition state theory (VTST), in particular canonical variational theory (CVT) and improved canonical variational theory (ICVT), and ABCRATE also includes the canonical unified statistical (CUS) model. All vibrational energy levels are quantized, and anharmonicity may be included by several options, including Morse and Wentzel-Kramers-Brillouin (WKB) anharmonicity for stretches and quartic and centrifugal oscillator anharmonicity for bends. Transmission coefficients to account for tunneling and nonclassical reflection may be included and the methods available for transmission coefficients include the minimum energy path semiclassical adiabatic ground-state method (MEPSAG, also called ZCT), the centrifugal-dominant small-curvature semiclassical adiabatic ground-state method (CD-SCSAG, also called SCT), the large-curvature ground- state method version 3 (LCG3, also called LCT), the least-action ground-state method (LAG, also called LAT), and the microcanonical optimized multidimensional tunneling method (muOMT). Reverse reaction rates are always determined by detailed balance.





 

ACES II is an ab initio Molecular Orbital program which uses many-body perturbation theory to derive correlation energy.

Contact:

Rodney Bartlett
Quantum Theory Project
University of Florida
362 Williamson Hall
Gainesville, FL 32611-8435
Tel: +1-352-392-1597
Fax: +1-352-392-8722
E-mail: aces2@qtp.ufl.edu




 

ADF (the Amsterdam Density Functional) program is available from:

Scientific Computing & Modelling NV
Theoretical Chemistry, Vrije Universiteit
De Boelelaan 1083
1081 HV Amsterdam, The Netherlands
http://www.scm.com
Tel: +31-20-5987626
Fax: +31-20-5987629
E-mail: sales@scm.com




 

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. Contact:

Michael Dupuis
IBM Corporation
Scientific and Engineering and Computations Department
Department 48B
Kingston, NY 12401 USA
Phone: 914-385-4965




 

AMPAC is a semiempirical quantum mechanics program developed by Michael Dewer 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. AMPAC is available as program number 506 from QCPE





 

AMPAC 4.0 with graphical user interface





 

AMSOL AMPAC with explicit solvation effects is available from:

Chris Cramer
The University of Minnesota
E-mail: cramer@maroon.tc.umn.edu
Web: QCPE

A commercial version also is available from

MakoLab, Computer Graphics Laboratory
Gdanska 80 Str., 90-613 Lodz, Poland
tel./fax (011)(48 42) 63 22 346, 63 99 716
US fax (909) 7526357
http://www.makolab.com/amsol




 

AOMix is a program for the molecular orbital (MO) analysis. It calculates the MO compositions in terms of the constituent chemical fragments (you can specify them as atoms, groups of atoms, atomic orbitals, fragment molecular orbitals, groups of atomic orbitals, etc.) in the molecule or atom. AOMix automatically processes output files of multiple quantum-chemical packages. AOMix also allows you to analyze chemical structure (bonding/antibonding nature of molecular orbitals) using overlap populations (total and per molecular orbital), 2-center (Mayer, Lowdin, Wiberg) and 3-center bond orders, charge decomposition analysis, CDA (total, per molecular orbital, per symmetry type), and condensed Fukui functions.





 

Argus is an electronic structure code; mainly for semi-empirical model Hamiltonians. It has been used mostly for spectroscopic calculations.





Ascalaph Quantum provides programs for a 3D graphic interface for the Quantum Mechanics program PC GAMESS as well as the generation and editing of molecular models.





 

Atomistix ToolKit (ATK) is a commercial package, made up of a state-of-the-art DFT code based on localized orbitals and a graphical user interface called Virtual NanoLab, linked together by a powerful Python-based scripting language, NanoLanguage. In addition to being able to compute the electronic structure of molecules and periodic systems, ATK has a unique capability to study open systems, where a finite bias is applied between two semi-infinite bulk-like electrodes. From these calculations, it is possible to extract the ballistic quantum tunneling current of nanoscale systems. This means that ATK can be used to investigate novel electronics application in carbon nanotubes, graphene, molecular electronics, nanowires, etc, as well as study the properties of complex interfaces, including high-k materials, and also magneto-tunnel junctions that e.g. can form the basis for future memory devices (MRAM). A particular focus of the development of the code is the ability to handle large-scale systems, meaning several thousand atoms. A new semi-empirical extension to ATK has just been released. More info at http://quantumwise.com/products/12-products/28-atk-se-200906

Kurt Stokbro
QuantumWise A/S
Nørre Søgade 27A, 1.th
1370 Copenhagen K
DENMARK
Tel: +45 699 01 888
Fax: +45 698 02 801
Email: info@quantumwise.com
URL: http://quantumwise.com




 

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. Contact:

Davide M. Proserpio
Universita di Milano Istituto di Chimica Strutturistica Inorganic Via Venezian 21
20133 Milano Italy
Tel: +38-2-70635120
Fax: +39-2-70635288




 

CADPAC (Cambridge Analytical Derivatives PACkage) is a quantum chemical program designed to calculate geometry, vibrational frequencies and a variety of molecular properties.

Roger Amos University Chemical Laboratory
Lensfield Road
Cambridge, CB2 1EW
Great Britian
Phone: 44-223-336384
Fax: 44-223-336362
E-mail at cadpac@theor.ch.cam.ac.uk




 

Cascade (Cascade Aids Semi-empiric Calculators Access Displays Eventually). Cascade V2 is a shell which converts semi-empirical data (from programs like MOPAC, AMPAC and VAMP) into several 3d graphic formats. It thus enables the user to visualize the resulting molecule geometry. The supported display programs are:3DV, Chemview, JMR, MOLWIN, MV, PC MODEL, PLUTON, POVRAY, RASWIN. You can get CASCADE via ftp at

Location 1 - CCL Archives

There are 3 files:

cascade2.rea -> the readme file (you have read in *)
cascade2.zip -> the program
install.exe -> this part installs CASCADE in the right way on your PC.

Please use the program install.exe to uncompress cascade.zip, otherwise you have to set the environment variables CASCADE and AWKDIR manually. If you have used install.exe, you can use cascade.bat to start cascade.

If you find any bugs or have any problems, think something should be changed, should be added or any thing else, feel free to contact:

Andreas Dosche at dosche@mi.uni-erlangen.de
Ralph Puchta at puchta@anorganik.chemie.uni-erlangen.de
Michael Reichenbacher at reichenb@mi.uni-erlangen.de




 

CASTEP (CAmbridge Serial Total Energy Package) is capable of simulating electronic relaxation to ground state for metals, insulators, or semiconductors. Using these techniques, CASTEP can calculate forces acting on atoms and stress on the unit cell. Atomic forces can be used either to find the equilibrium structure or to perform molecular dynamics simulation (either canonical or microcanonical ensemble).

The CETEP (Cambridge Edinburgh Total Energy Package) code is similar to CASTEP but designed to run on massively parallel supercomputers. This latter code was developed as part of the UKCP collaboration. Contact: Mike Payne, mcp1@phy.cam.ac.uk. URL: http://www.tcm.phy.cam.ac.uk/castep/





 

Cerius2 is a software environment designed to facilitate the chemical computing needs of R & D organizations. With Cerius2, scientists are able to apply the predictive power of computational chemistry to the critical issues in their research. WIth Cerius2 users can 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. QM modeling components include:

  • C2*ADF is an interface to the Amsterdam Density Functional Codes. C2*ADF allows you to perform electronic structure calculations that compute the structure, energetics, and properties of organic and inorganic molecules, transition-metals, and heavy-element compounds.

  • C2*CASTEP is 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. You can determine quantities such as geometric structure, energies, band-structures, and charge density.

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

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

The program is available from Accelrys





 

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. Obtain via anonymous FTP on our Internet node.

Contact:

Isaiah Shavitt
The Ohio State University
Department of Chemistry
120 West 18th Avenue
Columbus, OH 43210-1173 USA
Phone: 614-292-1668
Fax: 614-292-1685
shavitt@mps.ohio-state.edu (e-mail)




 

COSMOtherm is a QM based program which allows for general fluid phase property predicition (solubility, activity, partition coefficients, Henry's law constants, vapor pressure, pKa, etc...). We recently won the NIST competition on Fluid phase property predicition.

Contact

Dr. Andreas Klamt
COSMOlogic GmbH&CoKG
Burscheider Str. 515
51381 Leverkusen, Germany
Tel.: +49-2171-73168-1
Fax: +49-2171-73168-9
e-mail: klamt@cosmologic.de
web: http://www.cosmologic.de




--- D, E, F ---





 

Dalton is a complete, powerful quantum chemistry program for the calculation of molecular properties with SCF, MP2 or MCSCF wave functions. The strengths of the program are mainly in the areas of magnetic and (frequency-dependent) electric properties, and for studies of molecular potential energy surfaces, both for static and dynamical investigations, as well as stable algorithms for converging large MCSCF wave functions (also excited states). The program is distributed freely to all academic users, although we require all users to sign a copyright and license agreement. For more complete information on how to obtain a copy of the program, more information about what the program can and can not do, please check out our homepage at http://www.kjemi.uio.no/software/dalton/dalton.html, or send an e-mail to dalton-admin@kjemi.uio.no





 

DeFT can be obtained via ftp. However, it is NOT public domain software, and we'd ask you to observe the copyright and license agreement that come with the source code. All we ask in return is that all improvements be sent back to me so that we can make your improvements freely available to others. Such contributors will of course be appropriately recognized.

The code can basically locate local minima, locate transition states, perform vibrational analyses, with the use of analytic first derivatives. Sorry, no analytic second derivatives. DeFT uses gaussian functions and is therefore quite similar to DGauss. Both LSDA and NLSDA calculations can be performed.

The code can be obtained by ftp'ing theory.chem.uottawa.ca (137.122.43.156) with the username "DeFT_ftp". The filename is "DeFT_tarfile.Z", and it will be there in your home directory. However, to add an extra level of security, and to help me keep track of how many people are using the code, a password is required. People can obtain the password by e-mailing the following address:

request@theory.chem.uottawa.ca

Alain St-Amant will try to e-mail the password back as promptly as possible (hopefully, this should be within an hour or two, at worst, overnight if the request is sent late in the day). The password will remain valid for several days. The code, documentation, and sample inputs and outputs, once tar'ed and compressed, come out to about 800 kilobytes. Hopefully, the code will be of use to some, and improvements can be added by its new users.





 

DelPhi calculates electrostatic potential and solvation energy of both large and small molecules, including nucleic acids. The program uses an effective finite difference algorithm to solve the Poisson-Boltzmann equations. DelPhi is available from Accelrys





 

DMol is a density functional theory (DFT) based program for quantum mechanical calculations. It is available from Accelrys





 

ESOCS calculates the electronic and magnetic properties of solids. You can efficiently compute quantities such as the electronic structure of defects, optical absorption and reflection spectra, and magnetic properties of materials. ESOCS has wide application to metals, semiconductors, and inorganic pigments. It is also used for optimizing and designing magnetic materials in the disc drive industry. ESOCS is available from Accelrys





 

Fast Structure allows you to determine equilibrium geometries of crystals, interfaces, surfaces and molecules. It calculates structures using fast first principles density functional methods in conjunction with molecular dynamics, simulated annealing, and minimization techniques. FastStructure is used in the electronics, chemicals, petrochemicals, and glass industries. Fast Structure is available from Accelrys





--- G, H, I ---





 

GAMESS (General Atomic and Molecular Electronic Structure System) ab initio package.





 

GAR2PED is a Gaussian output postprocessing utility.





 

Gaussian 98 (®) provides a framework for the practical application of proven ab initio, density functional and semi-empirical electronic structure methods to chemical investigations. Detailed examination of molecular potential energy surface yields accurate molecular structures, properties, and reaction energetics. The properties that can be evaluated include vibrational frequencies, IR and Raman intensities, multipole moments, electrostatic potentials, polarizabilities, magnetic shielding tensors, magnetic susceptibilities, electron affinities, ionization potentials, and electrostatic potential derived charges. These results can then be used to predict thermodynamic properties, interpret molecular spectra, elucidate reaction mechanisms, and parameterize molecular mechanics calculations. Contact:

Gaussian, Inc.
Carnegie Office Park
Building Six
Pittsburgh, PA 15106 USA
Tel: 412-279-6700
Fax: 412-279-2118
E-mail: info@gaussian.com
http://www.gaussian.com/




 

GAUSSRATE is a set of FORTRAN subroutines and Unix scripts for interfacing the POLYRATE and GAUSSIAN 94 computer programs for the purpose of carrying out direct dynamics calculations of gas-phase chemical reaction rates of polyatomic species (and also atoms and diatoms as special cases) using the electronic structure methods available in GAUSSIAN 94 to calculate the potential energy surface and POLYRATE for the dynamics. The dynamical methods used are variational or conventional transition state theory and multidimensional semiclassical approximations for tunneling and nonclassical reflection. Rate constants may be calculated by any of the methods available in the POLYRATE program for canonical or microcanonical ensembles or for specific vibrational states of selected modes with translational, rotational, and other vibrational modes treated thermally. Bimolecular and unimolecular reactions are included. Both single-level and dual-level modes are available. In single-level mode, optimized geometries, potential energies, gradients and Hessians can be calculated by any of the ab initio or semiempirical methods in the GAUSSIAN 94 package. In dual-level mode, the lower-level data is calculated by GAUSSIAN 94, and the higher-level data is read from an external file.





 

Ghemical is a computational chemistry software package released under the GNU GPL. It means that full source code of the package is available, and users are free to study and modify the package. If you wonder about spelling in the package name, yes it's intentionally a bit "wrong" (originally inspired by the funny name of the excellent spreadsheet program Gnumeric), but feel free to pronounce it just in a way that is comfortable!



 

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. Contact:

Dr. Andrew Komornicki
Polyatomics Research Institute
1101 San Antonio Road, STE 420
Mountain View, CA 94043 USA
Tel: +1-415-964-4013




 

hmo10 is a Huckel molecular orbital calculator for students. It is available for DOS platforms free at http://www.simtel.net/pub/pd/42108.html or at the ftp address ftp://ftp.simtel.net/pub/simtelnet/msdos/chemistry/hmo10.zip





 

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. It is available as program number 544 from QCPE. The updated, commercial version (HONDO 95.3) is available from:

Michel Dupuis Dept. MLMA/MS078
IBM Corporation
Neighborhood Road
Kingston, New York 12401
Tel: 914-432-7996
Fax: 914-432-7373
E-mail: micheld@vnet.ibm. com




 

Huckel Calculator is available from Gerrit-Jan Linker. The user friendly Huckel calculator for Windows is available on the Huckel project pages. For general and download information check the web site at http://www.oraxcel.com/projects/huckel/

Features of Huckel:

  • Runs under Windows 3 and 95
  • Draw your structure formula as input
  • Receive results in graph and as text
  • Tutorial in help file
  • Huckel theory in help file

Comments or remarks can be sent to linker@ilovechocolate.com





 

ICON8 and FORTICON8 provide Extended Huckel 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. These programs are available as number 344 from QCPE





--- J, K, L ---





 

Jaguar Schrödinger, Inc.'s electronic structure software package, Jaguar (PS-GVB), is an extremely fast ab initio and density functional program that allows chemical accuracy for realistic systems in reasonable time for HF, DFT, MP2, GVB, GVB-RCI, and GVB-DFT methods. Most correlation methods in Jaguar can also be applied selectively to small areas of interest within a large system, reducing the cost of high-accuracy calculations significantly. The program can compute optimized geometries, transition states, frequencies, hyperpolarizabilities, electrostatic potential fitted charges, and numerous other properties. Jaguar's solvation module can compute accurate solvation energies, charges, geometries, and transition states for solvated systems. All of these calculation options are easily available to the user through a graphical user interface. Contact

Schrödinger, Inc.
1500 S.W. First Avenue, Suite 1180
Portland, OR 97201-5815
Phone: +1 503 299-1150
Fax: +1 503 299-4532
email: info@schrodinger.com
http://www.schrodinger.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. Contact:

Michael Dupuis
IBM Corporation
Scientific and Engineering and Computations Department
Department 48B
Kingston, NY 12401
Tel: 914-385-4965




--- M, N, O ---





 

SPARTAN'04 for Macintosh is the latest molecular modeling application from Wavefunction supporting G4 or higher and Intel Chip Macs running Tiger 10.4.6 OS or higher. This new version adds to user interface features including builders for organic and inorganic molecules, peptides and nucleotides. Included is the Spartan Molecular Database of over 60,000 molecules pre-calculated at up to 5 quantum mechanical theory levels. Offering substantial ease-of-use with internal spreadsheets and plotting tools for organizing your data, custom clipboards, and file import/export features including: SYBYL MOL and MOL2, PDB, MacroModel, SD Files, XYZ and Smiles files, with graphical export of JPEG, PNG, and QuickTime formats.

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

  • Mulliken, electrostatic-fit and natural-bond-orbital (NBO) charges
  • Dipole moments and higher moments
  • Polarizabilities and Hyperpolarizabilities
  • Ovality
  • Electronegativity and hardness
  • Enthalpies, entropies and free energies
  • Highest Occupied and Lowest Unoccupied Molecular Orbital Energies (and homo/lumo gaps)
  • Aqueous solvation energies
  • LogP
  • NMR Chemical shifts (Hartree-Fock)
  • UV/vis excitation energies from CIS and TDDFT models
  • Display of molecular orbitals, electron densities, contour displays
  • Display spin densities and electrostatic potentials as isosurfaces
  • Display ionization potentials
  • Composite surface maps
  • Ribbon displays for biopolymers
  • Display of hydrogen bonds

Available computational methods:

  • SYBYL, MMFF94, and MMFF(aq) molecular mechanics
  • MNDO, MNDO/d, AM1 and PM3 including PM3 parameters for transition metals Semi Empirical MO Models
  • Hartree-Fock molecular orbital
  • Local, SVWN, BP, BLYP, EDF1 and B3LYP density functional for ground and excited states
  • MP2, MP3, MP4, and LMP2
  • CCSD, CCSD(T), OD, and OD(T)
  • G2, G3, and G3 (MP2) Thermochemical Recipes
  • QCCD and QCCD(T)
  • QCISD and QCISD(T)
  • CIS and CIS(D), for excited states
  • STO-3G, 3-21G, 6-31G*, 6-311G*, cc-pVDZ, cc-pVTZ and cc-pVQZ all-electron basis sets, additional polarization and/or diffuse functions - additional and custom basis sets available Pseudopotential basis sets for calculations on molecules with heavy elements

Contact:

Sean Ohlinger/Nathan Dacuycuy/Kristin Robinson
Wavefunction, Inc.
18401 Von Karman Ave, Suite 370
Irvine, CA 92612
Tel: (949) 955 2120
Fax: (949) 955 2118
Email: sales@wavefun.com
URL: http://www.wavefun.com




 

MESSKit is a suite of highly modular ab initio electronic structure codes developed by Professor Jack Simons' group at the University of Utah. Please see the documentation on individual modules for specific functionalities. The programs are available via ftp at ftp.chem.utah.edu - (MESSKit is located in /pub/messkit). Login as user 'anonymous' and use your email address as the password. Make sure the transfer is binary,i.e. type 'binary' once logged in. The ftp daemon is a little picky, so you may not be able to see a 'full' directory listing (one generated by dir or ls -l), just use the 'ls' command. To get MESSKit, type the following at the ftp> prompt -- get MESSKIT-v2.021.tar.Z





 

MOLCAS is a general computer software for electron structure calculations, which emphasizes the use of high quality basis set, the importance of an adequate treatment of electron correlation, and general applicability to closed and open shell systems, to ground and excited states with a balanced treatment. Even if contains programs for single reference calculations, such as MP2, SDCI, Coupled Pair Functional (CPF) or full fourth order MBPT, the main emphasis is on the multiconfigurational approach to the electron correlation problem. The software includes codes for multiconfigurational SCF calculations, using both Complete and Restricted Active Space (CAS or RAS) type wave functions. These wave functions can be used as reference in subsequent Multi-Reference (MR) CI, or Average Coupled Pair Functional (ACPF) calculations. For additional information, check the MOLCAS Website at URL: http://www.teokem.lu.se/molcas/





 

MOLPRO is a complete system of ab initio programs for molecular electronic structure calculations, written and maintained by H.-J. Werner and P. J. Knowles, and containing contributions from a number of other authors. As distinct from other commonly used quantum chemistry packages, the emphasis is on highly accurate computations for small molecules, with extensive treatment of the electron correlation problem through the multiconfiguration-reference CI, coupled cluster and associated methods. The programs run on Cray (C90, Unicos 9.0), IBM (RS/6000, AIX 4.1.3), Hewlett-Packard (800 series, HP-UX 9.05), and Silicon Graphics (IRIX 6.2, R4000, R8000 and R10000) systems. Contact:

Prof. Peter J. Knowles
School of Chemistry
University of Birmingham
Edgbaston, Birmingham
B15 2TT, UK. Telephone: +44-121-414-7472
Fax: +44-121-414-7471,
E-mail: molpro-request@tc.bham.ac.uk
URL: http://www.tc.bham.ac.uk/molpro/




 

MOLSCAT is a code for quantum mechanical (coupled channel) solution of the nonreactive molecular scattering problem. Code is implemented for various types of collision partners. In addition to the essentially exact close coupling method several approximate methods, including the Coupled States and Infinite Order Sudden approximations, are provided. The code is in near standard FORTRAN 77 and has been ported to a large number of platforms. The source code supplied was run at this site on an IBM RS/6000 and also on IBM and compatible mainframes. It should work on most other machines; for the Cray, however, modifications to run in single precision should be made.





 

MOMEC a new program for modeling transition metal complexes. MOMEC was developed by Drs. Peter Comba and Trevor Hamley. The program is available from Heinz Hofmann, E-mail: 100411.2306@compuserve.com





 

MOPAC (Molecular Orbital PACkage) is a general purpose semiempirical molecular orbital package developed by J.J.P. Stewart and co-workers. 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 and is available from QCPE





 

Mopac 2000 is a general-purpose semiempirical quantum mechanics package for the study of chemical properties and reactions in gas, solution or solid-state. MOPAC 2000 directly predicts numerous chemical and physical properties such as Gibbs free energies, activation energies, reaction paths, dipole moments, non-linear optical properties and infrared spectra. It is also used as the basis of quantitative structure-property (or activity) relationships (QSAR), to predict a wide variety of biological and other properties such as carcinogenicity, vapor pressure, water solubility, and reaction rates. MOPAC 2000 is available from Schrödinger.





 

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.





 

Mulliken - an accurate, reliable ab initio calculations for large molecules with a powerful graphical interface and optimized performance. The product is no longer available.





--- P, Q, R ---





 

SPARTAN'06 for Windows is the latest molecular modeling application from Wavefunction supporting Windows 2000 or higher. This new version adds to user interface features including builders for organic and inorganic molecules, peptides and nucleotides, a substituent builder (for combinatorial libraries) and a 2-D builder utilizing ChemDraw (must be licensed separately). Included is the Spartan Molecular Database of over 1400,000 molecules pre-calculated at up to 8 quantum mechanical theory levels. Offering substantial ease-of-use with internal spreadsheets and plotting tools for organizing your data, custom clipboards, and file import/export features including: SYBYL MOL and MOL2, PDB, MacroModel, SD Files, ChemDraw Files, XYZ and Smiles files, with graphical export of BitMap, JPEG, PNG, and AVI formats.

Spartan for Windows will determine equilibrium and transition state geometries; identify lowest energy conformers and generate conformational and Boltzmann distributions (with optional use of NOE data); create conformational libraries of the minimum number of conformers to span conformational space, align molecules, score molecular similarities based on 3D superposition of atom positions of chemical function (pharmacophore) descriptors, scan geometrical coordinates; generate reaction sequences and generate and follow intrinsic reaction coordinates; calculate reaction and activation energies; calculate and plot IR, NMR, and UV/vis spectra and retrieve/plot experimental spectra data from NIST and University of Cologne web-based datasets; search the Spartan Molecular Database, the Cambridge Structural Database (requires separate license), retrieve structures from the Protein Data Bank and optionally extract bound small molecules. These tasks elucidate a host of numerical data, graphical data and properties including:

  • Mulliken, electrostatic-fit and natural-bond-orbital (NBO) charges
  • Dipole moments and higher moments
  • Polarizabilities and Hyperpolarizabilities
  • Ovality
  • Electronegativity and hardness
  • Enthalpies, entropies and free energies
  • Highest Occupied and Lowest Unoccupied Molecular Orbital Energies (and homo/lumo gaps)
  • Aqueous solvation energies
  • LogP
  • NMR Chemical shifts (Hartree-Fock)
  • UV/vis excitation energies from CIS and TDDFT models
  • Display of molecular orbitals, electron densities, contour displays
  • Display spin densities and electrostatic potentials as isosurfaces
  • Display ionization potentials
  • Composite surface maps
  • Ribbon displays for biopolymers
  • Display of hydrogen bonds

Available computational methods:

  • SYBYL, MMFF94, and MMFF(aq) molecular mechanics
  • MNDO, MNDO/d, AM1 and PM3 including PM3 parameters for transition metals Semi Empirical MO Models
  • Hartree-Fock molecular orbital
  • Local, SVWN, BP, BLYP, EDF1 and B3LYP density functional for ground and excited states
  • MP2, MP3, MP4, and LMP2
  • CCSD, CCSD(T), OD, and OD(T)
  • G2, G3, and G3 (MP2) Thermochemical Recipes
  • QCCD and QCCD(T)
  • QCISD and QCISD(T)
  • CIS and CIS(D), for excited states
  • STO-3G, 3-21G, 6-31G*, 6-311G*, cc-pVDZ, cc-pVTZ and cc-pVQZ all-electron basis sets, additional polarization and/or diffuse functions - additional and custom basis sets available Pseudopotential basis sets for calculations on molecules with heavy elements

Contact:

Sean Ohlinger/Nathan Dacuycuy/Kristin Robinson
Wavefunction, Inc.
18401 Von Karman Ave, Suite 370
Irvine, CA 92612
Tel: (949) 955 2120
Fax: (949) 955 2118
Email: sales@wavefun.com
URL: http://www.wavefun.com




SPARTAN'06 for Linux is the latest molecular modeling application from Wavefunction supporting RedHat Enterprise 4 or later, SUSE 9.1 orSLSE 0.0 or later with both 32 and 64 bit implementations. This new version adds to user interface features including builders for organic and inorganic molecules, peptides and nucleotides, and a substituent builder (for combinatorial libraries). Included is the Spartan Molecular Database of over 1400,000 molecules pre-calculated at up to 8 quantum mechanical theory levels. Offering substantial ease-of-use with internal spreadsheets and plotting tools for organizing your data, custom clipboards, and file import/export features including: SYBYL MOL and MOL2, PDB, MacroModel, SD Files, XYZ and Smiles files, with graphical export of BitMap, JPEG, and PNG formats.

Spartan for Linux will determine equilibrium and transition state geometries; identify lowest energy conformers and generate conformational and Boltzmann distributions (with optional use of NOE data); create conformational libraries of the minimum number of conformers to span conformational space, align molecules, score molecular similarities based on 3D superposition of atom positions of chemical function (pharmacophore) descriptors, scan geometrical coordinates; generate reaction sequences and generate and follow intrinsic reaction coordinates; calculate reaction and activation energies; calculate and plot IR, NMR, and UV/vis spectra and retrieve/plot experimental spectra data from NIST and University of Cologne web-based datasets; search the Spartan Molecular Database, the Cambridge Structural Database (requires separate license), retrieve structures from the Protein Data Bank and optionally extract bound small molecules. These tasks elucidate a host of numerical data, graphical data and properties including:

  • Mulliken, electrostatic-fit and natural-bond-orbital (NBO) charges
  • Dipole moments and higher moments
  • Polarizabilities and Hyperpolarizabilities
  • Ovality
  • Electronegativity and hardness
  • Enthalpies, entropies and free energies
  • Highest Occupied and Lowest Unoccupied Molecular Orbital Energies (and homo/lumo gaps)
  • Aqueous solvation energies
  • LogP
  • NMR Chemical shifts (Hartree-Fock)
  • UV/vis excitation energies from CIS and TDDFT models
  • Display of molecular orbitals, electron densities, contour displays
  • Display spin densities and electrostatic potentials as isosurfaces
  • Display ionization potentials
  • Composite surface maps
  • Ribbon displays for biopolymers
  • Display of hydrogen bonds

Available computational methods:

  • SYBYL, MMFF94, and MMFF(aq) molecular mechanics
  • MNDO, MNDO/d, AM1 and PM3 including PM3 parameters for transition metals Semi Empirical MO Models
  • Hartree-Fock molecular orbital
  • Local, SVWN, BP, BLYP, EDF1 and B3LYP density functional for ground and excited states
  • MP2, MP3, MP4, and LMP2
  • CCSD, CCSD(T), OD, and OD(T)
  • G2, G3, and G3 (MP2) Thermochemical Recipes
  • QCCD and QCCD(T)
  • QCISD and QCISD(T)
  • CIS and CIS(D), for excited states
  • STO-3G, 3-21G, 6-31G*, 6-311G*, cc-pVDZ, cc-pVTZ and cc-pVQZ all-electron basis sets, additional polarization and/or diffuse functions - additional and custom basis sets available Pseudopotential basis sets for calculations on molecules with heavy elements

Contact:

Sean Ohlinger/Nathan Dacuycuy/Kristin Robinson
Wavefunction, Inc.
18401 Von Karman Ave, Suite 370
Irvine, CA 92612
Tel: (949) 955 2120
Fax: (949) 955 2118
Email: sales@wavefun.com
URL: http://www.wavefun.com




 

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, ion charges, etc.) are handled transparently. Bond dipoles and lone pair sites can be included. A complete error analysis is made. Contact:

Donald E. Williams
Department of Chemistry
University of Louisville
Louisville, KY 40292
email:dewill01@homer.louisville.edu.




 

PDM97: Least-Squares Fitting of the Molecular Electrostatic Potential With Net Atomic Charges and/or Multipoles.





 

PSI-88 is a program used to plot wavefunctions in three dimensions from semi-empirical and most popular ab initio basis sets. Valence semi-empirical, STO-3G, 3-21++G(*) and 6-31++G(d,p) basis sets are implemented for atoms H-Ar. The program can be obtained by anonymous ftp from rani.chem.yale.edu Go to the /pub/psi88 directory to find the program and documentation. Contact:

William L. Jorgensen
Department of Chemistry
Yale University
P.O. Box 6666
New Haven, CT 06511, USA.
Phone (203) 432-6288
Fax (203) 432-6144




 

Q-Chem, an integrated ab initio quantum chemistry software package, greatly improves the speed and accuracy of calculations already being performed while accommodating far larger molecular structures than ever before possible. By solving theoretical problems far faster than other programs and with no loss in accuracy, Q-Chem will allow researchers to quickly and accurately analyze molecules of several hundred atoms, bringing the power of quantum chemistry to critical research projects for which this tool was previously unavailable. The current limit for most existing quantum chemistry software for practical research is approximately 100 atoms.

Q-Chem is interfaced with familiar graphical user interfaces (GUIs) including HyperChem(TM) from HyperCube, Inc. and UniChem(TM) from Oxford Molecular Group which will allow users an easier transition to the Q-Chem package.

Q-Chem incorporates advanced technology including the Continuous Fast Multipole Method (CFMM) for calculating the Coulomb energy and the latest version of Dr. Jon Baker's Optimize package containing a suite of state-of-the-art algorithms for geometry optimization. "Many of the capabilities for geometry optimization in Q-Chem are currently not available anywhere else", states Dr. Jon Baker.

Other Q-Chem features include the Quantum Chemical Tree Code (QCTC) for linear scaling calculations of the Coulomb matrix and ONX (order N computation of the Exact Exchange Matrix) which are algorithms that are numerically equivalent to conventional direct SCF, but scale linearly for complicated 3-D systems like water clusters and protein molecules.

Contact:

Jing Kong
Chief Scientist
Q-Chem, Inc.
Four Triangle Lane
Export, Pennsylvania
Telephone: 724-325-9969
Fax: 724-325-9560
Info@q-chem.com
http://q-chem.com/




 

Qmol is a program for viewing molecular structures and animating molecular trajectories. Originally based on the molview demo program by Mark Kilgard (from his book, Programming OpenGL for the X Window System) and inspired by the Xmol program. Qmol is similar to programs like VMD , MolMol , weblab, Swiss-Pdb Viewer, MolScript, RasMol, gOpenMol and ICM, but opts for a fast, easy to use user interface with a set of features focused on the display of proteins and small molecules. It supports the following (on the Windows platform - features under *uix are unfortunately rather limited):

  • Display wire frame, stick figure, ball and stick, point, space-filling, solid and flat ribbon, trace and tube molecular structures from a PDB file.
  • Display of multiple molecular models (as used in NMR).
  • Animate molecular trajectories stored in a DCD (i.e. CHARMm/Xplor binary trajectory) file in either big- or little-endian formats.
  • Kabsch rotate all structures in a trajectory against the initial structure.
  • Interactively measure bond lengths, bond angles and torsion angles.
  • Dynamically adjust user selected torsion angles.
  • Display atom labels.
  • Display coordinate axis.
  • Dynamic modification of the color scheme (including color-by-element, color-by-atom-number, color-by-residue-number, color-by-temperature and color-by-occupancy).
  • Dynamic lighting.
  • Adjust atomic radii (including radii-by-temperature and radii-by-occupancy).
  • Print to any Windows supported printer and copy images to the Windows clip board.
  • Generate AVI movies from a molecular trajectory.
  • Assign secondary structure via the STRIDE program.
  • Stereo view.
  • Directly query the Protein Data Bank and display the resulting structure.
  • Detect and display hydrogen bonds (using the energetic criterion of Kabsch and Sander).
  • Use the wheel mouse to zoom in and out.
  • NEW: User defined clipping plane with rendered sphere/plane intersections.
  • NEW: Paste temperature and occupancy PDB fields from the windows clipboard.

Qmol (written by Jason D. Gans) is available from DNAStar (http://www.dnastar.com/qmol/).



 

QuanteMM combines quantum mechanics and molecular mechanics, allowing you to use accurate first-principles methods to study a reaction center while taking the surrounding environment fully into account. Large and complex systems like zeolite pores, enzyme active sites, and metal oxide surfaces can be studied with high accuracy. It is available from Accelrys





 

Reaction Patterns visualizes, interprets, and analyzes chemical reactivity and reactions. It combines kinetic models and the analysis of quantum mechanical energy surfaces to give you an insight into fundamental chemical processes. It is available from Accelrys





 

RPAC Molecular Properties Package, Version 11.0 (1996) from the University of Copenhagen, Denmark. Contacts: Thomas D. Bouman, Aage E. Hansen, Keld L. Bak, Thomas B. Pedersen, and Robert A. Kirby. The program is Copyright 1996 by:

Aage E. Hansen
Department of Chemistry
H.C. Orsted Institute
University of Copenhagen
DK-2100 Copenhagen, Denmark

Program RPAC is a post-SCF package that computes electronic excitation and response properties in first-order (RPA/CHF) and second-order (SOPPA/SOLO) linear response theory. Electronic excitation properties include transition energies, oscillator and rotatory strengths, rotatory strength tensors, transition densities and excitation charge rearrangements. Electronic ground state response properties include nuclear magnetic shielding tensors, atomic polar and axial tensors for vibrational circular dichroism (CHF level only), and static and dynamic dipole polarizabilities. It provides analyses in molecular structural terms (not implemented for rotatory strength tensors) and output for graphic displays. Routines for graphical displays are included as stand alone programs in the distribution package. As a post-SCF package, RPAC 11.0 must be interfaced to an appropriate SCF program and it is assumed that such SCF packages are operated under proper license.

Distribution Policy: RPAC 11.0 is distributed free of charge and is ported onto a number platforms. The user is provided with source code, test files, and manual. To obtain a copy of RPAC 11.0, e-mail to Dr. Aa. E. Hansen at aaeh@rpac.ki.ku.dk and request the appropriate release form. When this form has been signed by the user and a responsible officer then ftp site information will be provided which will permit one to obtain RPAC 11.0.





--- S, T, U ---





 

SciAn (Scientific Visualization and Animation is a scientific visualization and animation package for Silicon Graphics workstations and IBM RS/6000 workstations with the GL option. It is being developed at the Supercomputer Computations Research Institute at Florida State University with the support of the U. S. Department of Energy and the State of Florida.

SciAn brings together the power of 3-dimensional scientific visualization and movie making with the ease of use and familiarity of object-oriented drawing packages. SciAn makes it very easy to apply visualization to new data by minimizing the work a researcher needs to do before seeing the first image on the screen. Once there is an image to work with, the researcher can modify the visualization to bring out details in the data using a wide variety of controls. The immediacy and directness of SciAn encourages the use of visualization as an important part of the research process itself.

In addition, there is a collection of 3 academic programs which facilitate visualization of some G94 output files data using SciAn. The programs are:

  • Transcube : convert G94 "CUBE" files to SciAn "STF" files, in order to visualize electronic density, electrostatic potential, or molecular orbitals.

  • transfreq : convert G94 output files (with vibrational analysis), in order to visualize vibrational frequencies (as arrows) with SciAn. (you must have an "NFF" file (created with Molnff for example) to visualize your molecule).

  • Molnff : creates SciAn "NFF" file from a G94 output, in order to visualize your molecule with SciAn (this is a first version, the next one will automatize the molecule creation).

These programs are available at URL: http://134.157.11.11/Pages/LECA/GP/Laurent/soft.html. Please notify Laurent Joubert (E-mail: joubert@ext.jussieu.fr) before downloading the files. Contact:

Laurent Joubert
Ecole Nationale Superieure de Chimie de Paris
Laboratoire d'Electrochimie et de Chimie Analytique
11 rue Pierre et Marie Curie
75231 PARIS CEDEX 05- FRANCE
Tel : 44-27-66-94
Fax : 44-27-67-50




 

SIBFA (Sum of Interactions Between Fragments Ab initio computed) is available at:

http://www.ccl.net/cca/software/SOURCES/FORTRAN/sibfa/
and
ftp://ftp.ccl.net/pub/chemistry/software/SOURCES/FORTRAN/sibfa/

SIBFA is molecular mechanics procedure which was formulated and calibrated on the basis of ab initio computations. Its purpose is the computation of inter- and intramolecular interactions involving molecules of biological interest, and molecules of interest in organic chemistry. The package includes the Fortran computer program, and several sample input data. Comments about the present package are welcome. Please address them to:

Nohad Gresh
Laboratoire de Pharmacochimie Moleculaire
UMR 8600 CNRS, U266 INSERM
4, Avenue de l'Observatoire
75006 Paris, France.
e-mail: gresh@bisance.citi2.fr
Fax. 011 33 1 43 26 69 18




 

SPARTAN, 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. Contact:

Shawn Butler/Jim Parisi
Wavefunction, Inc.
18401 Von Karman, Suite 370
Irvine, CA 92715
Tel: (714)660-6101
Fax: (714)955-2118
e-mail: macsales@wavefun.com
URL: http://www.wavefun.com




 

Titan is the union of Wavefunction's versatile, easy-to-use Spartan interface with fast, computational algorithms from Schrödinger's Jaguar. It is available from Schrödinger.





 

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. The program is available from COSMOlogic.





 

UniChem is a set of Cray-based ab initio programs. UniChem was last supported by Oxford Molecular Group, which is now a part of Accelrys.





--- V, W ---





 

Vamp - an exceptionally powerful semiempirical molecular orbital package. Available from Accelrys





--- X, Y, Z ---





 

ZINDO is a semi-empirical molecular-orbital program for studying the spectroscopic properties of molecules and complexes. ZINDO can be applied to a wide range of compounds, including organic and inorganic molecules, polymers, and organometallic complexes. ZINDO is available from Accelrys



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