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Software Collection at the Emerson Center

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The Emerson Center application software packages can be divided into three difference categories:

Electronic Structure Codes Biomolecular Modeling & Visualization Software Databases
Gaussian-03 Cerius2_4.2 QCLDB
Molpro-2006 Sybyl_6.7 MDL
Gamess-2006 MacroModel_7.1 Cambridge Crystall Database
Dalton_2.0 AMBER_6.0  
AcesII_4.0 HyperChem  
Molcas_4.0 Spartan  
Mopac-7 MM3  
Columbus-5.7 Mathematica_5.2  
TurboMol TINKER 4.2  
Hondo Molden  

I. Electronic Structure Codes:

Gaussian_03: Gaussian is a powerful electronic structure program. It is designed to model a broad range of molecular systems under a variety condition. Gaussian can predict the energies, molecular structures, vibrational frequencies and numerous molecular properties for systems in the gas phase and in solution, and it can model both their ground state and excited states. Chemists can apply these fundamental results to their own investigations, using it to explore chemical phenomena like substituent effects, reaction mechanisms and electronic transitions. Users with experimental background can use this program to study molecules and reactions of definite or potential interest, including both stable species and those compounds which are difficult or impossible to observe experimentally (short-lived intermediates and so on). Gaussian includes many features specially designed to bring large molecular systems within reach of electronic structure methods. Advanced optimization algorithms and other efficiency innovations make semi-empirical geometry optimizations practical for larger molecules than ever before. See:
How to use, see:

Gamess_2006. This code, like Gaussian, allows to (a) optimize the geometries of the molecules, (b) search for transition states, (c) calculate the energetic, transition dipoles, vibrational frequencies, force constants, intensities for vibrations, polarizabilities and hyperpolarizibities, Mulliken population analysis, multipole moments, electrostatic potential, atomic charges, (d) thermochemistry using arbitrary isotopes, temperature and pressure, etc. This package includes Effective-Fragmentation-Method for large molecule calculation, while Gaussian includes ONIOM method. Gamess also includes the (a) Vibrational Self-Consistent-Field (VSCF) method, (b) Methods for evaluation of spin-orbit coupled constants, (c) Methods evaluating analytic frequency dependent non-linear optical polarizability properties, (d) Methods allowing to take into account the solvent effects, effective fragment potentials (EFP), polarizable continuum model (PCM), conductor-like screening model (COSMO), and self-consistent reaction field (SCRF).
How to use, see:

Molpro_2006. This program design for calculation of the spectroscopic parameters of small systems with high accuracy. As distinct from other commonly used quantum chemistry packages, the emphasis is on highly accurate computations, with extensive treatment of the electron correlation problem through the multiconfigurational reference CI, coupled cluster and associated methods. The heart of the program consists of the multiconfgurational SCF, multireference CI, and coupled cluster routines, and these are accompanied by a full set of supporting features. See:
How to use, see;

AcesII_3.0. Major strengths of this program are in performing calculations using "many-body" methods to treat electron correlation. These approaches, broadly categorized as many-body perturbation theory (MBPT) and the coupled-cluster (CC) approximation, offer a reliable treatment of correlation and have the attractive property of size-extensivity, meaning that energies scale properly with the size of the system. As a result of this property, MBPT and CC methods are ideally suited for the study of chemical reactions. See:
How to use, see:

Dalton_2.0: This program allows to calculate the molecular properties based on SCF, MP2, MCSCF, and CCSD reference wavefunctions. Using this program you can calculate: (a) Geometries and transition states, (b) Frequencies, (c) Electric properties (Dipole, Quadruple moments, nuclear quadruple coupling constants, polarizabilties), (d) Magnetic properties (magnetizabilities, nuclear shielding constants, rotational g tensor, nuclear spin-rotation constants, spin-spin coupling constants, hyperfine coupling tensors), (e) Optical and Raman properties (Vibrational Circular Dichrosm, electronic Circular Dichroism, electronic adsorption, Raman Optical Activity), and more. See:

How to use, see;

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 toclosed and open shell systems, to ground and excited states with a balanced treatment. Even if Molcas contains programs for single reference calculations, such as MP2, ci-sd, cpf or MBPT, the main emphasis is on the multiconfigurational approach to the electron correlation. The software includes codes for multiconfigurational SCF calculations, using both Complete and Restricted Active Space (CAS and RAS) type wave functions. However, the unique feature of Molcas is the possibility to use multiconfigurational second order perturbation theory (CASPT2). See:
How to use,see EC staff.

HONDO. Hondo uses single configurational SCF, generalized valence bond GVB, multiconfigurational SCF and CI wavefunctions to calculate geometries, frequencies, one-electron properties of the middle-sized molecules and potential energy surfaces of the chemical reactions. The unique feature of Hondo is the possibility to calculate seam-of-crossing of different potential energy surfaces. How to use, see EC staff.

CADPAC. Cambridge Analytic Derivatives PACkage is a suite programs which originate from the Hondo. Its gradient routines have been altered from those in the original Hondo, the method have been changed to one which is more efficient and easier to extend to Higher-order derivatives. These routines also work for f-function. Using this program you can calculate energies, wavefunction, geometries, frequencies, and highest-order derivatives of energy.
How to use, see:

II. Biomolecular Modeling and Visualization Software:

Sybyl_6.7. Sybyl/UNITE is a suite of molecular mechanics and molecular dynamics programs. Our version of Sybyl includes, Sybyl/Base, Advances Computing, Biopolymers, Dynamics, Molcad, FlexX, QSAR, UNITY and many other modules. The foundation of the Sybyl design and analysis environment, Sybyl/Base, includes comprehensive tools for molecular modeling: structure building, optimization and comparison; visualization of structures and associated data; annotation, hardcopy and screen capture capabilities. A wide range of force fields is provided including, Tropos, Amber, MMFF94 and MMFF94s. Sybyl supports detailed molecular analysis with the chemically-aware Molecular Spreadsheet to organize, visualize and interpret results. Sybyl Programming Language makes Sybyl/Base a dynamic computing environment for building tools and customizing strategies to achieve discovery goals. Advance Computing module provides a wide range of tools for conformational analysis that enumerate all possible torsional states of a molecule or identify just its low-energy conformations. The Dynamic component of Advance Computing simulates the movements of atoms for purposes of conformational sampling, understanding molecular movements over time, and reproducing thermodynamic propoerties. Molcad generates striking displays that communicate key surface properties of both large and small molecules. It creates electron density and Connolly solvent-accessible surfaces onto it maps lipophilicity, electrostatic potential, hydrogen bonding sites and other properties. Confort performs exhaustive yet rapid conformational analyses of drug-sized molecules. It generates a maximally diverse subset of conformers, identifies the global minimum energy conformer, or loctes all local minima within a user-specified energy range. Confort's diverse conformers can be used for receptor-ligand docking studies, Unity-3D database searches starting from multiple conformations, pharmacophore perception using DISCOtech, and multi-conformer 3D-QSAR methods in QSAR with CoMFA. Unity locate compounds in databases that match a pharmacophore or fit a receptor site. FlexX flexibly docks ligands into binding sites, allowing virtual screening of compound databases. Biopolymer delivers an extensive set of tools for building, visualizing, manipulating and predicting the 3D structure of biological molecules including proteins, peptides, nucleaic acids and polysaccharidies. See:
How to use, see EC staff.

MacroModel_7.1. MacroModel is designed to minimize the energy of one or series of structures, to eliminate duplicate conformations, to do conformational search and to conduct molecular dynamic simulations, including free-energy perturbation methods and mixed-mode Monte-Carlo/stochastic dynamic procedures. It includes MM2, MM3, Amber, OPLS, OPLS-AA, and MMFF94s force fields. User-friendly, front-end Maestro makes preparation of input files and analysis of the output files very easier.
How to use, see: EC staff

Amber_6.0. Amber_6.0 is an another molecular mechanics and molecular dynamics program. Briefly, user could perform minimization of different conformer using original amber force fields, as well as to do: (a) the particle-mesh-Ewald analysis for molecular dynamics, (b) NMR refinements, which can be carried out with restraints derived from residual dipolar coupling measurements, or with "ambiquous" restraints whose corresponding NMR spectra are not fully assigned, or for "multiple-conformer" models generated using the LES algorithm, (c)Solvent interactions can be approximated with a pairwise generalized Born model that uses continuum solvent ideas to simulate the electrostatic effects of water and of added counterions, (d) The trajectory analysis could be perform, including time correlation functions of interest in NMR and fluorescene anisotropy decay, and many others.
How to use, see: EC staff

Cerius2_4.2. This software package also includes multiple modules. Our version includes, Visualiser, CrystalBuilder, Open force field, Molecular Dynamics and Molecular Mechanics minimizer. Using these modules you can build a crystal from molecules, minimize structures, run dynamic simulation, visualize your results and more. See:
How to use, see: EC staff

HyperChem. A molecular modeling and simulation program that lets to perform complex chemical calculations. It includes many fuctions such as: constructing proteins and nucleic acids from standard residues; solvating molecules in a periodic box; drawing molecules from atoms and converting them to three-dimentional models; determining of isotop effects and much more. See:
How to use, see: EC staff

IDL. Interactive Data Language is a complete computing environment for the interactive analysis and visualization of data. It integrates a powerful, array-oriented language with numerous mathematical analysis and graphic display techniques. Programming in IDL is a timesaving alternative to programming in Fortran or C. IDL includes many numerical and statistical analysis routines (such as Numerical Recipes routines) are provided for analysis and simulation of data. Its flexible input/output facilities allow you to read any type of custom data format. See:
How to use, see: EC staff

DL_POLY. This is a general purpose serial/parallel molecular dynamics simulation package.
For more details, see:
How to use, see: EC staff

Molden. Displaying Molecular Density from the Ab Initio packages GAMESS and GAUSSIAN, and the Semi-Empiricalpackages Mopac/Ampac, it also supports a number of other programs via the Molden Format. Molden reads all the required information from the GAMESS /GAUSSIAN output file. Molden is capable of displaying Molecular Orbitals, the electron density and the Molecular minus Atomic density. Either the spherically averaged atomic density or the oriented ground state atomic density can be subtracted for a number of standard basis sets. Molden supports contour plots, 3-d grid plots with hidden lines and a combination of both. It can write a variety of graphics instructions; postscript, XWindows, VRML, povray, OpenGL, tekronix4014, hpgl, hp2392 and Figure. The Xwindows version of Molden is also capable of importing and displaying of chemx, PDB, and a variety of mopac/ampac files and lots of other formats. It also can animate reaction paths and molecular vibrations. It can calculate and display the true or Multipole Derived Electrostatic Potential and atomic charges can be fitted to the Electrostatic Potential calculated on a Connolly surface. See:
How to use, see: EC staff

Mathematica is the world's most powerful technical computing system. Mathematica combines fast, high-precision numeric and symbolic computation with easy-to-use data visualization and programming capabilities. Mathematica creates publication-quality documents with its customizable, cross-platform file format. From simple calculator operations to large-scale programming and interactive document preparation, Mathematica is the tool of choice at the frontiers of scientific research, in engineering analysis and modeling, in technical education from high school to graduate school, and wherever quantitative methods are used. For more details see:
How to use, see EC staff

TINKER. The TINKER (v4.2) molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as AMBER94/96, CHARMM27, MM2(1991), MM3(2000), OPLS-AA and OPLS-UA. Parameter sets for other standard force fields such as UFF, ENCAD, MMFF and MM4 are under consideration. In addition, we are actively developing our own TINKER force field based upon polarizable atomic multipole electrostatics. The TINKER package includes a variety of novel algorithms such as a new distance geometry metrization method that has greater speed and better sampling than standard methods, Elber's reaction path methods, several of our Potential Smoothing and Search (PSS) methods for global optimization, an efficient potential surface scanning procedure, a flexible implementation of atomic multipole-based electrostatics with explicit dipole polarizability, a selection of continuum solvation treatments including several variants of the generalized Born (GB/SA) model, an efficient truncated Newton (TNCG) local optimizer, surface areas and volumes with derivatives, a simple free energy perturbation facility, normal mode analysis, minimization in Cartesian, torsional or rigid body space, velocity Verlet stochastic dynamics, an improved spheric, energy cutoff method, Particle Mesh Ewald summation for partial charges and regular Ewald for polarizable multipoles, a novel reaction field treatment of long range electrostatics. For more details, see
How to use, see EC staff

GaussView helps the user to visualize Gaussian input and output data.
For more details, see:
How to use, please see EC staff.

Spartan. At its core, Spartan is a seamless integration of computational modeling tools ranging from molecular mechanics to quantum methods such as semi-empirical, ab initio, and density functional theory. This core functionality is augmented by the ability to perform transition state searches, develop combinatorial libraries, and even compare molecules using spreadsheets and 2D graphs.
For more details, see:
How use it, please see EC staff.

III. Databases:

QCLDB: This database, Quantum Chemical Literature Database, on-line application and allows to search the quantum chemical literature. This database includes all quantum chemical papers published up to 2001. It includes about 60,000 references.
How to use, see:

MDL: Product of the MDL Information Systems Inc.. This database contains various databases (such as ORGSYN, Available Chemical Directory (ACD), Solid-Phase Organic Reaction (SPORE), ChemInform Reaction Library, Reference Library of Synthetic Methodology and Comprehensive Heterocyclic Chemistry (CHC) which include (up to a first half of year 2001) information about chemical reactions, chemical references, chemical suppliers etc. See:
How to use, see: How to use, see: EC staff

Cambridge Crystallographic Database: This is a Crystallographic Database, which includes tens of thousands crystallographic Data (until September 2001). See:

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