
Software Collection at the Emerson Center
The Queueing System  FAQ
 Hardware Specification  Software
Description  How to get an account
The Emerson Center application software packages can be divided into
three difference categories:
Electronic Structure Codes 
Biomolecular Modeling & Visualization
Software 
Databases 
Gaussian03 
Cerius2_4.2 
QCLDB 
Molpro2006 
Sybyl_6.7 
MDL 
Gamess2006 
MacroModel_7.1 
Cambridge Crystall Database 
Dalton_2.0 
AMBER_6.0 

AcesII_4.0 
HyperChem 

Molcas_4.0 
Spartan 

Mopac7 
MM3 

Columbus5.7 
Mathematica_5.2 

CADPAC 
IDL_5.0 

TurboMol 
TINKER 4.2 

Hondo 
Molden 


GaussView 


DL_POLY 




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 (shortlived
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 semiempirical geometry optimizations practical for larger molecules
than ever before. See: http://www.gaussian.com
How to use, see: http://www.emerson.emory.edu/local/appsoft/G98.html
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 EffectiveFragmentationMethod
for large molecule calculation, while Gaussian includes ONIOM method.
Gamess also includes the (a) Vibrational SelfConsistentField (VSCF)
method, (b) Methods for evaluation of spinorbit coupled constants, (c)
Methods evaluating analytic frequency dependent nonlinear optical polarizability
properties, (d) Methods allowing to take into account the solvent effects,
effective fragment potentials (EFP), polarizable continuum model (PCM),
conductorlike screening model (COSMO), and selfconsistent reaction field
(SCRF).
See: http://www.msg.ameslab.gov/GAMESS/GAMESS.html
How to use, see: http://www.emerson.emory.edu/local/appsoft/GAMESS96.html
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: http://www.tc.bham.ac.uk/molpro
How to use, see; http://www.emerson.emory.edu/local/appsoft/M98.html
AcesII_3.0. Major strengths of this program are in performing
calculations using "manybody" methods to treat electron correlation.
These approaches, broadly categorized as manybody perturbation theory
(MBPT) and the coupledcluster (CC) approximation, offer a reliable treatment
of correlation and have the attractive property of sizeextensivity, 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: http://www.qtp.ufl.edu/Aces2
How to use, see: http://www.emerson.emory.edu/local/appsoft/ACES30.html
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 spinrotation constants, spinspin coupling constants, hyperfine
coupling tensors), (e) Optical and Raman properties (Vibrational Circular
Dichrosm, electronic Circular Dichroism, electronic adsorption, Raman
Optical Activity), and more. See: http://www.kjemi.uio.no/software/dalton
How to use, see; http://www.emerson.emory.edu/local/appsoft/Dalton.html
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, cisd, 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: http://www.teokem.lu.se/molcas
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, oneelectron properties of the middlesized molecules
and potential energy surfaces of the chemical reactions. The unique feature
of Hondo is the possibility to calculate seamofcrossing 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 Higherorder derivatives.
These routines also work for ffunction. Using this program you can calculate
energies, wavefunction, geometries, frequencies, and highestorder derivatives
of energy.
See: http://wwwtheor.ch.cam.ac.uk/software/cadpac.html
How to use, see: http://www.emerson.emory.edu/local/appsoft/CADPAC.html
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 chemicallyaware
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 lowenergy 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 solventaccessible surfaces onto it maps lipophilicity,
electrostatic potential, hydrogen bonding sites and other properties.
Confort performs exhaustive yet rapid conformational analyses of drugsized
molecules. It generates a maximally diverse subset of conformers, identifies
the global minimum energy conformer, or loctes all local minima within
a userspecified energy range. Confort's diverse conformers can be used
for receptorligand docking studies, Unity3D database searches starting
from multiple conformations, pharmacophore perception using DISCOtech,
and multiconformer 3DQSAR 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: http://www.tripos.com
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 freeenergy perturbation methods and mixedmode MonteCarlo/stochastic
dynamic procedures. It includes MM2, MM3, Amber, OPLS, OPLSAA, and MMFF94s
force fields. Userfriendly, frontend Maestro makes preparation of input
files and analysis of the output files very easier.
See: http://www.schrodinger.com
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 particlemeshEwald 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 "multipleconformer"
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.
See: http://www.amber.ucsf.edu/amber/amber.html
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: http://www.accelrys.com/cerius2/index.html
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 threedimentional models; determining of isotop effects
and much more. See: http://www.hyper.com
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, arrayoriented 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: http://www.rsinc.com/idl
How to use, see: EC staff
DL_POLY. This is a general purpose serial/parallel molecular
dynamics simulation package.
For more details, see: http://www.dl.ac.uk/TCS/Software/DL_POLY
How to use, see: EC staff
Molden. Displaying Molecular Density from the Ab Initio
packages GAMESS and GAUSSIAN, and the SemiEmpiricalpackages 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, 3d
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: http://www.cmbi.nl/~schaft/molden/molden.html
How to use, see: EC staff
Mathematica is the world's most powerful technical computing
system. Mathematica combines fast, highprecision numeric and symbolic
computation with easytouse data visualization and programming capabilities.
Mathematica creates publicationquality documents with its customizable,
crossplatform file format. From simple calculator operations to largescale
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: http://www.hallogram.com/mathematica/mathematica
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), OPLSAA and OPLSUA. 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 multipolebased
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 http://dasher.wustl.edu/tinker
How to use, see EC staff
GaussView helps the user to visualize Gaussian input
and output data.
For more details, see: http://www.gaussian.com
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 semiempirical, 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: http://www.wavefun.com
How use it, please see EC staff.
III. Databases:
QCLDB: This database, Quantum Chemical Literature Database,
online 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.
See: http://qcldb.ims.ac.jp
How to use, see: http://www.emerson.emory.edu/local/appsoft/QCLDB99.html
MDL: Product of the MDL Information Systems Inc.. This
database contains various databases (such as ORGSYN, Available Chemical
Directory (ACD), SolidPhase 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: http://www.mdli.com
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: http://www.ccdc.cam.ac.uk
