Debian Science Chemistry packages

Adun is a biomolecular simulator that also includes data management and analysis capabilities. It was developed at the Computational Biophysics and Biochemistry Laboratory, a part of the Research Unit on Biomedical Informatics of the UPF.

APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including:

• simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics,
• implicit solvent molecular dynamics of biomolecules ,
• solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design,
• and biomolecular titration studies.

APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms.

Avogadro is a molecular graphics and modelling system targetted at molecules and biomolecules. It can visualize properties like molecular orbitals or electrostatic potentials and features an intuitive molecular builder.

Features include:

• Molecular modeller with automatic force-field based geometry optimization
• Molecular Mechanics including constraints and conformer searches
• Visualization of molecular orbitals and general isosurfaces
• Visualization of vibrations and plotting of vibrational spectra
• Support for crystallographic unit cells
• Input generation for the Gaussian, GAMESS and MOLPRO quantum chemistry packages
• Flexible plugin architecture and Python scripting

File formats Avogadro can read include PDB, XYZ, CML, CIF, Molden, as well as Gaussian, GAMESS and MOLPRO output.

BKchem is a free chemical drawing program, which is written in Python.

Some of the features, you can expect:

• Drawing (bond-by-bond drawing; templates for common rings; expanding of common-groups; draws radicals, charges, arrows; color support ...)
• Editing (unlimited undo and redo capabilities; aligning; scaling; rotation (2D, 3D) ...)
• Export/Import (fully supported SVG-, OpenOffice.org-Draw-, EPS-export; basic support for CML1 and CML2 import and export)

Common repository of chemical and physical facts that aim to increase interoperability between chemistry programs. See DOI 10.1021/ci050400b.

chemeq is a basic standalone filter written in C language, flex and bison. It inputs strings like:

 2H2 + O2 ---> 2 H2O
then it outputs LaTeX code and messages about the equilibrium of a

chemical reaction.

 example:~/src$ echo "2H2 + O2 ---> 2 H2O" | chemeq -lc
 2\,H_{2}\,+\,O_{2}\,\rightarrow\,2\,H_{2}O
 OK

Chemical MIME type integration for KDE, GNOME and possibly ROX desktops, based on Henry Rzepa's list at http://www.ch.ic.ac.uk/chemime/. Support is granted for KDE 3.x, GNOME 2.x and freedesktop.org systems.

Chemtool is a GTK+ based 2D chemical structure editor for X11. It supports many bond styles, most forms of text needed for chemical typesetting and splines/arcs/curved arrows.

Drawings can be exported to MOL and PDB format, SVG or XFig format for further annotation, as a PiCTeX drawing, as a bitmap or as Postscript files (several of these through XFig's companion program transfig).

The package also contains a helper program, cht, to calculate sum formula and (exact) molecular weight from a chemtool drawing file. Cht can either be called directly by Chemtool or on the console.

DRAWxtl reads a basic description of the crystal structure, which includes unit-cell parameters, space group, atomic coordinates, thermal parameters or a Fourier map, and outputs a geometry object that contains polyhedra, planes, lone-pair cones, spheres or ellipsoids, bonds, iso-surface Fourier contours and the unit-cell boundary.

Four forms of graphics are produced:

• an OpenGL window for immediate viewing
• the Persistence of Vision Ray Tracer (POV-RAY) scene language for publication-quality drawings
• the Virtual Reality Modeling Language (VRML) for dissemination across the Internet
• a Postscript rendering of the OpenGL window for those who want high-quality output but do not have POV-RAY installed.

File formats DRAWxtl can read include CIF, FDAT, FullProf (pcr), GSAS, SCHAKAL, SHELX, DISCUS and WIEN2k.

EasyChem is a program that helps you creating high quality diagrams of molecules and 2D chemical formulas that can be exported to PDF, PS, LaTeX and fig.

EasyChem was originally developed to create diagrams for chemistry books and is now frequently used for this purpose in commercial and non-commercial chemistry-related books.

Gabedit is a graphical user interface to computational chemistry packages like the Free Software package MPQC. Other (proprietary) packages supported include:

• GAMESS-US
• Gaussian
• Molcas
• Molpro
• Q-Chem

running locally or on a remote server (supporting FTP, RSH and SSH). It can display a variety of calculation results including support for most major molecular file formats. The advanced "Molecule Builder" allows to rapidly sketch in molecules and examine them in 3D. Graphics can be exported to various formats, including animations.

galculator is a scientific calculator. It supports different number bases (DEC/HEX/OCT/BIN) and angles bases (DEG/RAD/GRAD) and features a wide range of mathematical (basic arithmetic operations, trigonometric functions, etc) and other useful functions (memory, etc) at the moment. galculator can be used in algebraic mode as well as in Reverse Polish Notation.

GAMGI provides a graphic interface to build and analyse atomic structures. The program is aimed at the scientific community, who needs a graphic interface to study atomic structures and to prepare images for presentations, and for teaching the atomic structure of matter.

Garlic is written for the investigation of membrane proteins. It may be used to visualize other proteins, as well as some geometric objects. This version of garlic recognizes PDB format version 2.1. Garlic may also be used to analyze protein sequences.

It only depends on the X libraries, no other libraries are needed.

Features include:

• The slab position and thickness are visible in a small window.
• Atomic bonds as well as atoms are treated as independent drawable objects.
• The atomic and bond colors depend on position. Five mapping modes are available (as for slab).
• Capable to display stereo image.
• Capable to display other geometric objects, like membrane.
• Atomic information is available for atom covered by the mouse pointer. No click required, just move the mouse pointer over the structure!
• Capable to load more than one structure.
• Capable to draw Ramachandran plot, helical wheel, Venn diagram, averaged hydrophobicity and hydrophobic moment plot.
• The command prompt is available at the bottom of the main window. It is able to display one error message and one command string.

GaussSum parses the output files of ADF, GAMESS, GAMESS-UK, Gaussian, Jaguar and PC GAMESS calculations to extract useful information.

GaussSum uses GNUPlot to display the progress of geometry optimisations, density of states spectrum, UV-VIS spectra, IR spectra, Raman spectra, and electron density difference maps. It can also display all lines containing an arbitrary phrase and more.

GChemPaint is an editor for 2D chemical structures with a multiple document interface. Drawn molecules can be searched at NIST Webbook and PubChem.

GNOME Crystal is a light model visualizer for crystal-structures. It is based on the GNOME Chemistry Utils and should display models of all sorts of crystal microscopic structures using OpenGL.

The GNOME Chemistry Utils provide C++ classes and Gtk+-2 widgets related to chemistry. They will be used in future versions of both gcrystal and gchempaint.

This package provides 3 applications:

• a molecular structures viewer (GChem3D)
• a chemical calculator (GChemCalc)
• a periodic table of the elements (GChemTable)
• a ... (GSpectrum)

The GNOME Chemistry Utils provide C++ classes and Gtk+-2 widgets related to chemistry. They will be used in future versions of both gcrystal and gchempaint.

This package provides a browser plugin for Gecko-based browsers. It does not (yet) work with WebKit-based browsers.

A GTK+ based program for the display and manipulation of isolated molecules, periodic systems and crystalline habits. It is in development, but is nonetheless fairly functional. It has the following features:

• Support for several file types (CIF, BIOSYM, XYZ, XTL, MARVIN, and GULP)
• A simple molecular creation and manipulation tool
• A dialogue for creating starting configurations for molecular dynamics simulations
• Assorted tools for visualization (geometry information, region highlighting, etc.)
• Animation of BIOSYM files (also rendered animations, see below)

GDIS also allows you to perform the following functions through other packages:

• Model rendering (courtesy of POVRay)
• Energy minimization (courtesy of GULP)
• Morphology calculation (courtesy of cdd)
• Space group processing (courtesy of SgInfo)
• View the Periodic Table (courtesy of GPeriodic)
• Load additional filetypes, such as PDB (courtesy of Babel)

gpdc is a graphical program for visualising output data from molecular dynamics simulations. It reads input in the standard xyz format, as well as other custom formats, and can output pictures of each frame in JPG or PNG format.

gElemental is a GTK+ periodic table viewer that provides detailed information about chemical elements.

It features a table view which allows the elements to be coloured thematically by several properties, a sortable list view and an element properties dialog, displaying a variety of information, including historical, thermodynamic, electrochemical, and crystallographic properties.

This package contains the main application.

Ghemical is a computational chemistry software package written in C++. It has a graphical user interface and it supports both quantum- mechanics (semi-empirical) models and molecular mechanics models. Geometry optimization, molecular dynamics and a large set of visualization tools using OpenGL are currently available.

Ghemical relies on external code to provide the quantum-mechanical calculations. Semi-empirical methods MNDO, MINDO/3, AM1 and PM3 come from the MOPAC7 package (Public Domain), and are included in the package. The MPQC package is used to provide ab initio methods: the methods based on Hartree-Fock theory are currently supported with basis sets ranging from STO-3G to 6-31G.

GPeriodic is a small X/GTK+-based program which allows you to browse through a periodic table of chemical elements, and view somewhat detailed information on each of the elements. 118 elements are currently listed.

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non- biological systems, e.g. polymers.

GROMACS offers entirely too many features for a brief description to do it justice. A more complete listing is available at http://www.gromacs.org/content/view/12/176/.

This package is provided to automate the transition from the LAM-MPI implementation to its successor, OpenMPI. (On architectures where OpenMPI is unavailable, it will install MPICH2 instead.)

It may safely be removed from your system.

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non- biological systems, e.g. polymers.

This package contains only the core simulation engine with parallel support using the MPICH (v2) interface. It is suitable for nodes of a processing cluster, or for multiprocessor machines.

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non- biological systems, e.g. polymers.

This package contains only the core simulation engine with parallel support using the OpenMPI interface. It is suitable for nodes of a processing cluster, or for multiprocessor machines.

Kalzium is a full-featured chemistry application for KDE 4, including a Periodic Table of Elements, chemical reference, chemical equation solver, and 3D molecule viewer.

This package is part of the KDE 4 education module.

KAtomic is a puzzle game in which the player slides atoms around the board to assemble a molecule.

This package is part of the KDE games module.

The CDK is a library of Java classes used in computational and information chemistry and in bioinformatics. It includes renderers, file IO, SMILES generation/parsing, maximal common substructure algorithms, fingerprinting and much, much more.

massXpert is a program to simulate and analyse mass spectrometric data obtained on linear (bio-)polymers. It is the successor of GNU polyxmass.

Four modules allow:

• making brand new polymer chemistry definitions;
• using the definitions to perform easy calculations in a desktop calculator-like manner;
• performing sophisticated polymer sequence editing and simulations;
• perform m/z list comparisons;

Chemical simulations encompass cleavage (either chemical or enzymatic), gas-phase fragmentations, chemical modification of any monomer in the polymer sequence, cross-linking of monomers in the sequence, arbitrary mass searches, calculation of the isotopic pattern...

MOPAC provides routines to solve the electronic structure of molecules on a semi-empirical level. Available methods include MNDO, MINDO/3, AM1 and PM3.

This package contains the MOPAC7 binaries.

MPQC is an ab-inito quantum chemistry program. It is especially designed to compute molecules in a highly parallelized fashion.

It can compute energies and gradients for the following methods:

• Closed shell and general restricted open shell Hartree-Fock (HF)
• Density Functional Theory (DFT)
• Closed shell Moeller-Plesset pertubation theory (MP2)

Additionally, it can compute energies for the following methods:

• Second order open shell pertubation theory (OPT2[2])
• Z-averaged pertubation theory (ZAPT2)

It also includes an internal coordinate geometry optimizer.

MPQC is built upon the Scientific Computing Toolkit (SC).

MPQC is an ab-inito quantum chemistry program. It is especially designed to compute molecules in a highly parallelized fashion.

This package includes Perl modules to parse the output, Emacs-modes to facilitate editing mpqc files and molrender, a program to output the molecules in OOGL-format.

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It allows to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Features include:

• Hydrogen addition and deletion
• Support for Molecular Mechanics
• Support for SMARTS molecular matching syntax
• Automatic feature perception (rings, bonds, hybridization, aromaticity)
• Flexible atom typer and perception of multiple bonds from atomic coordinates
• Gasteiger-Marsili partial charge calculation

File formats Open Babel supports include PDB, XYZ, CIF, CML, SMILES, MDL Molfile, ChemDraw, Gaussian, GAMESS, MOPAC and MPQC.

This package includes the following utilities:

• babel: Convert between various chemical file formats
• obenergy: Calculate the energy for a molecule
• obminimize: Optimize the geometry, minimize the energy for a molecule
• obgrep: Molecular search program using SMARTS pattern
• obprop: Print standard molecular properties
• obfit: Superimpose two molecules based on a pattern
• obrotamer: Generate conformer/rotamer coordinates
• obchiral: Print molecular chirality information
• obrotate: Rotate dihedral angle of molecules in batch mode

GNU polyxmas is an official package of the GNU project. It is a fully integrated software suite to perform a wide variety of mass spectrometric and (bio-)polymer chemistry simulations. This software program is also useful to help analysing mass spectrometric data, such as data obtained on polymer sequences fragmented in the gas phase... This software program gives the user the ability to make brand new polymer chemistry definitions, use them in a molecular mass calculator, and edit polymer sequence files. Each action performed by the user automatically triggers recalculation of all the masses according to the mass calculation engine's configurations that were previously set by the user.

Chemical simulations encompass polymer sequence cleavage (either chemical or enzymatic), gas-phase fragmentations, chemical modification of any monomer in the polymer sequence...

This package is a dependency package. This package depends on the following three packages: polyxmass-bin (the GUI program), polyxmass-common (the fundamental chemical data required to run GNU polyxmass usefully) and polyxmass-data (supplementary chemical data).

Homepage: http://www.polyxmass.org

PSI3 is an ab-initio quantum chemistry program. It is especially designed to accurately compute properties of small to medium molecules using highly correlated techniques.

It can compute energies and gradients for the following methods:

• Closed shell and general restricted open shell Hartree-Fock (RHF/ROHF)
• Complete active space SCF (CASSCF)
• Coupled-cluster singles doubles (CCSD)
• Coupled-cluster singles doubles with pertubative triples (CCSD(T)) (only for unrestricted (UHF) reference wavefunctions)

Additionally, it can compute energies for the following methods:

• Unrestricted open shell Hartree-Fock (UHF)
• Closed/open shell Moeller-Plesset pertubation theory (MP2)
• Closed shell linear R12 Moeller-Plesset pertubation theory (MP2-R12)
• Multireference configuration-interaction (MRCI)
• Coupled-cluster singles doubles with pertubative triples (CCSD(T))
• Second-order approximate coupled-cluster singles doubles (CC2)
• Closed shell and general restricted open shell equation-of-motion coupled- cluster singles doubles (EOM-CCSD)

Further features include:

• Flexible, modular and customizable input format
• Excited state calculations with the CC2, EOM-CCSD, CASSCF and MRCI methods
• Internal coordinate geometry optimizer
• Harmonic frequencies calculations
• One-electron properties like dipole/quadrupole moments, natural orbitals, electrostatic potential, hyperfine coupling constants or spin density
• Utilization of molecular point-group symmetry to increase efficiency

PyMOL is a molecular graphics system targetted at medium to large biomolecules like proteins. It can generate high-quality publication-ready molecular graphics images and animations.

Features include:

• Visualization of molecules, molecular trajectories and surfaces of crystallography data or orbitals
• Molecular builder and sculptor
• Internal raytracer and movie generator
• Fully extensible and scriptable via a Python interface

File formats PyMOL can read include PDB, XYZ, CIF, MDL Molfile, ChemDraw, CCP4 maps, XPLOR maps and Gaussian cube maps.

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It allows to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Features include:

• Hydrogen addition and deletion
• Support for Molecular Mechanics
• Support for SMARTS molecular matching syntax
• Automatic feature perception (rings, bonds, hybridization, aromaticity)
• Flexible atom typer and perception of multiple bonds from atomic coordinates
• Gasteiger-Marsili partial charge calculation

File formats Open Babel supports include PDB, XYZ, CIF, CML, SMILES, MDL Molfile, ChemDraw, Gaussian, GAMESS, MOPAC and MPQC.

This package contains the Python binding.

RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.

The program reads in a molecule coordinate file and interactively displays the molecule on the screen in a variety of colour schemes and molecule representations. Currently available representations include depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick, solid and strand biomolecular ribbons, atom labels and dot surfaces.

Supported input file formats include Protein Data Bank (PDB), Tripos Associates' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's (MDL) Mol file format, Minnesota Supercomputer Center's (MSC) XYZ (XMol) format, CHARMm format, CIF format and mmCIF format files.

This package installs two versions of RasMol, rasmol-gtk has a modern GTK-based user interface and rasmol-classic is the version with the old Xlib GUI.

V_Sim visualizes atomic structures such as crystals, grain boundaries, molecules and so on (either in binary format, or in plain text format).

The rendering is done in pseudo-3D with spheres (atoms) or arrows (spins). The user can interact through many functions to choose the view, set the bindings, draw cutting planes, compute surfaces from scalar fields, duplicate nodes, measure geometry... Moreover V_Sim allows to export the view as images in PNG, JPG, PDF (bitmap), SVG (scheme) and other formats. Some tools are also available to colorize atoms from data values or to animate on screen many position files.

Viewmol is a graphical front end for computational chemistry programs. It is able to graphically aid in the generation of molecular structures for computations and to visualize their results.

At present Viewmol includes input filters for Discover, DMol3, Gamess, Gaussian 9x/03, Gulp, Mopac, PQS, Turbomole, and Vamp outputs as well as for PDB files. Structures can be saved as Accelrys' car-files, MDL files, and Turbomole coordinate files. Viewmol can generate input files for Gaussian 9x/03. Viewmol's file format has been added to OpenBabel so that OpenBabel can serve as an input as well as an output filter for coordinates.

xbs ball-and-sticks plotting program can create still and moving three dimensional models of molecules. X11 and PostScript output are available. Models can be rotated, scaled, etc. Various labeling, shading, lighting, coloring options are available.

Xdrawchem is a 2D editor for chemical structures and reactions. It mirrors the abilities of the commercial ChemDraw suite and has file compatibility with it as well as other chemical formats through OpenBabel.

XMakemol is a mouse-based program, written using the LessTif widget set, for viewing and manipulating atomic and other chemical systems. It reads XYZ input and renders atoms, bonds and hydrogen bonds.

Features include:

• Animating multiple frame files
• Interactive measurement of bond lengths, bond angles and torsion angles
• Control over atom/bond sizes
• Exporting to Xpm, Encapsulated PostScript and XYZ formats
• Toggling the visibility of groups of atoms
• Editing the positions of subsets of atoms

XMakemol is a mouse-based program, written using the LessTif widget set, for viewing and manipulating atomic and other chemical systems. It reads XYZ input and renders atoms, bonds and hydrogen bonds.

Features include:

• Animating multiple frame files
• Interactive measurement of bond lengths, bond angles and torsion angles
• Control over atom/bond sizes
• Exporting to Xpm, Encapsulated PostScript and XYZ formats
• Toggling the visibility of groups of atoms
• Editing the positions of subsets of atoms

This is the OpenGL-enabled XMakemol package. The images are rendered using true 3D graphics primitives, and can be exported using the Xpm format; red/blue stereo images can also be produced. The OpenGL package provides more display options, along with better support for displaying vectors. Ellipses can also be rendered.

gpdc is a graphical program for visualising output data from molecular dynamics simulations. It reads input in the standard xyz format, as well as other custom formats, and can output pictures of each frame in JPG or PNG format.

This package contains examples to be used by the gdpc program.

Jmol is a Java molecular viewer for three-dimensional chemical structures. Features include reading a variety of file types and output from quantum chemistry programs, and animation of multi-frame files and computed normal modes from quantum programs. It includes with features for chemicals, crystals, materials and biomolecules.

• The JmolApplet is a web browser applet that can be integrated into web pages.
• The Jmol application is a standalone Java application that runs on the desktop.
• The JmolViewer is a development tool kit that can be integrated into other Java applications.

For more detailed information about packaging status please see http://lists.debian.org/debian-med/2008/03/msg00097.html

MOLDEN is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the MOLDEN Format. MOLDEN reads all the required information from the GAMESS / GAUSSIAN outputfile. 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, X, VRML, povray, OpenGL, tekronix4014, hpgl, hp2392 and Figure. The X 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. MOLDEN has a powerful Z-matrix editor which give full control over the geometry and allows you to build molecules from scratch, including polypeptides. MOLDEN was also submitted to the QCPE (QCPE619), allthough the X version is considerably running behind on the current one.

The TINKER 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 Amber (ff94, ff96, ff98 and ff99), CHARMM (19 and 27), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA and OPLS-AA/L), Liam Dang's polarizable potentials, and our own AMOEBA polarizable atomic multipole force field. Parameter sets for other standard force fields such as GROMOS, UFF, ENCAD and MM4 are under consideration for future releases.

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 spherical 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, and more....

simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.

The EGAD Library is a modular, object oriented approach to rational protein design. It is platform-independent, written in C++ and, most importantly, free. Its raison d'etre is to serve as a tool for building protein design applications. It can also be used as a test-bed for the comparison of different energy functions and minimization algorithms under the same physical model.

Citations of EGAD Library should reference the paper in the Journal of Computational Chemistry. doi:10.1002/jcc.20727

Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. The idea of the library is to let computer write optimized code for computing such integrals. There are two primary advantages to this: much less human effort is required to write code for computing new integrals, and code can be optimized specifically for a particular computer architecture (e.g., vector processor).

Libint has been utilized to implement methods such as Hartree-Fock (HF) and Kohn-Sham density functional theory (KS DFT), second-order Moller-Plesset perturbation theory (MP2), coupled cluster singles and doubles (CCSD) method, as well as explicitly correlated R12 methods. The following software packages use Libint:

Improves mpqc (#409025) and psi3.

QuteMol is an open source (GPL), interactive, high quality molecular visualization system. QuteMol exploits the current GPU capabilites through OpenGL shaders to offers an array of innovative visual effects. QuteMol visualization techniques are aimed at improving clarity and an easier understanding of the 3D shape and structure of large molecules or complex proteins.

• Real Time Ambient Occlusion
• Depth Aware Silhouette Enhancement
• Ball and Sticks, Space-Fill and Liquorice visualization modes
• High resolution antialiased snapshots for creating publication quality renderings
• Automatic generation of animated gifs of rotating molecules for web pages animations
• Real-time rendering of large molecules and protein (>100k atoms)
• Standard PDB input
• Support as a plugins of the NanoEngineer-1 the modeling and simulation program for nano-composites This program needs the VCG library http://vcg.sourceforge.net which has to be packaged first.