http://www.redbrick.dcu.ie/~noel/linux4chemistry/The latest additions to Linux4Chemistry, the website of chemistry software available for LinuxSat, 02 Mar 2013 16:57:39 GMTPyRSS2Gen-1.1.0http://blogs.law.harvard.edu/tech/rsshttp://sketchel.sourceforge.net/SketchEl is an interactive chemical molecule sketching tool, designed for quick and simple entry of structures. The feature set is limited to those necessary to enter a single chemical species, in a form that might be used in a cheminformatic database, representing each atom and bond as a part of a labelled graph. This software is Open Source.Thu, 31 Aug 2006 16:15:13 GMThttp://pydespike.sourceforge.net/PyDespike is a program to graphically process (ie. despike) Raman and other spectroscopic data. It reduces the tedium involved in removing spikes in data due to artificial background fluctuations. This software is Open Source.Tue, 12 Sep 2006 15:08:47 GMThttp://www.unipress.waw.pl/fityk/fiytk is a tool for curve fitting and data analysis (e.g. baseline correction), used in crystallography, chromatography, photoluminescence or photoelectron spectroscopy, infrared or Raman spectroscopy, and in other fields. Common tasks can be automated with scripts. This software is Open Source.Tue, 17 Oct 2006 09:42:42 GMThttp://www.unipress.waw.pl/debyer/Debyer takes a file with atom positions as input, and outputs X-ray and neutron diffraction patterns, the total scattering structure function, the pair distribution function (PDF), and related functions such as the RDF (reduced PDF). It can be used for comparison of molecular dynamics simulations or other models of atomistic structure of the material with X-ray and neutron powder diffraction experiments. This software is Open Source.Tue, 17 Oct 2006 09:42:47 GMThttp://www2.autistici.org/interzona/index.php?mod=03_BistBist (Bidimensional Structures) is a chemical drawing program focussed on organic chemistry. Using the OpenBabel API, it can import/export in a wide variety of file formats including CML. A notable feature is that it can automatically parse linear fragments to create a 2D structure. This software is Open Source.Mon, 30 Oct 2006 16:17:04 GMThttp://objcryst.sourceforge.net/FoxFOX performs ab initio crystal structure solution from diffraction data (mostly powder diffraction data). Solutions can be constrained using angle or atom based constraints. Multiple powder patterns can be used simultaneously, and input is using a graphical user interface. This software is Open Source.Thu, 23 Nov 2006 13:05:45 GMThttp://qutemol.sourceforge.net/QuteMol is an open source (GPL), interactive, high quality molecular visualization system that aims to improve clarity and provide an easier understanding of the 3D shape and structure of large molecules or complex proteins. Its features include real time ambient occlusion, depth-aware silhouette enhancement, and automatic generation of animated gifs of rotating molecules for web page animations. This software is Open Source.http://qutemol.sourceforge.net/Tue, 06 Feb 2007 16:04:44 GMThttp://www.kdau.com/projects/gelemental/gElemental is a periodic table viewer derived from GPeriodic that provides detailed information on the chemical elements. It uses the GTK+ toolkit and is available for Linux and other GTK+ platforms. It also provides Python bindings to the data, which is stored in a separate data library. This software is Open Source.http://www.kdau.com/projects/gelemental/Tue, 06 Feb 2007 16:05:03 GMThttp://www.theochem.ethz.ch/software/snfSNF has been developed for the calculation of Infrared, Raman, and VROA spectra using the harmonic approximation for the frequencies and the double harmonic approximation for the intensities. Vibrational frequencies are determined using numerical differentiation of analytical gradients of the total electronic energy, while infrared, Raman, and VROA intensities are obtained by numerical differentiation of dipole moments and (generalized) polarizability tensor components with respect to nuclear coordinates. Single point calculations are carried out using Dalton, Gaussian, Molpro or Turbomole. This software is Open Source.http://www.theochem.ethz.ch/software/snfWed, 14 Feb 2007 11:25:45 GMThttp://www.ccdc.cam.ac.uk/products/life_sciences/gold/GOLD is a program for calculating the docking modes of small molecules into protein binding sites as part of a virtual screening application. Docking is performed using a genetic algorithm and incorporates full ligand flexibility and partial protein flexibility. The GoldScore and ChemScore scoring functions are available, or a custom scoring function can be implemented. Cavity-bound waters and constraints can be included as part of the docking procedure. This software is Commercial.http://www.ccdc.cam.ac.uk/products/life_sciences/gold/Wed, 28 Feb 2007 11:29:31 GMThttp://pyvib2.sf.net/PyVib2 is a program for analyzing vibrational motion and vibrational spectra, written in pure Python. PyVib2 permits the automatic correlation of vibrational motions of molecules thereby allowing an understanding of Raman, Raman optical activity (ROA), infrared vibrational absorption (IR), and vibrational circular dichroism (VCD) spectra. Features include a Versatile representation of vibrational motions, visualization of Raman/ROA and IR/VCD generation in molecules and the production of publication quality spectra. It currently supports DALTON and Gaussian output files. This software is Open Source.http://pyvib2.sf.net/Wed, 28 Feb 2007 11:29:42 GMThttp://molsketch.sourceforge.netmolsKetch is a molecular drawing tool for 2D molecular structures. Its goal is to help you draw molecules quick and easily. As well as allowing the user to export high quality images in a number of vector and bitmap formats, it can read and write multiple chemical file formats (using the Open Babel library). molsKetch features intelligent addition/removal of hydrogen atoms and a built-in library that provides quick access to regularly used molecules and functional groups. This software is Open Source.http://molsketch.sourceforge.netWed, 04 Apr 2007 12:58:41 GMThttp://www.atomistix.com/index.php?id=atkAtomistix ToolKit, ATK, is a first principles electronic structure program capable of modeling electrical properties of nanostructured systems coupled to semi-infinite electrodes (using non-equilibrium Green's functions). The key features are calculation of electrical properties of nanoscale devices, access to advanced DFT algorithms, support for molecular systems, bulk and periodic systems, and two probe systems. In addition there is a Python-based scripting environment. This software is Commercial.http://www.atomistix.com/index.php?id=atkWed, 04 Apr 2007 12:59:01 GMThttp://avogadro.sourceforge.net/wiki/Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers a flexible rendering engine and a powerful plugin architecture. This software is Open Source.http://avogadro.sourceforge.net/wiki/Thu, 07 Jun 2007 16:20:10 GMThttp://www.q-pharm.com/Quantum is a pure physics based molecular docking software which calculates Kd of a protein-ligand complex, and ligand position in the protein active site. This enables virtual screening of compound libraries. The calculation takes into account metals and other hetatoms in the protein active site as well as protein flexibility. This software is Commercial.http://www.q-pharm.com/Tue, 10 Jul 2007 12:46:12 GMThttp://www.agilemolecule.com/Products.htmlAGM Build can be used to build and prepare molecules for molecular mechanics calculations, while its companion program is a 3D viewer and conformational editor for molecular structures. Note that the add-on library of amino acids for AGM Build requires purchase. This software is Open Source.http://www.agilemolecule.com/Products.htmlMon, 03 Sep 2007 13:23:32 GMThttp://qmforge.sourceforge.net/QMForge is a program to analyze the results of quantum chemistry (DFT) calculations: Gaussian 98/03, ADF, GAMESS (US), GAMESS (UK), and PC-GAMESS files are supported. The following analyses are available for user-defined molecular fragments: Mulliken, C-squared and Overlap Population analyses, Fragment and Charge Decomposition Analyses. This software is Open Source.http://qmforge.sourceforge.net/Fri, 09 Nov 2007 13:39:01 GMThttp://www.molegro.com/products.phpMolegro Molecular Viewer is a free cross-platform application for visualization of molecules and analysis of protein-ligand interactions. This software is Freeware.http://www.molegro.com/products.phpThu, 24 Jan 2008 16:18:04 GMThttp://www.chemdoodle.com/ChemDoodle is an innovative 2D chemical drawing application which works on any operating system with Java installed. It contains an abbreviation library which can be extended, and can import and export many file formats including ChemDraw Exchange Format. This software is Commercial.http://www.chemdoodle.com/Wed, 16 Apr 2008 13:30:51 GMThttp://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.htmlJMolEditor is a Java-based molecular viewer for quantum chemistry calculations, with support for Gaussian, GAMESS, ADF and Q-Chem calculations. Molecules can be built, and input files can be prepared and submitted. Calculation results, including isosurfaces from cube files, can be displayed. This software is Freeware.http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.htmlWed, 16 Apr 2008 13:30:58 GMThttp://www.scinetec.com/VB2000 is an ab initio electronic structure package for performing modern Valence Bond (VB) calculations based on a highly efficient VB algorithm - the so called Algebrant Algorithm. It has also a general implementation of the Group Function (GF) Theory, in which a large molecule is described in terms of its constituent parts of physically identifiable "electron groups". It can be used as a stand-alone program, or as a plug-in module for GAMESS and Gaussian. This software is Free for academics.http://www.scinetec.com/Mon, 17 Nov 2008 10:57:41 GMThttp://www.zeden.orgZodiac is an advanced molecular editor for molecular modelling and computer aided drug design, that offers tools such as energy minimisation, database management, molecular property prediction and front ends to various docking and QM programs. It is cross platform and released under the GPL. This software is Open Source.http://www.zeden.orgMon, 17 Nov 2008 10:57:46 GMThttp://bionano.icm.edu.pl/software/RedMD (Reduced Molecular Dynamics) is an open source package for molecular dynamics simulations and normal mode analysis for coarse-grained models of proteins and nucleic acids. Force fields are based on one-bead elastic network models and their extensions. The code is written in C/C++ and is parallelized. This software is Open Source.http://bionano.icm.edu.pl/software/Fri, 09 Jan 2009 12:42:33 GMThttp://www.scienomics.com/products/maps_platform.phpMAPS (Materials And Processes Simulations) is a platform for performing materials modeling and simulations. It provides a flexible framework for accessing both proprietary and open-source simulation codes in the areas of quantum, classical, mesoscale and chemical engineering. MAPS serves as an integration tool for all modeling related tasks and data and offers a multi-user/multi-project modeling environment complete with data management. This software is Commercial.http://www.scienomics.com/products/maps_platform.phpThu, 12 Feb 2009 15:32:05 GMThttp://www.ing.unitn.it/~maud/MAUD (Material Analysis Using Diffraction) is a general diffraction/reflectivity analysis program mainly based on the Rietveld method. It has a GUI, and a wide range of features including ab initio structure solution, various optimisation algorithms, Le Bail fitting and microstruture analysis. This software is Freeware.http://www.ing.unitn.it/~maud/Thu, 12 Feb 2009 15:32:12 GMThttp://www.open-enventory.de/open enventory is an integrated laboratory journal and inventory program. It is a web application that runs in your browser. Automatic acquisition of freely accessible data from online databases makes manual data acquisition and catalogue searches obsolete, and price surveys can be done with a mouseclick. The laboratory journal uses the information available in the inventory database and makes the data available for all members of a workgroup. Both inventory and laboratory journal have the ability to allow data exchange between workgroups. This software is Open Source.http://www.open-enventory.de/Wed, 22 Apr 2009 09:42:55 GMThttp://code.google.com/p/metastudio/MeTA Studio is programmable IDE tailored for a computational chemist. It has support for BeanShell and Jython, and integrates Jmol. This software is Open Source.http://code.google.com/p/metastudio/Wed, 22 Apr 2009 09:43:01 GMThttp://openthermo.sourceforge.netOpenThermo is a program package for statistical thermodynamics computations beyond rigid rotor harmonic oscillator approximation (RRHOA), with taking into account internal rotations and vibration anharmonicity. In contrast to statistical subprograms integrated to QC packages, OpenThermo is designed to make the calculation transparent to user and give maximum control under the choice of used theories and approximations. This software is Open Source.http://openthermo.sourceforge.netThu, 27 Aug 2009 16:27:32 GMThttp://www.pdynamo.orgpDynamo is an open source program library that has been designed for the simulation of molecular systems using quantum chemical (QC), molecular mechanical (MM) and hybrid QC/MM potential energy functions. This software is Open Source.http://www.pdynamo.orgThu, 27 Aug 2009 16:27:39 GMThttp://www.massxpert.org/massXpert lets users analyse/predict mass spectrometric data on (bio)polymers. Notable features include ex nihilo polymer chemistry definitions, highly sophisticated editing of polymer sequences and chemical reaction simulations. This software is Open Source.http://www.massxpert.org/Thu, 27 Aug 2009 16:27:46 GMThttp://opensource.scitouch.net/indigoIndigo is a cheminformatics toolkit that includes a rendering library (Dingo), generation of canonical SMILES (Cano), an Oracle cartidge for searching molecular databses (Bingo) and R-Group deconvolution (Deco). It also can handle nucleotides (Nucleo). This software is Open Source.http://opensource.scitouch.net/indigoThu, 19 Nov 2009 17:20:18 GMThttp://www.yambo-code.org/Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. Yambo relies on the Kohn-Sham wavefunctions generated by the DFT codes abinit and Pwscf. This software is Open Source.http://www.yambo-code.org/Thu, 02 Dec 2010 21:44:49 GMThttp://olex2.opencryst.net/Olex2 is an easy-to-use program for small-molecule structure solution and refinement. It also includes many useful tools for structure analysis, archiving and report generation. All aspects of the structure determination and publication process are presented in a single, workflow-driven package - with the ultimate goal of producing an application which will be useful to both chemists and crystallographers. This software is Freeware.http://olex2.opencryst.net/Thu, 02 Dec 2010 21:44:53 GMThttp://espressomd.orgESPResSo (Extensible Simulation Package for Research on Soft matter) is a software package for the scientific simulation and analysis of coarse-grained atomistic or bead-spring models as they are used in soft matter research, with emphasis on charged systems. It can be driven by Tcl scripts. This software is Open Source.http://espressomd.orgThu, 06 Oct 2011 20:54:37 GMThttp://cp2k.berlios.de/CP2K can perform atomistic and molecular 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. This software is Open Source.http://cp2k.berlios.de/Thu, 06 Oct 2011 20:54:56 GMThttp://www.openchrom.netOpenChrom is a cross-platform GUI for chromatography and mass spectrometry. It is able to import binary and textual chromatographic data files, such as *.D chromatograms from Agilent Technologies or NetCDF. A basic set of methods to detect baselines, peaks and to integrate peaks in a chromatogram are implemented. Preprocessing steps, e.g. To remove certain mass fragments (m/z) such as nitrogen (28) or water (18), are supported by applying filters on the chromatogram or mass spectrum. Extensions are welcome, as OpenChrom is open source and uses a flexible approach, which allows others to implement their own methods, algorithms, filters, detectors or integrators. This software is Open Source.http://www.openchrom.netFri, 03 Feb 2012 16:53:40 GMThttp://www.ball-project.org/BallView is a cross-platform molecular visualization tool with support for molecular mechanics optimisation, molecular dynamics and molecular editing. It supports a large number of file formats, SMILES and SMARTS, as well as forcefields such as Amber, MMFF94 and Charmm. Its capabilities also include realtime raytracing and stereoscopic viewing. Actions can be automated using Python scripts. This software is Open Source.http://www.ball-project.org/Fri, 03 Feb 2012 16:53:46 GMThttp://www.physics.kku.ac.th/sq/Siam Quantum is an ab initio quantum chemistry program that uses quantum mechanics to determine the total energy and wave function of molecules within the framework of the Hartee-Fock method. The source code and documentation was originally designed to introduce students to electronic structure calculations. It can perform geometry optimisation and simple population analysis. Further developments are ongoing. This software is Open Source.http://www.physics.kku.ac.th/sq/Fri, 03 Feb 2012 16:54:01 GMThttp://ergoscf.org/Ergo is a quantum chemistry program for large-scale self-consistent field calculations. It performs electronic structure calculations using Hartree-Fock and Kohn-Sham density functional theory using Gaussian basis sets. Linear scaling techniques are employed such as fast multipole methods, hierarchic sparse matrix algebra, density matrix purification, and efficient integral screening. This software is Open Source.http://ergoscf.org/Fri, 03 Feb 2012 16:54:13 GMThttp://padel.nus.edu.sg/software/padeldescriptor/index.htmlPaDEL-Descriptor is a GUI for calculating molecular descriptors and fingerprints. The software currently calculates 856 descriptors (722 1D, 2D descriptors and 134 3D descriptors) and 10 types of fingerprints. The descriptors and fingerprints are calculated using the Chemistry Development Kit with some additional descriptors and fingerprints. These additions include atom type electrotopological state descriptors, extended topochemical atom (ETA) descriptors, McGowan volume, molecular linear free energy relation descriptors, ring counts, count of chemical substructures identified by Laggner, and binary fingerprints and count of chemical substructures identified by Klekota and Roth. This software is Open Source.http://padel.nus.edu.sg/software/padeldescriptor/index.htmlFri, 03 Feb 2012 16:59:37 GMThttp://cantera.googlecode.comCantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes. You can use Cantera from Python or Matlab to handle problems in areas such as combustion, flame structure, detonations, electrochemical energy conversion, fuel cells, aqueous electrolytes, plasmas and thin-film deposition. This software is Open Source.http://cantera.googlecode.comSat, 10 Mar 2012 12:34:53 GMThttps://www.atelgraphics.com/DENEB is a powerful graphical user interface to many DFT calculation packages as SIESTA, VASP and QE. It is capable of managing hundreds of projects, each containing hundreds of simulations applied to different samples, every one containing thousands of atoms. This software is Commercial.https://www.atelgraphics.com/Sat, 02 Mar 2013 16:57:12 GMThttp://www.ovito.org/OVITO (Open Visualization Tool) allows the analysis and visualization of large-scale atomistic datasets produced by molecular dynamics/statics and Monte-Carlo simulation codes. This software is Open Source.http://www.ovito.org/Sat, 02 Mar 2013 16:57:18 GMThttp://sourceforge.net/projects/qmol/qmol is a simple molecular weight calculator, available for Linux and Windows. You can enter a formula, (e.g. CH3(CH2)2OH) and get its molecular weight (60.0959 g/mol) and its elemental composition (C3H8O: C 59.96; H 13.42; O 26.62 %). This software is Open Source.http://sourceforge.net/projects/qmol/Sat, 02 Mar 2013 16:57:24 GMThttp://erkale.googlecode.comERKALE is a quantum chemistry program used to solve the electronic structure of atoms, molecules and molecular clusters. The main use of ERKALE is the computation of x-ray properties, such as ground-state electron momentum densities and Compton profiles, and core (x-ray absorption and x-ray Raman scattering) and valence electron excitation spectra of atoms and molecules. This software is Open Source.http://erkale.googlecode.comSat, 02 Mar 2013 16:57:39 GMT