Collaborative Computational Project Number 14 (CCP14) For Single Crystal and Powder Diffraction (Freely Available Crystallographic Software for Students and Academia)

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Agile Molecule - AGM View and AGM Build - Alexey Nikitin

• Contact: [email protected]
• AGM View - freeware (Windows and Linux - OpenGL required)
• 3 Dimensional molecular viewer which shows molecular models and provides some geometry editing capabilities.
• AGM Build - freeware - (Windows and Linux - OpenGL required)
• A molecular builder and conformational editor.
  • Geometry editing
  • Lattice building
  • Building of chain molecules
  • Chains with predetermined conformations
  • Charges and atom types according to selected Force Field
• AGM Build can be used for interactive model preparation for molecular dynamics simulations with package MDynaMix / MDX.
• The original website is at http://www.agilemolecule.com/index.htm
• The website also contains a commerical extension to AGM Build to include amino acids
• Performance and Evaluation of 3D Model Builders - Evaluation of 3D Structure Generators Revisited - http://vermeer.organik.uni-erlangen.de/software/corina/xrayeval.html

DPT Fast Stereolithography - http://www.dpt-fast.com/

• Rapid Prototyping using SLS, SLA, FDM, urethane casting, injection molding, and metal casting.
• Can take 3d CAD files and bring them to reality.

CORINA (COoRdINAtes): "A powerful and reliable tool for the generation of 3D atomic coordinates" (2D to 3D conversion)

• CORINA home page - http://www2.ccc.uni-erlangen.de/software/corina/corina.html
• Determine a "Thousand 3D-Structures for Free" using Corina on the Web for free (with Chemdraw/ISISDraw like Java 2D structure Editor or by inputting a SMILES string generated from another program)
  • At: http://www2.ccc.uni-erlangen.de/software/corina/free_struct.html

  • Or information given in the above page on how to send the 2D files via Email and get an E-mail response in a variety of formats including, "mol" (MDL Molfile), "xyz" (XYZ format), "pdb" (Protein Database Format), "smd" (Standard Molecular Data), "jcamp" (a spectroscopy standard), "vrml" (Virtual Reality Modelling Language), "compass", "ctx", "molgen", "sharc", "cascii" and "cbin".
  • 

• "Atomsmith Molecular Exploration Kit for Windows" - http://www.bitwixt.com/

• "SMILES is a simple yet comprehensive chemical nomenclature." - http://www.daylight.com/dayhtml/smiles/

• "WebMolecules - over 210,000 molecules that can be downloaded or viewed online" - http://www.webmolecules.com

• Enhanced NCI Database Browser (Database status: 246,182 open structures ready for searching) -
  • In Europe (with Chemdraw/ISISDraw like Java 2D structure Editor) : http://vermeer.organik.uni-erlangen.de/ncidb/frame.html
  • 2D and 3D Structural Information: The NCI has collected information on almost half a million structures in the past forty years. The following collections of structural information are freely available: http://dtp.nci.nih.gov/docs/3d_database/structural_information/structural_data.html
  • Selection of the Diversity Set: http://dtp.nci.nih.gov/branches/dscb/diversity_explaination.html

  http://www2.organik.uni-erlangen.de/services/index.html

• TORVS Research Team - Freely Accessible Chemical Internet Services - http://www2.organik.uni-erlangen.de/services/index.html
  • Includes:
  • 3D Coordinates for Chemical Structures: http://www2.organik.uni-erlangen.de/services/3d.html
  • GIFs of Chemical Structures: http://www2.organik.uni-erlangen.de/services/gifcreator/index.html
  • Calculation and 3D Visualization of Orbitals: http://www2.organik.uni-erlangen.de/services/orbital/index.html
  • The WWW Chemical Structures Database: http://www2.organik.uni-erlangen.de/services/webmol.html
  • The NCI enhanced Database Browser: http://www2.organik.uni-erlangen.de/ncidb/index.html
  • The TeleSpec Infrared Spectra Simulator: http://www2.organik.uni-erlangen.de/research/ir/index.html
  • Calculation of Physicochemical Properties: http://www2.organik.uni-erlangen.de/software/petra/access/index.html

• Pro Chemist Model - http://pro.chemist.online.fr

• Computer Aided Chemistry and Biotechnology Software for Silicon Graphics - http://www.chemie.fu-berlin.de/chemistry/misc/chemsoft.html

• Computational Chemistry Software - http://www.chamotlabs.com/cl/Freebies/Software.html

• Computational Chemistry Software - http://www.ccl.net/cca/documents/chamotlabs/Software.shtml

• Flash Fire Designs - http://www.flashfire.com/

• Molecular Modelling Software (with weblinks to mentioned software) - http://www.infochem.co.uk/software/modelling/index.htm

• Demo software and freeware (including IR software) with weblinks - http://www.softshell.com/FREE/IndexX.html

• Cobra 3D Model Builder (2D to 3D conversion) - Oxford Molecular - http://www.oxmol.com

• ChemWindow (2-D and 3-D Chemical Structure Presentations) - http://www.softshell.com/

• Molecules 3D from Molecular Arts Corporation (Windows and Mac): (2-D to 3-D Chemical Structure Presentations, Building and Optimisation) - http://www.molecules.com/products.shtml

• ChemDraw (2-D and 3-D Chemical Structure Presentations) - http://www.camsoft.com/

• ISISDraw (2-D Chemical Structure Presentations) - http://www.mdli.com/download/idrawdown.html

• Chemistry 4-D Draw (2-D Chemical Structure Presentations, Nomencalture) - http://www.cheminnovation.com/chem4dd.html

• ArgusLab Molecular Modeling Program - http://www.planaria-software.com

• The STR3DI Molecular Modelers by EXORGA (including the QVBMM molecular mechanics force field) - http://www.exorga.com | http://www.exorga.com/exorga0.htm. Downloadables: http://www.exorga.com/exorga6.htm.

• Beilstien Information (Organic Chemistry) - http://www.belstein.com/

• ACD/Labs: Windows-based structure drawing and analysis tools - ACD/ChemSketch - Advanced Chemistry Development Inc - http://www.acdlabs.com | http://acdlabs.co.uk/

• Chem-X - molecular modeling programs for Macintosh, PC (Windows, Windows/95) and UNIX computer systems - Chemical Design, Ltd. - http://www.netsci.org/Companies/CDL/top.html | http://www.oxmol.com | http://www.oxmol.com/prods/chem-x/

• Concord: quickly generate 3D structures from 2D or 2.5D connection tables - Tripos Associates - http://www.tripos.com

• MOE (Molecular Operating Environment) - Molecular Builders from the Chemical Computing Group - http://www.chemcomp.com/feature/builders.htm

• Galaxy: 2D and 3D molecule building software.- http://www.am-tech.com/galaxysummary.html

• SCARECROW (replaced by gOpenMol): A program for the display of molecular structures and the analysis of molecular dynamics trajectories - http://www.csc.fi/lul/chem/scarecrow/jmg_scare.html
  • "Cooperative effects in the transport of small molecules through an amorphous polymer matrix": http://www.csc.fi/lul/chem/movies/pib/pib_movies.html
  • gOpenMol: http://laaksonen.csc.fi/gopenmol/gopenmol.html

• ChemWeb - Draw GIFS of 2D Chemical Structures for the Web: http://www.softshell.com/FREE/ChemWeb/cw-pages.html

• List of Molecular Modelling Software: http://www.infochem.co.uk/software/modelling/index.htm

• Spock is a full-featured molecular graphics program, knows about crystallographic symmetry (and also allows shared screens/conferencing over the internet): http://quorum.tamu.edu/spock/
  • Image Gallery (looks very nifty) - http://quorum.tamu.edu/spock/images.html

• Spartan/PC Spartan: "Full range of computational methods, conformation searching, interfaces, and much more, this is our most powerful package. Organics, Inorganics, PolyPeptides" - http://www.wavefun.com/software/software.html

• ZINDO: "molecular electronic structure programs" - http://www.qtp.ufl.edu/zindo.html

• StrukEd (2D drawing and conversion to 3D) - http://www.softshell.com/FREE/ChemWeb/cw-pages.html

• CONVERTER - Biosym Technologies
• HyperChem
• Sketcher (in Insight II) : draws molecules in 2D and automatically convert them to 3D models.
• INTERCHEM is a molecular modeling system designed for use on Silicon Graphics workstations.
• Latticepatch is an interactive graphics program for data collection optimisation for CCD systems.
• MacroModel is a molecular mechanics/dynamics program - W. Clark Still, Columbia University.
• Molecular Presentation Graphics - Windows based chemical structure drawing program - ACS Software.

• MOPAC (Molecular Orbital PACkage) is a general purpose semiempirical molecular orbital package developed by J.J.P. Stewart and co-workers
  • Refer QCPE - Quantum Chemistry Exchange Program: http://www.ccl.net/cca/html_pages/qcpe/QCPE/index.html
  • Rules and Mailing List: http://www.ccl.net/chemistry/aboutccl/rules/index.shtml
  • QCPE Software Catalog: http://www.ccl.net/cca/html_pages/qcpe/QCPE/catalog.html.shtml
  • QCPE Software Catalog: Scattering and Crystallography : http://www.ccl.net/cca/html_pages/qcpe/QCPE/section06.html.shtml
    • 187. Coupled Channel Scattering Matrices
    • 229. CLASTR: Monte Carlo Quasi-Classical Trajectory Program
    • 187. Coupled Channel Scattering Matrices
    • 229. CLASTR: Monte Carlo Quasi-Classical Trajectory Program
    • 248. CTAMYM: Modification of the Atomic-Diatomic Quasi- Classical Trajectory Program CLASTR (QCPE 229)
    • 273. A+BC: General Trajectory Program
    • 305. MOLMOL: Potential Energy Surfaces for the Interaction of Two Linear Molecules
    • 316. MINI A+BC: Minicomputer-Adapted Version of the QCPE 273 General Trajectory Program
    • 352. RXN1D: A Program to Solve the Quantum Collinear Reactive Scattering Problem
    • 359. RXN1D: A Program to Solve the Quantum Collinear Reactive Scattering Problem (IBM Version)
    • 451. HOTATOM: Stochastic Program for Simulated Collision Events
    • 453. MERCURY: A General Monte Carlo Classical Trajectory Program
    • 472. TDPT: Exponential Time-Dependent Perturbation Theory for Inelastic Scattering
    • 46. SYMPRO: Symmetry Projection Program
    • 149. CARTCORD: Cartesian Coordinates for Lattice Atoms in a Crystal
    • 163. IRREP: Description of a FORTRAN Program for the Calculations of Irreducible Representations of Finite Groups
    • 201. CRYSMO: CNDO-MO Calculations on Hydrogen-Bonded Molecular Crystals
    • 215. DIHEDR: Subroutine to Calculate the Value and the Sign of the Dihedral Angle of 4 Atoms Bonded L1-L2-L3-L4
    • 216. Crystal-Field Splitting Calculations for Trivalent Lanthanide Ions (Main Program and Eleven Subroutines)
    • 222. MADE: Coulombic Lattice Energy of an Ionic Crystal
    • 259. SYMPRJ/SYMPW: Symmetry Projection Programs
    • 325. MCA: A General Program for Molecular Crystals Analysis
    • 331. PPUR: Powder Pattern Program
    • 345. GHMC: A Computer Program for Generating Hydrogen Atom Positions
    • 373. PCK5/PCK6: Molecular Packing Analysis in Crystals
    • 377. Programs for the Calculation of Normal Modes and Structure Factors for Crystals and Molecules
    • 392. JKNIFE: A Nonparametric Statistical Test of Variance
    • 442. ANVPDA: Analysis of N Vertex Polyhedral Dihedral Angles
    • 467. PARST: Routines for Calculating Molecular Parameters from Results of Crystal-Structure Analysis
    • 481. PCK83: A Crystal Molecular Packing Analysis Program
    • 520. POWDRFIT: Derivation of Unit-Cell Parameters from Powder Pattern
    • 521. CLUST: Simulation of the Intensity Diffracted by a Spherical Cluster
    • 548. PCK83: A Crystal Molecular Packing Analysis Program (IBM 3090 Version)
    • 550. PDM87: Least-Squares Net Atomic Charges or Site Multipoles from the Surrounding Molecular Electric Potential