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Molecular Modeling

Commercial Software

  • 3D Viewer: converts 2D structures into 3D with simple MM2
  • Alchemy 2000: semi empirical, QSAR, Protein, Polymer, LogP
  • AMPAC: semiempirical quantum mechanical program
  • AMSOL: semi empirical, solvation models for free energies of solvation in aqueous solutions and in alkane solvents
  • Personal CAChe: visualize molecules in 3D, search for conformations, analyze chemical reactivity and predict properties of compounds
  • Quantum CAChe: Personal CaChe plus molecular dynamics and semi-empirical MOPAC and ZINDO quantum mechanics
  • Chem3D: MOPAC and Gaussian integration, ChemProp, ...
  • Gaussian 98W: MP2, MP3, MP4, MP5, HF, CASSCF, GVB, QCISD, BD, CCSD, G1, G2, ZINDO, ONIOM calculations, DFT excited states, VCD intensities, ...
  • GROMOS: general-purpose molecular dynamics computer simulation package for the study of biomolecular systems
  • Hyperchem Suite: semi empirical, RMS Fit, Molecule Presentations, Sequence Editor, Crystal Builder, Sugar Builder, Conformational Search, QSAR Properties, Script Editor ...(Hyperchem Pro, Hyperchem Std.)
  • Jaguar: electronic structure calculation
  • MacroModel: allows the graphical construction of complex chemical structures mechanics and dynamics techniques in vacuo or in solution
  • MOPAC 2000: the latest version of MOPAC
  • Spartan: MM, semiempirical, ab initio, DFT, ...
  • Titan: TITAN is the union of Wavefunction's versatile, easy-to-use interface with fast, computational algorithms from Schrödinger's Jaguar
  • WinMOPAC: based on MOPAC
  • Shareware/Freeware

  • 3D Viewer for ISIS Draw: converts 2D structures into 3D with simple MM2
  • Biomer: online java applet, model builders for polynucleotides (DNA/RNA), polysaccharides and proteins, interactive molecule editor, AMBER force-field based geometry optimization, simulated annealing with molecular dynamics, and the ability to save gif, jpeg, and ppm images
  • Chem3D Net: demo version of Chem3D
  • COLUMBUS: high-level ab initio molecular electronic structure calculations
  • Dalton: quantum chemistry program
  • GAMESOL: calculate free energies of solvation based on fixed, gas-phase solute geometries interfacing GAMESS
  • GAMESS: General Atomic and Molecular Electronic Structure System is a general ab initio quantum chemistry package
  • Gaussian Basis Set: get any Gaussian basis set you can imagine
  • GROMACS: fully automated topology builder for proteins, molecular dynamics, leap-frog integrator, position langevin dynamics, normal mode analysis, electrostatics, non-equilibrium MD, NMR refinement with NOE data, large number of powerful analysis tools, ...
  • Hückel: constructs the Hückel matrix, the programs then calculate, display
  • MOIL: molecular modeling, energy minimization and molecular dynamics simulation for biomolecules like proteins
  • Moldy: molecular dynamics simulation program, liquids, solids, rigid surfaces
  • MOPAC: general purpose semiempirical molecular orbital package for the study of chemical structures and reactions
  • MOPAC 5.08mn: modified version of MOPAC
  • NWChem: quantum package for supercomputers and Linux, SCF, RHF, UHF, DFT, CASSCF, interface to Python programming language
  • OMNISOL: calculating free energies of solvation for organic molecules containing H, C, N, O, F, S, Cl, Br, and I in water and organic solvents
  • PC GAMESS: GAMESS for the Intel community
  • Q: molecular dynamics package designed for free energy calculations in biomolecular system
  • Tinker: molecular modeling software is a complete and general package for molecular mechanics and dynamics

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