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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