Molecular modeling software

11 Jul

One of the very useful things I’ve learned at DTU is how to use several kinds of molecular modeling and computational chemistry software. Among them are:

Spartan – commercial, but there’s a trial available. Can do molecular mechanics, semi-empirical methods, ab initio models, DFT methods, post Hartree-Fock methods, and quantum chem composite methods.

Pymol – free, open source, Python-based. Allows you to create pretty images of proteins.

VMD (Visual Molecular Dynamics) – open source and free to academics. A molecular visualization program for displaying, animating, and analyzing large biomolecular systems -f.ex., ligand-binding.

Schrödinger Suite, including Maestro, MacroModel, and Jaguar – commercial. Maestro is a nice, user-friendly, visual interface for molecular modeling and reaction simulation. Macromodel (accessible through Maestro) uses force field methods to calculate pretty accurate relative energies for your chemical systems. Even more powerful is Jaguar, which employs ab initio QM methods to characterize reactions mechanisms and transition states.


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