- NAMD
http://www.ks.uiuc.edu/Research/namd/
A parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code.
- AMMP
http://www.cs.gsu.edu/~cscrwh/ammp/ammp.html
A free program suite for molecular mechanics, dynamics and modeling with some special features like docking or ab initio DFT calculations. Runs under Linux/Unix and Win9x. The site provides access to the documentation and offers on-line tutorials.
- B: On-line Molecular Modeling
http://www.scripps.edu/case/Biomer/
"B" (formerly known as Biomer) is a Java-based molecular modeling program for small organic molecules and biopolymers. Supports nucleic acids (DNA/RNA), polypeptides, polysaccharides, the AMBER force field, geometry optimization, simulated annealing. Exports jpeg, gif, and ppm images.
- Ghemical
http://www.uku.fi/~thassine/ghemical/
An easy-to-use molecular editor and modeling package with all-atoms molecular mechanics, reduced protein models and links to many common chemistry programs. Ghemical is released under the GNU GPL and includes source code.
- TINKER
http://dasher.wustl.edu/tinker/
A free molecular modeling package for molecular mechanics and dynamics, with some special features for biopolymers. Distributed as source code and as binaries for Windows9x, Linux and Mac.
- Genmol
http://www.3dgenoscience.com/index.php
Genmol is a 3D molecular modeling software for measuring resistance/affinity between a ligand and a target, used for Disease Management, Drug Discovery and Development of molecules.
- Amber
http://amber.ch.ic.ac.uk/
A general purpose molecular mechanics and molecular dynamics package with the capability to compute free-energy changes.
- YASARA
http://www.yasara.org/
(Yet Another Scientific Artificial Reality Application) is an interactive real-time molecular dynamics program.
- PDB Viewer
http://www.geocities.com/pdbviewer/
Downloads for Windows and Linux, to visualize three dimensional structure of macromolecules, using protein data bank format for atom coordinates, from ex-student at University of Manchester, England.
|
