TINKER :-Molecular modelling

TINKER a molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for polypeptides. TINKER has the ability to use any of several common parameter sets, such as AMBER-95, CHARMM22, MM2(1991), MM3(2000), OPLS-AA and OPLS-UA.

Tessellator :- Molecular volume visualisation

Tessellator is an application for the tessellation of 3D volume in and around biological molecules. It creates Tcl script files which are run within VMD to visualize volumes in context with their associated molecular structures

Tonto :- Quantum Chemistry

Tonto is a free package for doing quantum chemistry simulations. The main objective of Tonto is to be simple--simple to understand, simple to use, and most importantly, simple to hack

TmoleX :- GUI for Turbomole

COSMOlogic provides a graphical user interface for Turbomole, TmoleX 2.1, as a cost-free add on for the Windows, Linux and MacOS X version of Turbomole 6.0.
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TurboMole :- DFT & ab initio Quantum Chemistry

TURBOMOLE is one of the fastest and most stable quantum chemistry codes available. With over 20 years of development on HF, DFT and MP2,  its RI-DFT method is up to 10 times faster than many comparable codes. TURBOMOLE was developed by Prof. Ahlrich's group at the University of Karlsruhe to deal with practical applications and large systems (> 100 atoms), and to create accurate COSMO (input) files for COSMOtherm.

VASP :- Vienna Ab-Initio Simulation Package

VASP is a Fortran90 plane-wave DFT code which can be run as a single-cpu or MPI-parallel code. It runs on many platforms, too many in fact for the VASP group to test and support VASP on all of them. Peter Klaver ported VASP to MacOSX using LAM-MPI and the IBM XLF/XLC compilers for MacOSX (now using gcc instead of XLC for MacOSX 10.4 'Tiger'). Performance is excellent and he has written a 'How to install+run VASP for dummies' instruction

Viewmol :-Molecule viewer

Viewmol is a graphical front end for computational chemistry programs. It is able to graphically aid in the generation of molecular structures for computations and to visualize their results

VMD :-Molecule viewer

VMD 1.8.5 VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X,and now uses native windowing and hardware acceleration. The vmd-xplor package is a combination of VMD with the xplor structure determination package
From Clipboard

Vortex:- Cheminformatics Data Analysis

Vortex can import files in a variety of formats, it provides depiction and structure based searching, together with property calculations tightly integrated with excellent charting and analysis tools.

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WebMo:- Front end to Computational Chem

WebMO is a free World Wide Web-based interface to computational chemistry packages.
  • Support for Gamess 1999+, Gaussian 94/98/03, MolPro 2002/2006, Mopac 7/93/200X, NWChem 4/5, PQS 3.3, QChem 2/3, and Tinker 4
  • Users draw structures in a 3D java editor, run calculations, and view results, all from their web browser
  • No software to install on the client. WebMO is installed only on the single web server that runs or accesses the computational chemistry programs
  • All administrative tasks (user accounts, program configuration, job time limits, etc) are performed through a web browser interface
  • Simple enough for undergraduate computational chemistry curriculum: reasonable default values and results are presented on web pages
  • Flexible enough for computational chemistry research: full access to input and output files
  • Works fully with Internet Explorer 4.0+ (Windows), Safari (Mac), Mozilla Firefox (Windows, Mac, Linux/unix), and other browsers

Widgets :- A collection of widgets

A collection of widgets, if you see any I've missed please let me know

XDrawChem :-Structure drawing

XDrawChem is a two-dimensional molecule drawing program for Unix operating systems. It is similar in functionality to other molecule drawing programs such as ChemDraw (TM, CambridgeSoft). It can read and write MDL Molfiles, and read ChemDraw text and binary files, to allow sharing between XDrawChem and other chemistry applications, and it can create images in popular formats like PNG and EPS.

X-score :-Calc binding affinity

X-score is a scoring function that computes the binding affinities of ligands to a target protein (Dr. Xueliang Fang and Dr. Renxiao Wang J. Med. Chem. 2003, 46 2287) whilst it was written for SGI it compiles fine with either Apples GCC or the IBM c++ compiler.

Zodiac :- Human steered molecular docking

Zodiac is the result of work by Nicola Zonta on developing an environment for human steered computation approaches to drug design. The application is built upon OpenBabel and the aim is to use simple input devices to allow the user to interact with a molecule and guide it into an active site. To date they have implemented haptic device support so you can feel when the molecule bumps into the receptor, and wiimote head tracking for 3D visulisation.
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The application is still in early development but already has impressive graphics capabilities. In addition Zodiac now includes a front-end to the PLANTS docking engine.
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Zem:- Molecular Editor

The first beta release of Zem a molecular editor is now available.

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Zephyr:- Molecular Mechanics

OpenMM Zephyr is a freely available molecular simulation application with an easy-to-use graphical user interface. It is built on top of the visualization tool VMD and a special version of the molecular dynamics code GROMACS. This version of GROMACS uses the OpenMM API for GPU-accelerated molecular simulations. The new release is able to run on Mac OSX and further simplifies the installation process. See the Zephyr website at http://simtk.org/home/zephyr for a list of other features that were added and to download.

With version 0.9.2, OpenMM Zephyr makes it even easier to run molecular dynamics simulations. OpenMM Zephyr is a freely available molecular simulation application with an easy-to-use graphical user interface and GPU-acceleration capabilities on both NVIDIA and ATI GPUs. This latest version of OpenMM Zephyr has automated many of the steps for converting PDB molecule files into the format required for the simulations.

M. S. Friedrichs, P. Eastman, V. Vaidyanathan, M. Houston, S. LeGrand, A. L. Beberg, D. L. Ensign, C. M. Bruns, V. S. Pande. “Accelerating Molecular Dynamic Simulation on Graphics Processing Units.” J. Comp. Chem., (2009), 30(6):864-872 (2009)