1. Open Babel http://openbabel.org/wiki/Main_Page
2. BuildQSAR BuildQSAR is a free program designed to help the QSAR practitioner on the task of building and analyzing quantitative models through regression analysis. The main part of the program is a spreadsheet, in which the user can enter with the data set composed by the structure definition of the compounds, one or more types of biological activity values and many physicochemical properties.
3. Pymol www.pymol.org
4. MOPAC http://openmopac.net/Download_MOPAC_Executable_Step2.html
5. Marvin sketch: https://chemaxon.com/products/marvin
ADF: Amsterdam Density Functional software SCM: Scientific Computing and Modeling URL: http://www.scm.com/
Schrodinger URL: http://www.schrodinger.com
MedeA URL: http://www.materialsdesign.com
Chem3D for Windows URL: http://www.cambridgesoft.com/
WebMO & WebMO Pro URL: http://www.webmo.net/index.html
JSmol (free) is a very popular versatile JAVA-based program that allows structures to be examined in detail, including molecular orbitals. If keyword HTML is used, MOPAC will write a simple web-page that can be opened using JSmol. For examples, see Molecules, Solids, and Animations. http://jmol.sourceforge.net/
Other GUIs for MOPAC2016™ (either untested or unsupported)
Avogadro (free) is an excellent editor for preparing MOPAC input data-sets and for viewing results. Runs on Windows, Mac, and Linux. https://avogadro.cc/
Molden (free) is a good pre/post processing program of molecular and electronic structure that runs on Windows, Mac, and Linux. Z-matrix editing of geometries. http://www.cmbi.ru.nl/molden/molden.html
MoCalc2012 (free) Graphical User Interface for MOPAC, GAMESS (US), Firefly and ORCA http://sourceforge.net/projects/mocalc2012/
Pcmodel by Serena Software is a pre/post processing program of molecular and electronic structure that runs on Windows, Linux, and Macintosh. http://www.serenasoft.com/ http://www.serenasoft.com/prices.html
MolWorks (free) is a molecular builder and pre/post interface to MOPAC and other programs. It runs on Windows, Linux, and Mac. http://www.molworks.com/en/
Winmostar (free for students) is a Japanese and English language pre/post processing program of molecular and electronic structure that runs on Windows. http://winmostar.com/
Facio (free) is a 3D-Graphics program for molecular modeling and visualization of quantum chemical calculations. Facio is available only for Windows platform . http://www1.bbiq.jp/zzzfelis/Facio.html
HyperChem is a complete molecular modeling suite that runs under Windows and Mac. Allows editing, e.g. adding hydrogens. http://www.hyper.com/
AOMix (free) is software for molecular orbital (MO) analysis. It generates total, partial, and overlap population density-of-states (DOS) plots. http://www.sg-chem.net/aomix/