1. VMD, which is free of charge:
a. Main webpage: https://www.ks.uiuc.edu/Research/vmd/
b. Tutorials. http://www.ks.uiuc.edu/Training/Tutorials/vmd-index.html
c. Using VMD in AMBER: http://ambermd.org/tutorials/basic/tutorial2/
d. Plugins: http://www.ks.uiuc.edu/Research/vmd/plugins/
2. GaussView, which is developed by the Gaussian, Inc.:
a. Main webpage: https://gaussian.com/gaussview6/
b. Gaussian & GaussView tutorials: https://gaussian.com/videos/
3. Pymol:
a. A version that is developed by the Schrödinger, Inc.: https://pymol.org/2/
b. A version can be downloaded through conda: "conda install -c mw pymol"
c. Downloaded from Sourceforge: https://sourceforge.net/projects/pymol/
d. Pymol for beginners: https://pymolwiki.org/index.php/Practical_Pymol_for_Beginners
e. Pymol Wiki: ymolwiki.org/index.php/Main_Page
f. Pymol Wiki Gallery: https://pymolwiki.org/index.php/Gallery
4. UCSF Chimera, which is free of charge:
a. Main webpage: https://www.cgl.ucsf.edu/chimera/
b. Chimera tutorials: https://www.cgl.ucsf.edu/chimera/tutorials.html
5. Molekel, which is free of charge:
a. Main webpage: https://ugovaretto.github.io/molekel/
b. Video tutorials: https://ugovaretto.github.io/molekel/wiki/pmwiki.php/Main/VideoTutorials.html
6. Avogadro, which is free of charge:
a. Main webpage: https://avogadro.cc/
b. Manual: https://avogadro.cc/docs/
7. Molden, which is free of charge:
a. Main webpage: http://cheminf.cmbi.ru.nl/molden/
b. Install Moden 5.7 on a Mac: https://people.unica.it/massimilianoarca/2018/02/13/compiling-molden-5-7-on-macos-high-sierra-how-to/
Note: one may need to change the "X11R6" strings to "X11" in the make file before installing.
8. IboView:
a. Main webpage: http://www.iboview.org/
9. Macs in Chemistry, a lot of programs are introduced there:
a. Main webpage: https://www.macinchem.org/
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