Many times Geometry optimization gets very time consuming ( even with access to super-computers ). I have seen some pre-optimized libraries for biomolecules like proteins that you can easily download machine optimized files from.

I use Avogadro, GAMESS and McMolPlt for my quantum calculations. I am thinking such libraries should exist for some complex chemical structures ( usable on softwares mentioned above ) but couldn't find any.

At this point I am specifically interested in " Hydroxyapatite Crystals ". Does anyone know such resources ?


2 Answers 2


Short answer: we're building one for molecules

In your case, you don't actually want molecules. You're mentioning crystals. In that case, I suggest the Crystallography Open Database or if you have access, try the commercial Cambridge Crystal Structure Database. The COD is planning a theoretical crystal database, but I don't think it's online yet. These are experimental x-ray structures, but should be good starting structures for solid-state simulations.

For molecules, my group is building one. It's the Pitt Quantum Repository There are a few related efforts that I'm aware of.

With the PQR, you can either search through the website (even on mobile). The database is keyed by InChI keys, so if you have an existing structure you can generate the InChIKey and then get the structure, e.g.:

The long answer is that some commercial software vendors consider such libraries as violations of the license. No joke, I've planned this for years to augment Avogadro, but the company behind a leading program told me that they would void my license to distribute output files in this fashion.

With the rise of community and open source quantum chemistry software, this is moot. Use programs that let you distribute output files. What remained was:

  • Gathering the 3D coordinates (i.e., a low-energy conformer) of X thousand/million molecules
  • Obtaining the computer time to optimize all of them
  • Devoting a server and disk space to serving them
  • Having a great website to help view, browse, and search them
  • $\begingroup$ Thank you ! We have done some simulations in Colorado and I will be more than happy if I can contribute to that repository project. $\endgroup$
    – Aug
    Feb 7, 2015 at 5:25
  • $\begingroup$ Incidentally, we only have ~64k molecules right now at the PM7 semiempirical level and growing, so PQR may not be right for every purpose. $\endgroup$ Jul 6, 2015 at 16:31
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    $\begingroup$ @GeoffHutchison, anyway, I wish your group good luck with the PQR project. $\endgroup$
    – Wildcat
    Jul 6, 2015 at 21:04
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    $\begingroup$ @Wildcat It's further ironic, since the founder of the "unmentionable program" actually wanted to have something exactly like PQR. We'll be adding more model chemistries for people to compare and contrast later this year. $\endgroup$ Jul 7, 2015 at 2:00
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    $\begingroup$ What is your guys' favorite probability distribution? Lorentzian? Binomial? Boltzmann? It's got to be one of those, right? No? Which one did I leave out? $\endgroup$
    – Curt F.
    Jul 7, 2015 at 21:48

You could try figshare.com for comp chem files and http://www.ccdc.cam.ac.uk/pages/Home.aspx for crystal structures.


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