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I'm searching for a workflow for extracting cartesian coordinates for multiple moelcules from both a single file (e.g., several conformers from one .spartan file or one multiple molecules, each from multiple Gaussian output files). Any insight would be appreciated. I'm using Ubuntu (14- & 16.04), on a machine on which I do not have either Gaussian or Spartan installed.

Thank you kindly

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  • $\begingroup$ Hello. The common approach is invert some minutes in codding a simple script (using bash, python, perl, for example). It can be done in less than 15 lines of code. $\endgroup$ – user1420303 Aug 31 '16 at 18:37
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The only tool that I know for reading Spartan files (besides Spartan) is Jmol. With some programming or scripting, you will probably be able to save conformers to other files in a workflow - I don't think there is a pre-existing script.

There are multiple open source tools that read Gaussian output files. I would suggest either:

For example to extract a bunch of Gaussian files to XYZ Cartesian:

obabel *.log -oxyz -m

The -m flag indicates "multiple" and the -oxyz indicates that you want XYZ-format files. More is in the manual.

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