It seems that the Gaussian output provides the Cavity area only. Is it possible for using Gaussian to get accessible surface area for organic compounds? Do I need to add any keyword in the input file to enable this calculation? Or is there anybody could provide the method of obtaining accessible surface area from Spartan calculation?
Thank you!
When it comes to anything "solid" like "a surface of some-thing" (which is a useful concept), isn't QM somewhat lost as to what is a surface and, if it can define it, where the surface is?
Hi Muxue,
Convert your Gaussian output file to PDB file by OpenBabel.
http://openbabel.org/wiki/Main_Page
Then calculate its ASA. Check the following links:
https://en.wikipedia.org/wiki/Accessible_surface_area
http://freesasa.github.io/
http://mgltools.scripps.edu/packages/MSMS/
. . . except that PDB file does not contain any quantum-mechanical information. The coordinates of the centers of the atoms are metaphysical rather than physical for at the center of anything there is not the thing to which the center is both its center and source of its manifestation.
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