CCL:G: Overlaying conformers for visualization

[Michel Petitjean <petitjean.chiral|gmail.com>]

 Sent to CCL by: Michel Petitjean [petitjean.chiral : gmail.com]
 Dear Andrew,
 There are two cases:
 (1) The atom numbering is the same for all conformers.
 (2) The atom numbering is different.
 In case (1), there are many softwares which perform an optimal
 superposition of two conformers  (optimal, in the sense of minimizing
 the RMSD).
 E.g., ARMS do that and outputs the coordinates of the moved conformer
 superposed on the reference one.
 http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ARMS
 In case (2), CSR retrieves the pairwise correspondence and then
 computes the minimized RMSD, as in ARMS.
 http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#CSR
 Pls be careful: in both cases you must define one of your conformers
 as the reference one, because, when conformer 2 is optimally
 superposed on conformer 1 and conformer 3 is also optimally superposed
 on conformer 1, then in general conformer 3 is not optimally
 superposed on conformer 2.
 Best regards,
 Michel Petitjean
 Université Paris Cité, BFA, CNRS UMR 8251, INSERM ERL U1133, F-75013
 Paris, France
 Phone: +331 5727 8434; Fax: +331 5727 8372
 E-mail: petitjean.chiral.[-].gmail.com (preferred),
         michel.petitjean.[-].u-paris.fr
 http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html
 Le mer. 27 avr. 2022 à 05:09, Andrew DeYoung
 andrewdaviddeyoung**gmail.com <owner-chemistry.[-].ccl.net> a écrit :
 >
 > Hi,
 >
 > I'm a postdoc and quantum chemistry novice.  I've run geometry optimization
 ("Opt") using Gaussian to find several molecular geometries
 corresponding to local minima on the potential energy surface for a single
 molecule.  The geometries are similar but not exact.  I'd like to overlay
 several geometries in order to visualize, qualitatively, how they differ.  In
 other words I want to overlay multiple conformers.
 >
 > Could someone please suggest a relatively simple way to overlay geometries
 for visualization?  I have access to GaussView, Avogadro, VMD, and any other
 freeware applications you can think of.  The molecular geometries are in
 separate .log files (i.e., output from Gaussian), but of course it is easy to
 convert these to almost any other chemical file format, using Avogadro or the
 like.
 >
 > I realize, though, that "overlaying several conformers" is not a
 unique specification; one would need to specify which atom(s) to try to overlap
 exactly.  Is there an algorithm in a computational chemistry program that does
 this?
 >
 > Thank you for any guidance you can provide!
 >
 > Andrew
 >
 > Andrew DeYoung, PhD
 > Department of Chemistry
 > Carnegie Mellon University