CCL:G: Overlaying conformers for visualization

[Anson Thomas <thomasanson53-#-gmail.com>]

Dear Andrew, there are multiple ways to accomplish this.

1. You may open the structure files separately which you want to overlay (say in the xyz format) in Avogadro. Copy all the atoms of one structure and paste them into the other structure window. This will show both the conformers together. You can adjust the orientation of the pasted structure as per your choice.

2. This can also be done using VMD. After opening up VMD, you can load the two structures by going to Files -> New Molecule. This will show the two conformers together.

3. Importing the two structures into Pymol can also help achieve the same. In case you want to get more quantitative information, such as the RMSD, you may enter this command after importing the two structures (say, 1.xyz and http://2.xyz">2.xyz):

align 1, 2, cycles=0, transform=0

This will align the atoms and give you the RMSD value on the terminal. 

Hope this helps.

On Wed, Apr 27, 2022 at 9:20 AM Andrew DeYoung andrewdaviddeyoung**gmail.com <owner-chemistry.:.ccl.net> wrote:

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

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Anson Thomas

M.Sc. Chemistry, IIT Roorkee