Re: Removal H--H bond paths in AIM topoloy using Multiwfn and VMD

dummy@example.com (sobereva) — Tue, 20 May 2025 16:26:22 +0000

To delete it in Multiwfn, in the topology analysis interface, choose " -5 Modify or print detail or export paths, or plot property along a path", and then "3 Delete some paths", then follow the prompts to input.

You can also choose to show/hidden some topology paths in VMD. In the paths.pdb exported by Multiwfn, you can find different paths correpond to different residue index. So, in VMD, you can enter "Graphics" - "Representation", and in "Selected Molecule" select the ID used to showing paths, then if you input e.g. "not resid 3" in the "Selected Atoms" box, then the 3rd path will be invisible.

Deleting H-H bond path is often acceptable, as it usually only implies an extremely weak interaction (except for case of dihydrogen bond, which is a relatively prominent interaction and the strength is often comparable to H-bond).

Removal H--H bond paths in AIM topoloy using Multiwfn and VMD

dummy@example.com (baymor) — Tue, 20 May 2025 13:05:27 +0000

Hello Dear Prof Tian,

I am plotting an AIM topology map for a complex using Multiwfn and VMD; however, I see some H--H bond paths that I want to delete.

Please, how can I delete the H--H bond paths using both Multiwfn and VMD?

Also, is it appropriate to delete H--H bond paths when we use AIM topology as an image to inteprete?

Thank you in advance.