VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Mar 30 2022 - 08:15:31 CDT

VMD uses the topology information provided in your input and if there is no
topology data, it will do a heuristic bond search based on a list of
covalent radii with the constraint that any atom whose name starts with H
is considered a hydrogen and then can have only one bond.

Where things can go wrong is when:
- there is no explicit bond topology information in the file you read
- there is no "name" associated with the atoms or something that is not
equivalent to the element so the bond guess is wrong
- the list of covalent radii has no specific value for your elements and
thus VMD uses a default value (which may not be suitable)

You can use atom selections to change names and radii as needed and then
issue the "mol bondsrecalc" command to redo the heuristics.
Or you figure out some other way to get the bond topology data and store it
in a suitable file (e.g. a .psf) file and load that before loading your
actual file.

On Wed, Mar 30, 2022 at 9:08 AM maxim todoru <mtodoru_at_gmail.com> wrote:

> Hi there,
> I performed a wave function analysis for some organic compounds, and I
> need to visualize the results, for that I used VMD, but I found that some
> C-H bonds don't show up. Is there the possibility to change bond length
> maximum in VMD in order to show the missing bonds ? I could use the
> "Topotools", but it's tedious to pick a pair of atoms every time and add
> the bond, especially when the molecule is large.
> Just a note : I found the feature "Custom Bonding Parameters" in Gaussview
> program, which enables us to change the bond length limit between any two
> atoms in the periodic table, but Gaussview doesn't suit me in my work,
> especially in the visualisation.
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!pITLfMciKpDjWUCaJot-5Vzi5TuwqWn43Tuf5F1FRMhSgjhW8Y6EemFICJJD1CDD0g$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.