VMD-L Mailing List

From: maxim todoru (mtodoru_at_gmail.com)
Date: Tue Mar 29 2022 - 20:04:45 CDT

The structure was stored in .xyz format.

Le mer. 30 mars 2022 à 13:15, Axel Kohlmeyer <akohlmey_at_gmail.com> a écrit :

> 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!oPgQeI5z7a7Hvo8IAhSG0D2JuypOyUWCTH7f_x0dzeO7NJUANlTOLJSiE-g_Z8639w$
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>