VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Dec 27 2022 - 16:12:10 CST

Camps,

The bond search heuristics in VMD use the "radius" property of atoms for
the bond search, so you can tweak its behavior by changing that property.
The default (covalent) radius for carbon atom is set to be 1.5 \AA. So you
can try with 1.6 \AA through the following commands after loading the files.

set sel [atomselect top "name C"]
$sel set radius 1.6
mol bondsrecalc top

Axel.

On Tue, Dec 27, 2022 at 4:32 PM I. Camps <icamps_at_gmail.com> wrote:

> Hi John,
>
> My trajectories are in PDB multimode format without the atom connectivity
> information.
> I did a MD using xTB starting with a PDB with all the connections ok.
>
> []'s,
>
> Camps
>
>
> On Tue, Dec 27, 2022 at 1:10 PM John Stone <johns_at_ks.uiuc.edu> wrote:
>
>> Hi,
>> VMD uses a distance based bond determination heuristic when you
>> load files that don't otherwise provide explicit bond connectivity
>> information. The best way to resolve this kind of problem is to use
>> a file format that actually specifies bond connectivity. Since you
>> didn't state what file format you used, my assumption is that it was
>> something like PDB that lacks this information.
>>
>> Best,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Wed, Dec 21, 2022 at 04:49:48PM -0300, I. Camps wrote:
>> > Hello, all,
>> > I have three systems (three carbon nanotubes with different
>> chiralities)
>> > that, when visualized in VMD, some bonds are broken, looking as if
>> the
>> > structure has holes.
>> > Visualizing the same structures in other softwares like Maestro,
>> Jmol,
>> > Avogadro and Chimera, the structures look right: all bonds are drawn
>> and
>> > there are no holes.
>> > Is there any place in VMD where we can manually change the threshold
>> bond
>> > parameters to "fix" this issue?
>> > Thanks in advance.
>> > Camps
>>
>> --
>> Research Affiliate, NIH Center for Macromolecular Modeling and
>> Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> http://www.ks.uiuc.edu/~johns/
>> http://www.ks.uiuc.edu/Research/vmd/
>>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!8FzGgBR1497x-K-SSiF3Crzu3hT-byL9mT7kgkWfRQrd7_7dLR7qhUYtxn8fbMv60zmEsviYxvkBIkAz-Q$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.