From: I. Camps (icamps_at_gmail.com)
Date: Tue Dec 27 2022 - 14:54:19 CST

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/
>