From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 07 2006 - 10:55:23 CST

Hi,
  At present, VMD doesn't calculate the bond order, it either gets this
information from a loaded file which contains bond order information
(such as Biograf, MOL2, etc..) or it sets the bond order to a default value
of 1.0 if VMD's automatic bond determination code ends up being invoked.
You can set the bond orders yourself using atom selections if you have
a way of calculating them. The automatic bond calculation code in VMD
is just a relatively simple heuristic which can potentially be tricked by
unusual atom names, bad VDW radii, or other bad parameters, so if you really
need accurate bond information, the best thing to do is to provide it to
VMD in the structure files you load. That said however, you can change
the bond information in VMD on the fly as you wish, either by manually
correcting any incorrect bonds with the mouse, or by writing scripts.
Let us know if you need more help with this.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 07, 2006 at 01:25:53AM -0800, Weiqiang Wang wrote:
> Hi
>
> Is there a way of changing the default cutoff distance used in calculating the bond order in VMD?
> This way, I wish VMD would be able to give me a different numbond value other than the one calculated from the default cutoff distance.
>
> Thanks.
>
> Weiqiang Wang

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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