VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 02 2004 - 10:36:41 CST

Hi,
  Generally speaking, if you want correct bonding you'll need to supply
files that contain bond information, such as PSF files. When loading
a PDB file or similar file formats, VMD ends up having to "guess" the
bonds with a distance-based bond determination heuristic. This heuristic
is not foolproof, and will sometimes make bad choices. The dynamic bonds
rep does the same thing, except that the bonds are re-evaluated for each
timestep in a trajectory, and you have control over the cutoff distance
scaling factor. Let me know if you need more help with this.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Apr 02, 2004 at 03:27:38PM +0300, Arturas wrote:
> Hi,
>
> I have installed VMD 1.8.2 in my Suse 8.2 pro.
>
> When I load *.gro or *.pdb protein molecule into VMD, molecule's bonds
> are extremly long and are disoriented with 'line' type in 'drawing
> method'. Some fragments of protein are drawed correctly.
>
> When I change to to 'bond', 'Hbond' and etc., I see a correct structure.
> In Windows XP VMD works fine.
>
> Any commenst or suggestions.... ?
>
> Have a nice weekend
> Arturas
>
> 

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