From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Sep 19 2010 - 19:46:44 CDT

Hi,
  This is because you're using an XYZ file, and the waters are so
close together that VMD thinks they are bonded. This is also related
to the choice of atom names, as VMD guesses atom radii and other
properties from atom names, but only if they are specified using the
Protein Databank (PDB) conventions. Otherwise it uses some simpler
guesses, and in your case it is guessing wrong. You can fix this by
setting the atomic element types and/or atom radii manually, or by
loading a file format that includes explicit bond information.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Sep 17, 2010 at 03:37:03PM +0800, Cun Zhang wrote:
> hi, John
> I find vmd can't display water molecules rightly in some case( vmd
> 1.8.8a7).
> Some molecues are regarded as one molecule. It's so weird.
>
> Thank you!
>
> Cun Zhang
>
> The following is th testing file. And a screenshot is attached.
>
> cunzhang_at_Debian:$ cat test.xyz
> 12
> generated by VMD
> OW 140.621994 122.303001 119.871002
> HW 140.358002 121.397003 119.541000
> HW 140.434998 122.984001 119.163002
> OW 143.095993 122.399002 121.165001
> HW 142.190002 122.556000 120.774002
> HW 143.725006 123.107002 120.845001
> OW 142.955002 119.873001 120.723999
> HW 143.567001 119.393997 121.352997
> HW 143.102005 120.859001 120.802002
> OW 140.755005 119.730003 119.224998
> HW 141.153000 120.091003 118.382004
> HW 141.460007 119.676003 119.931000
>
> --
> Blog: http://www.edwardpku.com/cun

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