VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 03 2002 - 14:01:36 CST

Dear Phuong,
  VMD isn't really designed to work with structures that have
overlapping or otherwise duplicated atoms. The distance based
search is exactly the reason you're having the problems with the
bonds. It finds phantom bonds from atoms to their duplicates,
among others. If you really want them to overlap like this, but
to have any semblance of correct bonds then you're going to have
to use a PSF file, the distance based search can't do anything
reasonable with duplicated atoms. I don't know why you need to have
these duplicate atoms, but VMD just isn't designed to work with
structures like that. Perhaps you can explain why you need the
duplicates within a single molecule?? You could always load the
duplicates as separate molecules rather than as the same molecule,
which would at least eliminate half of your problems.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Apr 03, 2002 at 08:49:57PM +0200, Nguyen Hoang Phuong wrote:
>
> Dear Paul,
>
> I know that my pdb files have many ideltical water molecules but that is
> my purpose. VMD works fine for each pdb file (even though there are
> duplicate waters in that file). If VMD use the criterion distance to make
> the bonds for each pdb file then there will be no problem, isn't it?
>
> Regards,
>
> Phuong
> -----
>
> On 3 Apr 2002, Paul Grayson wrote:
>
> > John wasn't clear about this in his email: your pdb files have many
> > duplicate copies of water molecules (you have only 10 waters but 66
> > atoms!) Fix that and the problem will go away.
> >
> > -Paul
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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