VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jul 31 2002 - 08:12:28 CDT

Dear Pascal,
  You could probably modify the "pick_bonds" script from the
VMD script library to do this for you pretty easily. It is
intended to be used interactively, but by reading the User's
guide and looking at the pick_bonds script, you should be able
to write your own script that does whatever you want, by combining
an atom selection with some looping to delete the bonds you don't
want. The "pick_bonds" script is available on our web site here:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/pickbond/

The "setbonds" command which can be used on an atom selection
is in the User's guide in the section on the atomselect keywords:
  http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node108.html#ug:ui:text:atomselect

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jul 31, 2002 at 12:52:07PM +0100, Pascal Bonnet wrote:
> Hi,
>
> When I download a topology file and a AMBER6 trajectory file, bonds
> are drawn between the two hydrogens of the TIP3P water model.
>
> Is it possible to delete all the bonds in a quick way?
> The residue name of water is WAT
> the atom name are H1 H2 and O
>
> Thanks
>
> pascal 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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