VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 24 2005 - 10:21:05 CDT

Hi,
  Have you checked to make sure you have the right units in your
PDB/XYZ file? VMD assumes the units are in Angstroms. That would
easily cause problems with bond determination. When using autobonds 0
you'll want to display the molecule using VDW or one of the other space
filling reps since the atoms will otherwise be drawn as tiny points when
you use the default "lines" mode since there aren't any bonds to draw.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 24, 2005 at 11:06:09AM -0400, Jindal Shah wrote:
> Hello,
> I am trying to view trajectory of water molecules in VMD. When I load a pdb
> or xyz file, the bonds are automatically generated which returns errors due
> to maximum number of bonds exceeded. I checked the vmd mailing list and
> found that the following solution was suggested
>
> mol new myfile.pdb autobonds 0
>
> However, it does not work for me? My pdb or xyz file does not contain any
> information.
>
> Any suggestions?
> Thank you.
>
> Jindal 

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