From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 09 2015 - 11:49:16 CDT

Hi,
  XYZ files don't include bond information and neither do DCD files.
If you don't want VMD to have to guess the bonds, you will need to provide
it with a file that actually contains bond information (e.g. like a PSF
file, a mol2 file, or similar).

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 09, 2015 at 10:43:10AM -0400, Bharat Sharma wrote:
> Hello everyone,
> During the post-production from dcd file, I encountered with "Determining
> bond structure from bond search" after running some steps. I don't get if I
> have few frames.
>
> I am using xyz file initially and loaded dcd file. Since psf is not
> provided, VMD calculates bonds with bond search technique (this is what I
> found on web).
>
> Is there any solution to fix this problem? It may be fine if I use psf
> file. How can I make psf file from xyz format?
>
> I only have water molecules in my xyz file.
>
> Thank you .
>
> Bharat

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
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