VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 09 2015 - 11:49:16 CDT
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).
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 .
-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/