From: Bharat Sharma (
Date: Thu Apr 09 2015 - 09:43:10 CDT

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 .