From: Vasiliy Triandafilidi (
Date: Thu Apr 09 2015 - 19:25:44 CDT

Bharat what software do you use for your simulations? LAMMPS? if yes, then you can use topotools to transform the .data file into a .psf file.
Please have a look here: <>

Another way would be to guess your bonds just as John said, luckily topotools can do that as well. <>


> On Apr 9, 2015, at 9:49 AM, John Stone <> wrote:
> 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
> 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
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