VMD-L Mailing List

From: Vasiliy Triandafilidi (vasiliy.triandafilidi_at_phystech.edu)
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: http://bazilevs31.github.io/using_vmd.html <http://bazilevs31.github.io/using_vmd.html>

Another way would be to guess your bonds just as John said, luckily topotools can do that as well. https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-1 <https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-1>

Cheers,
Vasiliy

> On Apr 9, 2015, at 9:49 AM, John Stone <johns_at_ks.uiuc.edu> 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
> 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
> 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/
>