VMD-L Mailing List

From: Bharat Sharma (bharatsolbridge_at_gmail.com)
Date: Thu Apr 09 2015 - 20:01:46 CDT

Thank you John. I don't mind vmd guesses the bonds but at some point it
stops saying "determining bond distance from distant search". It works fine
for few hundred frames and suddenly stuck there. I am not sure whether vmd
is not able to guess bonds or not.

Vasiliy: I use CP2K. I will check topotools-tutorial. Thank you.

Best regards,
Bharat

On Thu, Apr 9, 2015 at 8:25 PM, Vasiliy Triandafilidi <
vasiliy.triandafilidi_at_phystech.edu> wrote:

> 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
>
> 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
>
> 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/
>
>
>