VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jun 05 2015 - 02:04:34 CDT

On Fri, Jun 5, 2015 at 2:04 AM, SaeeD PourasaD <saeedpourasad_at_gmail.com> wrote:
> Dear VMD users ,
>
> I Have a XYZ trajectory file and I want to analyse breaking / forming
> hydrogen bonds with using of VMD .
>
> I tried to use h.bonds plugin of vmd but unfortunately I couldn't !

that is not very helpful description.

> Can you please let me know what I have to do ?

the hydrogen bonds plugin is effectively a GUI wrapper around the
measure hbonds command in VMD
http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.2/ug/node138.html
thus it is subject to the same limitations and requirements, e.g. your
input has to conform to the naming conventions expected by VMD
(typically CHARMM based)

most likely your file doesn't conform to the expectations of VMD, so
it cannot identify potential H-bond donors and acceptors and possibly
not even the hydrogens itself.

> I have attached my file with this Email.

no, you didn't.

> Best ,
> Saeed.
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.