VMD-L Mailing List

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Sun Jan 24 2010 - 13:22:31 CST

Dear Mert,

On Sun, Jan 24, 2010 at 1:17 PM, Mert Gür <gurmert_at_gmail.com> wrote:
> Dear all,
> I have performed MD in water and loaded my trajectory file into VMD. I can
> see the hydrogen bonds by selecting "within 3 of protein" and "hbonds" as
> the drawing method (Unfortunately I also see the hydrogen bonds among water
> molecules.Also a solution for that would be nice)
> I would like to determine for each time frame how many hyrdogen bonds there
> are between the protein and the water molecules of the solvent.

See http://www.ks.uiuc.edu/Research/vmd/plugins/hbonds/

Cheers,
Leo

> Thanks in advance,
>
> Mert Gur
> CMSE
> Koc University 

-- 
Leonardo Trabuco, Ph.D. candidate
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign