VMD-L Mailing List

From: Mert Gür (gurmert_at_gmail.com)
Date: Sun Jan 24 2010 - 14:00:32 CST

Thanks a lot Leonardo,
I didn't had that option in my current version of VMD.
Best,
Mert

On Sun, Jan 24, 2010 at 9:22 PM, Leonardo Trabuco <ltrabuco_at_ks.uiuc.edu>wrote:

> 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
>