VMD-L Mailing List

From: Mert Gür (gurmert_at_gmail.com)
Date: Mon Jan 25 2010 - 07:50:25 CST

Dear Leonardo,
I have read and tried the link you posted.
I think there have been an misunderstanding. Let's say 1/3th of my protein
is outside the water box (Not visually wrapped arround to the other side)
and the rest 2/3th is inside of it. So this 1/3th of my protein is wiggling
outside the box (Not on the other side). So there seem to be no water
molecules around it.
Best,
Mert

On Mon, Jan 25, 2010 at 12:42 AM, Leonardo Trabuco <ltrabuco_at_ks.uiuc.edu>wrote:

> Hi Mert,
>
> On Sun, Jan 24, 2010 at 2:25 PM, Mert Gür <gurmert_at_gmail.com> wrote:
> > One last question. My protein leaves the waterbox at some period . So
> there
> > is a part of my protein in the imaginary water box next to it. Do you
> know
> > if the hydrogen bonds of this part are included in the given number of
> > hydrogen bond output? I am asking that because I think there are not. If
> it
> > is so do you know a solution to it.
>
> You can avoid this problem by unwrapping your protein throughout the
> trajectory using the pbctools plugin
> (http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/).
>
> Best,
> Leo
>
> > Best,
> > Mert
> >
> > On Sun, Jan 24, 2010 at 10:00 PM, Mert Gür <gurmert_at_gmail.com> wrote:
> >>
> >> 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
> >>
> >
> >
>
>
>
> --
> Leonardo Trabuco, Ph.D. candidate
> Theoretical and Computational Biophysics Group
> University of Illinois at Urbana-Champaign
>