VMD-L Mailing List

From: Mert Gür (gurmert_at_gmail.com)
Date: Sun Jan 24 2010 - 14:25:52 CST

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.
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
>>
>
>