VMD-L Mailing List

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Sun Jan 24 2010 - 16:42:01 CST

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