[gmx-users] water-medited hydrogen bonds - %exist hydrogen bonds

[Justin A. Lemkul]

leila karami wrote:
> Dear Justin
> 
> very thanks for your reply.
> 
> I used for script two times:
> 
> 1) between proten and interfacial waters.
> 
> 2) between dna and same water molecules.
> 
> using what I said above, can I obtain what water molecules form 
> water-mediated hydrogen bond between protein and dna?
> 
> if my way is wrong, please guide me about that.
> 

My script will not calculate such a sophisticated quantity.  What it would need 
to do would be to determine if a hydrogen bond to the protein and to the DNA was 
present at the same time frame.  Right now, all you know is that a given water 
molecule may form a hydrogen bond with a protein residue for X% of the time and 
then with DNA for Y% of the time, but you have no indication of whether X and Y 
overlap.  The script could probably be extended to do this, since the frame work 
for reading all the necessary files is there already.

-Justin

> any suggestion will highly appreciated.
> 
> -- 
> 
> Leila Karami
> Ph.D. student of Physical Chemistry
> 
> K.N. Toosi University of Technology
> Theoretical Physical Chemistry Group
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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