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

Justin A. Lemkul jalemkul at vt.edu
Thu Feb 24 16:35:46 CET 2011

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.


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


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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