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
--
========================================
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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