Raja Pandian wrote:
Dear All,
I’m doing research in the field of Protein-DNA interaction. I have gone
through these papers,
*A “Solvated Rotamer” Approach to Modeling Water-Mediated Hydrogen Bonds
at Protein–Protein Interfaces*
*“Effect on DNA relaxation of the single Thr718Ala mutation in human
topoisomerase I: a functional and molecular dynamics study”*
*“Molecular Dynamics Simulation Study of Interaction between Model Rough
Hydrophobic Surfaces.”*
*“Prediction of Protein Binding to DNA in the Presence of Water-Mediated
Hydrogen Bonds”*
I have found lot of interesting things on these papers that will be
useful for the progress of my research carrier.
I have been looking for water mediated hydrogen bond in my simulation
when i use g_hbond the -ins option it dose not showing the water
mediated hydrogen bond could you please tell me how to get the hydrogen
mediated hydrogen bond and water mediated free energy in Gromacs ?
Is there any way to calculate water mediated hydrogen bond between
Protein-DNA using Gromacs tools?
If it is possible, please send your program (water mediated hydrogen
bond derivation program) to me and also the program operating procedure.
This has been discussed several times in the list archive, for instance one
solution is:
http://lists.gromacs.org/pipermail/gmx-users/2011-May/061296.html
Search "water mediated hydrogen bonds" and you will find many more posts about
the same topic.
-Justin
Eagerly waiting for your reply.
Thanking You
Faithfully
Raja
--
========================================
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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