Raja Pandian wrote:
Dear Justin,
Thanks for your mail.
I don't have the programing knowledge.
It is exceptionally rare to find all of the software you already need in place
and freely available. You'd be well-advised to learn a language (or maybe even
a few) that suit your needs. For instance, Perl is handy for dealing with text
files in the way I suggested in the previous post.
If it is possible, please send your program (water mediated hydrogen
bond derivation program) to me and also the program operating procedure.
I don't have such a program. Perhaps someone else does.
-Justin
On Sat, Jul 2, 2011 at 5:24 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
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
<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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
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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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