[gmx-users] Water-Mediated Hydrogen Bonds

[Justin A. Lemkul]

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 <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> 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

========================================