[gmx-users] Water-Mediated Hydrogen Bonds

[Justin A. Lemkul]

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
> 

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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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