[gmx-users] Water-Mediated Hydrogen Bonds

Raja Pandian chemistryraj at gmail.com
Sat Jul 2 08:31:21 CEST 2011

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.

Eagerly waiting for your reply.

Thanking You


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