[gmx-users] Water-Mediated Hydrogen Bonds

Erik Marklund erikm at xray.bmc.uu.se
Mon Jul 4 17:02:54 CEST 2011

-ins doesn't work as far as I know, and I believe the help text says so.


2 jul 2011 kl. 08.31 skrev Raja Pandian:

> 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
> Faithfully
> Raja
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Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se

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