[gmx-users] Water-Mediated Hydrogen Bonds

Francesco Oteri francesco.oteri at gmail.com
Mon Jul 4 17:48:11 CEST 2011

Hi Raja,
You can perform the job calculating h-bond between Protein and Water and 
between DNA and Water.
Now you have to select water that, in the same frame, form h-bond with 
protein and DNA.

The residue information can be found in hbmap.xpm e hbond.log files.
There is a perl script in the Justin's webpage 
that extract information
from this files. You should modify it to reach your goal


Il 04/07/2011 17:02, Erik Marklund ha scritto:
> -ins doesn't work as far as I know, and I believe the help text says so.
> Erik
> 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 iuse 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 <mailto:erikm at xray.bmc.uu.se>
> http://www2.icm.uu.se/molbio/elflab/index.html

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