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
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/Scripts/plot_hbmap.txt)
that extract information
from this files. You should modify it to reach your goal
Francesco
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
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