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Hi Raja,<br>
You can perform the job calculating h-bond between Protein and Water
and between DNA and Water.<br>
Now you have to select water that, in the same frame, form h-bond
with protein and DNA. <br>
<br>
The residue information can be found in hbmap.xpm e hbond.log files.
<br>
There is a perl script in the Justin's webpage
(<a class="moz-txt-link-freetext" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/Scripts/plot_hbmap.txt">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/Scripts/plot_hbmap.txt</a>)
that extract information <br>
from this files. You should modify it to reach your goal<br>
<br>
<br>
Francesco <br>
<br>
Il 04/07/2011 17:02, Erik Marklund ha scritto:
<blockquote
cite="mid:7BCD2037-0760-4C46-A6A7-E509764CA56D@xray.bmc.uu.se"
type="cite">-ins doesn't work as far as I know, and I believe the
help text says so.
<div><br>
</div>
<div>Erik</div>
<div><br>
<div>
<div>2 jul 2011 kl. 08.31 skrev Raja Pandian:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<p class="MsoNormal" style="margin-bottom: 0.0001pt;
text-align: justify; line-height: 150%;">Dear All,</p>
<div style="margin-bottom: 0.0001pt; text-align: justify;
line-height: 150%;"> <br class="webkit-block-placeholder">
</div>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;
text-align: justify; line-height: 150%;">I’m doing
research in the field of Protein-DNA
interaction. I have gone through these papers,</p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;
text-align: justify; line-height: 150%;"><b style="">A
“Solvated
Rotamer” Approach to Modeling Water-Mediated Hydrogen
Bonds at Protein–Protein
Interfaces</b></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;
text-align: justify; line-height: 150%;"><b style="">“Effect
on DNA
relaxation of the single Thr718Ala mutation in human
topoisomerase I: a
functional and molecular dynamics study”</b></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;
text-align: justify; line-height: 150%;"><b style="">“Molecular
Dynamics
Simulation Study of Interaction between Model Rough
Hydrophobic
Surfaces.”</b></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;
text-align: justify; line-height: 150%;"><b style="">“Prediction
of
Protein Binding to DNA in the Presence of Water-Mediated
Hydrogen Bonds”</b></p>
<div style="margin-bottom: 0.0001pt; text-align: justify;
line-height: 150%;"> <br class="webkit-block-placeholder">
</div>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;
text-align: justify; line-height: 150%;">I have found lot
of interesting things on these
papers that will be useful for the progress of my research
carrier.</p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;
text-align: justify; line-height: 150%;">I have been
looking for water mediated hydrogen bond
in my simulation when i<span style=""> </span>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 ?</p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;
text-align: justify; line-height: 150%;">Is there any way
to calculate water mediated hydrogen
bond between Protein-DNA using Gromacs tools?</p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;
text-align: justify; line-height: 150%;">If it is
possible, please send your program (water
mediated hydrogen bond derivation program) to me and also
the program operating
procedure.</p>
<div style="margin-bottom: 0.0001pt; text-align: justify;
line-height: 150%;"> <br class="webkit-block-placeholder">
</div>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;
text-align: justify; line-height: 150%;">Eagerly waiting
for your reply.</p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;
text-align: justify; line-height: 150%;">Thanking You</p>
<div style="margin-bottom: 0.0001pt; text-align: justify;
line-height: 150%;"> <br class="webkit-block-placeholder">
</div>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;
text-align: justify; line-height: 150%;">Faithfully</p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;
text-align: justify; line-height: 150%;">Raja</p>
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<div>-----------------------------------------------</div>
<div>Erik Marklund, PhD student</div>
<div>Dept. of Cell and Molecular Biology, Uppsala
University.</div>
<div>Husargatan 3, Box 596, 75124 Uppsala, Sweden</div>
<div>phone: +46 18 471 4537 fax: +46 18 511 755</div>
<div><a moz-do-not-send="true"
href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a></div>
<div><a moz-do-not-send="true"
href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a></div>
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