<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">-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:0cm;margin-bottom:.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:0cm;margin-bottom:.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:0cm;margin-bottom:.0001pt;text-align:
justify;line-height:150%"><b style="mso-bidi-font-weight:normal">A “Solvated
Rotamer” Approach to Modeling Water-Mediated Hydrogen Bonds at Protein–Protein
Interfaces</b></p><p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;text-align:
justify;line-height:150%"><b style="mso-bidi-font-weight:normal">“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:0cm;margin-bottom:.0001pt;text-align:
justify;line-height:150%"><b style="mso-bidi-font-weight:normal">“Molecular
Dynamics Simulation Study of Interaction between Model Rough Hydrophobic
Surfaces.”</b></p><p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;text-align:
justify;line-height:150%"><b style="mso-bidi-font-weight:normal">“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:0cm;margin-bottom:.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:0cm;margin-bottom:.0001pt;text-align:
justify;line-height:150%">I have been looking for water mediated hydrogen bond
in my simulation when i<span style="mso-spacerun:yes"> </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:0cm;margin-bottom:.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:0cm;margin-bottom:.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:0cm;margin-bottom:.0001pt;text-align:
justify;line-height:150%">Eagerly waiting for your reply.</p><p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.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:0cm;margin-bottom:.0001pt;text-align:
justify;line-height:150%">Faithfully</p><p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;text-align:
justify;line-height:150%">Raja</p>
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<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><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 href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a></div><div><a href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a></div></span>
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