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Hi,<br>
You can use g_hbond -num and write a small script to calculate the
percentage of h-bond existence per frame by calculating the number of
frames for which a h-bond exists.<br>
Good luck,<br>
Ran.<br>
<br>
Moutusi Manna wrote:
<blockquote cite="mid693813.38100.qm@web94305.mail.in2.yahoo.com"
type="cite">
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style="font-family: 'Times New Roman','serif';">
<p class="PreformattedText"
style="margin: 0in 0in 0pt; text-align: justify;"><span
style="font-family: 'Arial','sans-serif';">Dear all,<o:p></o:p></span>
</p>
<p class="PreformattedText"
style="margin: 0in 0in 0pt; text-align: justify;"><span
style="font-family: 'Arial','sans-serif';"><span style=""> </span>I
am dealing with a POPC+PEPTDE+WATER system. Basic residues of the
peptide make hydrogen bonds with lipid headgroup (as reflected from
g_rdf analysis) and the number of hydrogen bonds formed can be
calculated from g_hbond program. Now, i want to calculate the % of
trajectory time for which a bond between a particular group (say LYS
and lipid headgroup po4) exist. -hbm gives a .xpm matrix, on solving
(using xpm2ps) that i got a .eps file, which is a picture file of
h_bond existence map, but the data sheet is not given.<o:p></o:p></span>
</p>
<p class="PreformattedText"
style="margin: 0in 0in 0pt; text-align: justify;"><span
style="font-family: 'Arial','sans-serif';">Can any one help me to
solve this problem?<o:p></o:p></span>
</p>
<p class="PreformattedText"
style="margin: 0in 0in 0pt; text-align: justify;"><span
style="font-family: 'Arial','sans-serif';">With regards,<o:p></o:p></span>
</p>
<p class="PreformattedText"
style="margin: 0in 0in 0pt; text-align: justify;"><span
style="font-family: 'Arial','sans-serif';"><o:p> </o:p></span>
</p>
<p class="PreformattedText"
style="margin: 0in 0in 0pt; text-align: justify;"><span
style="font-family: 'Arial','sans-serif';">Moutusi Manna<o:p></o:p></span>
</p>
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<br>
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