Hi everyone,<br><br>actually Erik is right. My problem is that I wasn't using the "-nomerge" option.<br>So g-hbond was printing the wrong number of hydrogen atom and so all my results were not matching.<br>Now that I used "-nomerge", all my H-bonds match even in my concatenated trajectory.<br>
<br>Thanks to all,<br>It took me a long time to figure it out, thanks for your patience,<br>Carla<br><br><div class="gmail_quote">On Thu, Nov 11, 2010 at 4:26 PM, Erik Marklund <span dir="ltr"><<a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Hi,<br>
<br>
I'm thinking it *may* have something to do with how search_donors() and the -merge flag work. The hydrogen must be part of the index group you provide. Nothing strange there. But the hydrogen that is printed to the index file may in fact *not* be the hydrogen bonding one if the -merge flag is set (default). Would the vanishing h-bonds happen to have donors with multiple hydrogens? There are two things you could try: either add all the donor's hydrogen to the index group when validating single h-bonds, or use -nomerge to generate a complete list of h-bonds and do your validation on that list.<br>
<br>
Erik<br>
<br>
Carla Jamous skrev 2010-11-09 15.08:<div><div></div><div class="h5"><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi everyone,<br>
<br>
I ran g_hbond on a trajectory. When g_hbond asks for two groups in the index file, I give:<br>
group1: "Protein"<br>
group2: "ligand"<br>
The output .ndx file contains 44 Hbonds.<br>
<br>
In order to verify my result on each and every Hbond, I ran g_hbond on the same trajectory but this time in my index file, I gave atom triplets, so when g_hbond asks for two groups, I give for example:<br>
group1: "a4810_a4811_a1857"<br>
group2: "a4810_a4811_a1857"<br>
Surprisingly, 10 of the 44 Hbonds are not found using this method.<br>
<br>
Am I doing something wrong or is there a problem with g_hbond?<br>
<br>
Thank you,<br>
<br>
Carla<br>
</blockquote>
<br>
<br></div></div><div><div></div><div class="h5">
-- <br>
-----------------------------------------------<br>
Erik Marklund, PhD student<br>
Dept. of Cell and Molecular Biology, Uppsala University.<br>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>
phone: +46 18 471 4537 fax: +46 18 511 755<br>
<a href="mailto:erikm@xray.bmc.uu.se" target="_blank">erikm@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se/</a><br>
<br>
</div></div></blockquote></div><br>