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Hi,<br>
<br>
Let me have a look at the files off-list and I'll probably see
what's going on.<br>
<br>
Erik<br>
<br>
Carla Jamous skrev 2010-11-04 11.32:
<blockquote
cite="mid:AANLkTikVf+T5VXBRqzEXehG1nL=fTLJc27kjQ964HC02@mail.gmail.com"
type="cite">Hi Erik,<br>
<br>
I tried what you said: I made index groups containing only the
atoms involved in that hbond and ran g_hbond again. The problem
didn't persist.<br>
So I wanted to check if I misinterpreted the map: for that, I
compared my 4 index files: the one of my concatenated trajectory
and the three of the separate trajectories.<br>
When I look at this comparison table and then at my concatenated
hbond map, the results don't match: for example, the Hbond that
has the number 1 in my concatenated trajectory doesn't appear in
my concatenated map (it means that in my map, next to y=1, nothing
appears), however, this same H-bond (same number of atoms
involved) exists in my first and my third trajectories' index
files. So please could you explain how to interpret the map and if
next to some y value in my map, nothing appears, is this value
taken into account in my index file?<br>
<br>
Thank you,<br>
Carla<br>
<br>
<div class="gmail_quote">On Tue, Nov 2, 2010 at 8:36 PM, Erik
Marklund <span dir="ltr"><<a moz-do-not-send="true"
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;">
Erik Marklund skrev 2010-11-02 20.33:
<div class="im"><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Carla Jamous skrev 2010-11-02 17.35:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Hi to all,<br>
<br>
I'm sorry I'm asking again a question I asked a week ago
but I still haven't found my answer:<br>
<br>
I concatenated 3 trajectories of 3 different molecules
(that have the same number of atoms) with trjcat: trjcat
-settime<br>
<br>
Then I ran g_hbond on the concatenated trajectory, I got
an index.ndx file that contains an H-bond between the
Thr121 of my protein and an atom N2 of my ligand. This
H_bond figures in the 3 trajectories when I look at the
hbmap of my concatenated trajectory.<br>
<br>
On the other hand, I ran g_hbond on each of the 3
different trajectories. This H_bond doesn't exist in the
index files of two of my trajectories. So it doesn't
match the result I get with my concatenated trajectory.<br>
<br>
To be sure that this result is right, I calculated the
angle and the r of my H-bond in VMD during each of the 3
trajectories and the results indicate that this H-bond
doesn't exist (I consider that r must be < or equal
to 0.35 nm and angle < or equal to 30 degrees).<br>
<br>
Please can anyone tell me why the results of g_hbond in
my concatenated trajectory don't match the results of
g_hbond on each of my trajectories?<br>
<br>
Thank you<br>
<br>
Carla<br>
</blockquote>
Hi,<br>
<br>
This sounds strange. Could you file a bugzilla and either
upload the trajectories+tpr, or, if the files are huge,
make them available my other means? I need to have a
closer look, perhaps through a debugger.<br>
<br>
</blockquote>
</div>
A simple test you could do yourself is to make index groups
containing only the atoms involved in that hbond and run
g_hbond again. If the problem persists, then it looks like a
bug. If not, then I still can't rule out misinterpretation of
the matrix.<br>
<font color="#888888">
<br>
Erik</font>
<div>
<div class="h5"><br>
<br>
-- <br>
-----------------------------------------------<br>
Erik Marklund, PhD student<br>
Dept. of Cell and Molecular Biology, Uppsala University.<br>
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</blockquote>
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<br>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
<a class="moz-txt-link-abbreviated" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a class="moz-txt-link-freetext" href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a>
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