Hi,
I have looked at the files to sent me, and I can't spot any errors.
There *is* a hydrogen bond at y=1. It only occurs in 5 frames though, so
they're really hard to find when isnpecting the xpm in e.g. Gimp, since
the image is 60000 pixels wide. So, I got tired of sqinting in front of
Gimp and went for a bit of comandline work instead. Here's what I did:
>> tail -1 map_concatenated.xpm | tr 'o' '\n' > lastline
>> head -1 lastline | wc -c
16749
>> head -2 lastline | wc -c
16936
>> head -3 lastline | wc -c
40226
>> head -4 lastline | wc -c
45019
>> head -5 lastline | wc -c
58565
>> head -6 lastline | wc -c
60001
The numbers I got (except for the last one) are the frames where the
hbond manifests. I verified the first one in gimp. You can check the
other's if you wish. I also found two frames in map1.xpm and three in
map3.xpm using the same method.
Erik
Carla Jamous skrev 2010-11-04 11.32:
Hi Erik,
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.
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.
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?
Thank you,
Carla
On Tue, Nov 2, 2010 at 8:36 PM, Erik Marklund <[email protected]
<mailto:[email protected]>> wrote:
Erik Marklund skrev 2010-11-02 20.33:
Carla Jamous skrev 2010-11-02 17.35:
Hi to all,
I'm sorry I'm asking again a question I asked a week ago
but I still haven't found my answer:
I concatenated 3 trajectories of 3 different molecules
(that have the same number of atoms) with trjcat: trjcat
-settime
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.
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.
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).
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?
Thank you
Carla
Hi,
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.
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.
Erik
--
-----------------------------------------------
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
[email protected] <mailto:[email protected]>
http://folding.bmc.uu.se/
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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
[email protected] http://folding.bmc.uu.se/
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