erikm at xray.bmc.uu.se
Thu Nov 11 17:04:34 CET 2010
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
>> head -2 lastline | wc -c
>> head -3 lastline | wc -c
>> head -4 lastline | wc -c
>> head -5 lastline | wc -c
>> head -6 lastline | wc -c
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.
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,
> On Tue, Nov 2, 2010 at 8:36 PM, Erik Marklund <erikm at xray.bmc.uu.se
> <mailto:erikm at xray.bmc.uu.se>> 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
> 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
> 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 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
> erikm at xray.bmc.uu.se <mailto:erikm at xray.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
erikm at xray.bmc.uu.se http://folding.bmc.uu.se/
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