[gmx-users] g_hbond

Erik Marklund erikm at xray.bmc.uu.se
Thu Nov 11 17:04:34 CET 2010 

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 <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
>             -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
>     erikm at xray.bmc.uu.se <mailto:erikm at xray.bmc.uu.se>
>     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
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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