[gmx-users] g_hbond

[Erik Marklund]

Oliver Grant skrev 2010-11-11 11.45:
> Hi Carla,
>
> I've seen this behavior too but I didn't look at the code. I figured 
> with the hydrogen included it checks the angle too or if the hydrogen 
> is between the two heavy atoms. So the first pass just looks at 
> distances between donor and acceptor atoms and doesn't consider that 
> the hydrogen may be completely on the wrong side of the donor atom.
>
It always looks at the angle unless you use the -contact flag.

/Erik
> Did you look at any of the bonds that were left out in the 2nd pass?
>
> Oliver
>
> On 9 November 2010 14:08, Carla Jamous <carlajamous at gmail.com 
> <mailto:carlajamous at gmail.com>> wrote:
>
>     Hi everyone,
>
>     I ran g_hbond on a trajectory. When g_hbond asks for two groups in
>     the index file, I give:
>     group1: "Protein"
>     group2: "ligand"
>     The output .ndx file contains 44 Hbonds.
>
>     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:
>     group1: "a4810_a4811_a1857"
>     group2: "a4810_a4811_a1857"
>     Surprisingly, 10 of the 44 Hbonds are not found using this method.
>
>     Am I doing something wrong or is there a problem with g_hbond?
>
>     Thank you,
>
>     Carla
>
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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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