erikm at xray.bmc.uu.se
Thu Nov 11 16:07:55 CET 2010
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.
> Did you look at any of the bonds that were left out in the 2nd pass?
> 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,
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Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
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erikm at xray.bmc.uu.se http://folding.bmc.uu.se/
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