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 <[email protected]
<mailto:[email protected]>> 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
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