[gmx-users] g_hbond

Erik Marklund erikm at xray.bmc.uu.se
Thu Nov 11 16:26:31 CET 2010


I'm thinking it *may* have something to do with how search_donors() and 
the -merge flag work. The hydrogen must be part of the index group you 
provide. Nothing strange there. But the hydrogen that is printed to the 
index file may in fact *not* be the hydrogen bonding one if the -merge 
flag is set (default). Would the vanishing h-bonds happen to have donors 
with multiple hydrogens? There are two things you could try: either add 
all the donor's hydrogen to the index group when validating single 
h-bonds, or use -nomerge to generate a complete list of h-bonds and do 
your validation on that list.


Carla Jamous skrev 2010-11-09 15.08:
> 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

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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