Hi,
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.
Erik
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
[email protected] http://folding.bmc.uu.se/
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
