Hi everyone, actually Erik is right. My problem is that I wasn't using the "-nomerge" option. So g-hbond was printing the wrong number of hydrogen atom and so all my results were not matching. Now that I used "-nomerge", all my H-bonds match even in my concatenated trajectory.
Thanks to all, It took me a long time to figure it out, thanks for your patience, Carla On Thu, Nov 11, 2010 at 4:26 PM, Erik Marklund <[email protected]> wrote: > 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/ > >
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