erikm at xray.bmc.uu.se
Tue Nov 2 20:33:08 CET 2010
Carla Jamous skrev 2010-11-02 17.35:
> Hi to all,
> I'm sorry I'm asking again a question I asked a week ago but I still
> haven't found my answer:
> I concatenated 3 trajectories of 3 different molecules (that have the
> same number of atoms) with trjcat: trjcat -settime
> Then I ran g_hbond on the concatenated trajectory, I got an index.ndx
> file that contains an H-bond between the Thr121 of my protein and an
> atom N2 of my ligand. This H_bond figures in the 3 trajectories when
> I look at the hbmap of my concatenated trajectory.
> On the other hand, I ran g_hbond on each of the 3 different
> trajectories. This H_bond doesn't exist in the index files of two of
> my trajectories. So it doesn't match the result I get with my
> concatenated trajectory.
> To be sure that this result is right, I calculated the angle and the r
> of my H-bond in VMD during each of the 3 trajectories and the results
> indicate that this H-bond doesn't exist (I consider that r must be <
> or equal to 0.35 nm and angle < or equal to 30 degrees).
> Please can anyone tell me why the results of g_hbond in my
> concatenated trajectory don't match the results of g_hbond on each of
> my trajectories?
> Thank you
This sounds strange. Could you file a bugzilla and either upload the
trajectories+tpr, or, if the files are huge, make them available my
other means? I need to have a closer look, perhaps through a debugger.
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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