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
Carla
Hi,
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.
--
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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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