erikm at xray.bmc.uu.se
Tue Nov 2 20:36:03 CET 2010
Erik Marklund skrev 2010-11-02 20.33:
> 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.
A simple test you could do yourself is to make index groups containing
only the atoms involved in that hbond and run g_hbond again. If the
problem persists, then it looks like a bug. If not, then I still can't
rule out misinterpretation of the matrix.
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/
More information about the gromacs.org_gmx-users