[gmx-users] g_hbond

Erik Marklund 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
> Carla

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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