[gmx-users] g_hbond

Erik Marklund 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
>> 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.
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/

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