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
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