Hi everyone, I ran g_hbond on a trajectory. When g_hbond asks for two groups in the index file, I give: group1: "Protein" group2: "ligand" The output .ndx file contains 44 Hbonds.
In order to verify my result on each and every Hbond, I ran g_hbond on the same trajectory but this time in my index file, I gave atom triplets, so when g_hbond asks for two groups, I give for example: group1: "a4810_a4811_a1857" group2: "a4810_a4811_a1857" Surprisingly, 10 of the 44 Hbonds are not found using this method. Am I doing something wrong or is there a problem with g_hbond? Thank you, Carla
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