[gmx-users] g_hbond

[Nidhi Katyal]

Hi all,

I have created hydrogen bond existence map. In the index file generated
using hbn option I can see following lines at the end:
   1      2   1598
      1      2   1851
      1      2   1852
      1      2   1862
     10     11   1643
     10     11   1651
     10     11   1658
     10     11   1664
     10     11   1682
     10     11   1748
     10     11   1754
     10     11   1761
     10     11   1762
     10     11   1772
     10     11   1830
     10     11   1831
     10     11   1838
     10     11   1851
     10     11   1862

There are 19 lines in total and also in the existence map created using hbm
option, I could see 19 lines. But when I generate index file with a2 and
calculate hydrogen bond with my ligand moleules, I can see zero bonds. Am I
doing something wrong?

Thanks
Nidhi