[gmx-users] HBOND probability

[Poojari, Chetan]

Hello Justin,

I wanted to find the probability of hydrogen bond formed between my peptide and water molecules over time. So I used your plot_hbmap.pl script.

As mentioned in the script file, my index file contained atom numbers only from the  [hbonds...] section, rest were deleted.

Heres my short output after running the script:

#    Donor                        Acceptor                   % Exist.
                                                                     0.004
      ALAA               N                                           0.004
      ALAA               N                                           0.016
      ALAA               N                                           0.012
      ALAA               N                                           0.008
                                      ALAA               O           0.008
                                      ASNA      OD1          0.012
                                      GLYA               O           0.008
                                      ALAA               O           0.008



Please can I know if this is the expected output from the script ??? if not please can I know what might be wrong in my input ????



Kind regards,
chetan.


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