[gmx-users] Hydrogen bonds

soumadwip ghosh soumadwipghosh at gmail.com
Sat Jul 4 12:33:12 CEST 2015

As a said the -hbn option in g_hbond is probably not informative in your
case. First tell us what do you really want to observe? The no. of hydrogen
bonds between specific amino acid residues and your ligand binding sites?
If yes, use g_hbond with -num option that will give you the exact no of
hydrogen bonds (second column of the num.xvg output file) and if you want
to perform a kinetic analysis of hydrogen bond formation use the -ac flag.
>From the part of the file you sent in the previous mail I can not
understand what exactly you want to achieve from g_hbond.


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