I am trying to determine the hydrogen bonds in the protein backbone. For that I made an index file with donor amide H (HN) and acceptor carbonyl (0) using this command: gmx make_ndx -f MD.tpr -o backbone_hbond.ndx. This ndx file contains the HN group as well as carbonyl O , however when i try to determine the number of H-bonds using this command :
gmx hbond -s MD.tpr -f MD_center.xtc -num hb_hn_o_backbone.xvg -backbone_hbond.ndx, it shows an error which says
‘Program: gmx hbond, version 2025.1 Source file: src/gromacs/trajectoryanalysis/modules/hbond.cpp (line 622) Function: static void gmx::analysismodules::{anonymous}::Hbond::linkDA(gmx::analysismodules::{anonymous}::t_info*) Inconsistency in user input: Selection HN’ has no donors AND has no acceptors! Nothing to be done.
Even i tried to determine the H-bond betwee the protein bacbone and just protein, it shows zero H-bonds. What am i doing wrong.
Thanks in advance.