H-bond calculation

[FarzaneJP]

Please define different groups in your index file (*.ndx) and make sure you’re using the latest GROMACS version, 2023.2. Here is a discussion that might be helpful to you:

Hbond for docked protein-protein complex

GROMACS version: 2020.2 GROMACS modification: No Hi, I have a docked protein-protein complex and performed md simulations. I want to make a hydrogen bond study between these 2 proteins using gmx hbond ( gmx hbond -f md.xtc -s md.tpr -num hbnum_Pro-Pro.xvg and issuing Protein , Protein (same atom numbers for both)) however, I believe this way I’m looking at intraprotein H bonds instead of interprotein H bonds, right? The md simulation was run using a pdb file with the two protein chains in it…