GROMACS version: 2024.2
GROMACS modification: No
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I have run MD simulation of a docked membrane protein ligand complex embedded in POPC bilayer through CHARMM GUI and GROMACS for 100ns.
My ligand forms a conventional hydrogen bond with LEU182 residue of protein when visualized in Discovery Studio (H-bond distance was 4.57 A).
After running the MD Simulation, I visualized the trajectory in VMD, and found the same LEU182 residue interacting with my ligand, along with a few more interactions (cutoff distance: 0.35nm, angle cutoff: 20).
But when I calculated H-bond in gmx hbond or gmx hbond-legacy usng the same cutoff, it says, no H-bond found, Ligand doesn’t have any donor or acceptor.
I tried with increasing the distance cutoff (default if 0.35nm in gmx hbond), decreasing the angle cutoff (default is 30 in gmx hbond), even added “nitacc” flag, but still cannot find any H-bond.
I understand there might be differences in VMD and gmx hbond how they calculate the H-bond, but even after applying same cutoff why there are no H-bond found in gmx hbond?