Hello GROMACS community,
I’ve recently encountered an issue regarding hydrogen bonding analysis between a ligand and protein in my simulation. Initially. After running a short simulation (around 1 ns), I’m now facing a new issue with hydrogen bond detection.
I used the command:
gmx hbond -s md.tpr -f md_center.xtc -num hb-w.xvg -tu ns
But the program outputs the following error:
Program: gmx hbond, version 2024.2
Source file: src/gromacs/trajectoryanalysis/modules/hbond.cpp (line 572)
Function: static void gmx::analysismodules::{anonymous}::Hbond::linkDA(gmx::analysismodules::{anonymous}::t_info*)Inconsistency in user input:
Selection ‘LIG’ has no donors AND has no acceptors! Nothing to be done.
I’ve checked my setup multiple times, tried different ligands and molecules, and even experimented with both the AMBER99SB-ILDN and CHARMM36 force fields. However, I still encounter the same issue. I also tested hydrogen bonding between water and the ligand, but the error persists.
Some additional details:
- I always set periodic boundary conditions.
- Before creating the complex, I align the
xyzcoordinates of both the protein and ligand to ensure they are close together, as randomly placed, they tend to be far apart.
Despite these adjustments, I continue to see this “no donors or acceptors” error, even with a short 1 ns simulation to just check quickly.
I’ve attached the entire small simulation directory. Could someone please take a look and offer any advice? Any help would be greatly appreciated!
Here is the FILE
NB : This issue make false the entire result even for rmsd, rmsf etc.