Gmx-hbond: No donors No acceptors

User discussions
1

GROMACS version: 2024.2-dev
apt1_OL21_solv-neu_GMX.top (2.0 MB)

GROMACS modification: Yes/No
Hi,
I can’t understand why gmx-hbond return the error:

Checking for overlap in atoms between DNA (2709 atoms) and DNA (2709 atoms)
WARNING: Selection 'DNA' has no acceptors!
WARNING: Selection 'DNA' has no donors!

While hbond-legacy gives no problem; don’t know if relevant but for the same system if I use OPC instead of TIP3P the command works properly.

I’ve attached topology file: I’m still using tleap to build the system with ff OL21.

Any suggestions?

Best regards

2

I came across the same issue too. But tried a few times later, I noticed it would work well if I change the tpr file. Initially I used a gro file for -s flag input. The program could run, but complained for no acceptors no donors. Changing the tpr file to another file could work for me.