From: Ata Madanchi (
Date: Thu Nov 03 2022 - 14:28:43 CDT


I have a simulation of water molecules and I want to extract the hydrogen bond information between each molecule, I managed to visualize these bonds with Graphic Representation and Drawing method: HBond. now how can I retrieve these connections? I don't see them to be saved in mol2 or pdb data format. I am aware of hydrogen bond plugin which does write hydrogen bond info into a .dat file, but I can't get it to work. in selection1 criteria I write name H, and name O for selection 2, but zero bond is being found regardless of the cut-offs. Could you give me any hint?