VMD-L Mailing List

From: Josh Vermaas (vermaasj_at_msu.edu)
Date: Thu Nov 03 2022 - 15:29:05 CDT

Hi Ata,

The hydrogen bond plugin picks hydrogen bonds between heavy atoms. I
recall (but would need to check) that if you just want all the water,
you'd put "water" as selection1, and leave selection2 blank.

-Josh

On 11/3/22 15:28, Ata Madanchi wrote:
> Hello,
>
> 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?
>
> Best
> A