VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Sat Sep 08 2018 - 21:45:52 CDT

The measure h-bonds command? Or ask the plugin for detailed output?

-Josh

On 2018-09-08 02:16:24-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:

Dear all,
          I want to calculate the hydrogen bonds between protein and dna atomwise in vmd. So I used vmd for this calculation but vmd gives the hydrogen bonding in residue wise for an example residue-132-side with dna-11-side. But vmd does not give the hydrogen bond between atoms i.e. which atom in protein making hydrogen bond with which dna atom. So if you give any suggestion of how to calculate hydrogen bonds atomwise, it would be very much helpful.Thanks in advance.