VMD-L Mailing List

From: Sadegh Faramarzi Ganjabad (safaramarziganjabad_at_mix.wvu.edu)
Date: Thu Feb 23 2017 - 23:52:24 CST

Hello VMD users,

I am trying to find hydrogen bonds between oxygen atoms of a set of
detergents with sugar headgroups. The output shows 0 hbonds, which is
impossible. I suspect it is because the atom names are unusual. For
example, the hydrogen atoms are named as AH1, BH1 (I assume they should
start with 'H'),... or oxygen atoms are AO1, BO1,... Since hbonds are
calculated using simple geometrical criteria, I am wondering if there is
any other way to calculated them on VMD?

Thanks,
Sadegh