VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Feb 28 2017 - 17:02:52 CST
You might find that for the purposes of just the H-bond calculation,
renaming the affected atoms using an atom selection would be quick and easy.
Where did the atom naming scheme you're using come from, if I may ask?
On Fri, Feb 24, 2017 at 12:52:24AM -0500, Sadegh Faramarzi Ganjabad wrote:
> 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?
-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/