VMD-L Mailing List

From: Sadegh Faramarzi Ganjabad (safaramarziganjabad_at_mix.wvu.edu)
Date: Tue Feb 28 2017 - 18:34:33 CST

John,

Thanks for your replay. I am not sure how to rename an atom selection in a
trajectory. Would you please give an example?

We were using BDDM topology from toppar_all36_lipid_detergent.str to
generate psf of dodecyl-beta-D-maltoside detergent. The atom names start
with numbers, like 1C1, 2O1,... then psfgen was complaining about it and we
mistakenly replaced numbers with 'A' and 'B' letters.

Thanks,
Sadegh

On Tue, Feb 28, 2017 at 6:02 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> 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?
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> 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?
> > Thanks,
> > Sadegh
>
> --
> 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/
>