VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 02 2017 - 14:35:17 CST

Hi,
  You can rename any of the parts of a structure in VMD very easily:

set sel [atomselect top "name AH1"]
$sel set name "H1"
$sel delete

Once you have done the renaming, you can even write out new PDB/PSF files
with the new names.

The DCD trajectory files don't contain any names, so changes to the
names, or even writing new PDB/PSF files has no impact on the trajectory at all.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Feb 28, 2017 at 07:34:33PM -0500, Sadegh Faramarzi Ganjabad wrote:
> 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 <[1]johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> Â 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,
> Â John Stone
> Â [2]vmd_at_ks.uiuc.edu
>
> On Fri, Feb 24, 2017 at 12:52:24AM -0500, Sadegh Faramarzi Ganjabad
> wrote:
> >Â Â Hello VMD users,
> >Â Â I am trying to find hydrogen bonds between oxygen atoms of a set
> of
> >Â Â detergents with sugar headgroups. The output shows 0 hbonds,
> which is
> >Â Â impossible. I suspect it is because the atom names are unusual.
> For
> >Â Â example, the hydrogen atoms are named as AH1, BH1 (I assume they
> should
> >Â Â start with 'H'),... or oxygen atoms are AO1, BO1,.. Since hbonds
> are
> >Â Â calculated using simple geometrical criteria, I am wondering if
> there is
> >Â Â any other way to calculated them on VMD?
> >Â Â Thanks,
> >Â Â 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
> [3]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Phone: [4]217-244-3349
> [5]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. mailto:vmd_at_ks.uiuc.edu
> 3. http://www.ks.uiuc.edu/~johns/
> 4. file:///tmp/tel:217-244-3349
> 5. http://www.ks.uiuc.edu/Research/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/