VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 02 2017 - 14:37:04 CST

Hi,
  Oops, I realized I forgot to advise one more step:
After renaming parts of the structure, you may need to use the
"mol reanalyze" command to make all of the name changes take full effect:
  mol reanalyze top

Cheers,
  John

On Thu, Mar 02, 2017 at 02:35:17PM -0600, John Stone wrote:
> 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/ 

-- 
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/