VMD-L Mailing List

From: Sadegh Faramarzi Ganjabad (safaramarziganjabad_at_mix.wvu.edu)
Date: Thu Mar 02 2017 - 15:03:49 CST

John,

That works, thanks a lot.

Sadegh

On Thu, Mar 2, 2017 at 3:37 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> 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/
>