VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 24 2011 - 10:21:28 CDT

Hi,
  If you read the help page for the plugin, you can see the list
of residue names it recognizes for detection of chiral centers.
The plugin currently won't detect errors in any residues other than the
ones on that list:
  http://www.ks.uiuc.edu/Research/vmd/plugins/chirality/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 24, 2011 at 10:08:41AM -0500, Ling Wu wrote:
> Hi John,
>
> Thanks a lot for your reply. Does this plugin also work for lipid system or only works for protein and DNA?
>
>
> Emilia
>
> On Aug 23, 2011, at 5:05 PM, John Stone wrote:
>
> >
> > Hi,
> > If you want to use the new Chirality plugin in VMD 1.9, you must
> > first issue the command "package require chirality"
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Tue, Aug 23, 2011 at 04:13:53PM -0500, Ling Wu wrote:
> >> Hi All,
> >> I want to use extrabonds command to restrain some dihedral angles in my
> >> lipid system, so I can have the correct chirality and Cis-trans isomerism
> >> through MD simulation. I noticed that VMD can generate corresponding
> >> extrabonds.txt file, but It did not work for me, I tried chirality
> >> restrain -o chirality-extrabonds.txt in VMD TkConsole, it gave me this
> >> message "invalid command name "chirality"". Since my system has a lot of
> >> lipids, so I am trying to avoid writing those atom numbers by myself. Does
> >> anyone have any experience about this?
> >> Thanks in advance!
> >> Emilia
> >
> > --
> > NIH Resource 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/ Fax: 217-244-6078
> 

-- 
NIH Resource 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/       Fax: 217-244-6078