VMD-L Mailing List

From: Lorenzo Gontrani (lorenzo.gontrani_at_gmail.com)
Date: Tue Apr 29 2014 - 11:15:35 CDT

If you start from SMILES string, I find it very convenient to use Marvin
sketch (free, from MarvinBeans). I successfully use it to build whatever
polymer. It has both a 2D and 3D "cleaner", but don't forget to make
hydrogen atoms EXPLICIT.

HTH

Lorenzo

2014-04-29 17:01 GMT+02:00 Norman Geist <norman.geist_at_uni-greifswald.de>:

> I don't think this is possible even with scripting, as "building" tools do
> usually have a database with coordinate templates. How could you otherwise
> determine the position of the atoms while adding them? VMD is more a
> visualization-, than a building-tool, although it can be used for
> parameterization.
>
> Norman Geist.
>
> > -----Ursprüngliche Nachricht-----
> > Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im
> > Auftrag von Jean-Patrick Francoia
> > Gesendet: Dienstag, 29. April 2014 14:49
> > An: vmd-l_at_ks.uiuc.edu
> > Betreff: vmd-l: Visualize a SMILES string
> >
> > Hello,
> >
> > I wonder if there is a way to visualize a SMILES string in VMD, and
> > possibly in 3D. I did a bit of digging but found nothing clear.
> >
> > How do you do that ?
> >
> > Regards
> >
> > JP
>
>
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-- 
==========================================
 Lorenzo Gontrani
 Research associate of CNR-ISM (Rome Tor Vergata)
 EDXD group of University of Rome "La Sapienza"
 GSM +39 338 7615798
 Email lorenzo DOT gontrani AT gmail DOT com
 Webpage: http://webcaminiti/gontrani.html
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