VMD-L Mailing List

From: Mauricio Carrillo Tripp (trippm_at_gmail.com)
Date: Mon Oct 03 2005 - 14:23:04 CDT

The problem I saw when trying to implement some kind of
'fancy' representation for lipids is that there is no standard naming
of all different lipids among different force fields (and therefore
pdb files), one can divide the lipid molecule in many different ways
or not at all, the naming of the atoms can change from one force filed to
another too. I guess if there was some kind of standardization,
things would be much easier. Meanwhile, I'm also going to try that hack...

On 10/3/05, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>
> Hi,
> There's no built-in rep to do what you describe presently, but it's
> conceivable that I could add something along these lines if there's
> enough interest. In the short term, you might be able to hack your
> structure as you're suggesting and trick VMD into drawing a ribbon/cartoon
> for it.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Sep 29, 2005 at 01:22:51AM +0200, nsapay_at_ibcp.fr wrote:
> > Dear VMD users,
> > I am working with a system made of water, peptides and membrane
> bilayers. I can
> > use tube, cylinder or cartoon representation for the peptide... But is
> there a
> > trick to represent lipid molecules in a fancier representation than CPK
> or VDW?
> > For example, if I rename carbon atoms of a POPC molecule in the same way
> than a
> > protein backbone, would it be possible to use the tube representation?
> In fact,
> > I am looking for a representation that "smoothes" the lipid hydrophobic
> tails
> >
> > Cheers
> >
> > Nicolas
> >
> > -------------------------------------------------
> > This mail sent through IMP: http://horde.org/imp/
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> 

--
Mauricio Carrillo Tripp, PhD
Department of Chemistry
Wabash College
trippm_at_wabash.edu
http://trippm.bajacast.com/