VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Sep 14 2006 - 18:26:45 CDT

On 9/14/06, L. Michel Espinoza-Fonseca <mef_at_ddt.biochem.umn.edu> wrote:
> What about the suggestion made by Alessadro?? Here is his post:
>
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/4514.html

furthermore, from looking a the code it seems, that with rather little
effort, the membrane plugin in VMD could be taught to handle
additional lipids, if the corresponding parameters and pre-equilibrated
configurations do exitst. it looks rather modular...

any takers?

axel.

>
> Michel
>
>
> 2006/9/14, Ting Wang <twang_at_ucdavis.edu>:
> >
> >
> > Hi Akshay,
> >
> > VMD can not generate DPPC bilayer. Peter Tieleman's coordinates are fine but
> > you will probably later have problems of embedding your protein into the
> > membrane. A easier way is to generate POPC bilayer in VMD and use VMD
> > scripts to do later on jobs. I have 118 POPC lipids for my GPCR protein.
> >
> > Ting
> >
> > ----- Original Message -----
> > From: Akshay Patny
> > To: vmd-l_at_ks.uiuc.edu
> > Sent: Thursday, September 14, 2006 11:49 AM
> > Subject: vmd-l: DPPC Bilayer Size
> >
> >
> >
> >
> > Hi All
> >
> >
> >
> > I am trying to simulate a GPCR protein belonging to the rhodopsin family
> > with amino acid length of 320 residues. Also, I would be using the
> > pre-hydrated DPPC bilayer, can somebody suggest that for a GPCR protein of
> > roughly 320 aa, how big DPPC bilayer would be appropriate to use e.g. 128
> > DPPC bilayer is available from Peter Tieleman's website
> > http://moose.bio.ucalgary.ca/index.php?page=Main .
> >
> >
> >
> > Also, can VMD 'membrane' van generate DPPC bilayer?
> >
> >
> >
> > Thanks
> >
> > Akshay Patny
> >
> >
> >
> > Graduate Research Assistant
> > Faser Hall 417, Department of Medicinal Chemistry
> >
> > Research Institute of Pharmaceutical Sciences
> > University of Mississippi
> > University, MS 38677
> > E-mail: akshay17_at_olemiss.edu
> > Tel: 662-915-1286 (office); Web: www.olemiss.edu
> >
> >
>
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.