VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Thu Sep 14 2006 - 18:11:28 CDT

What about the suggestion made by Alessadro?? Here is his post:

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/4514.html

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
>
>