VMD-L Mailing List

From: Ting Wang (twang_at_ucdavis.edu)
Date: Thu Sep 14 2006 - 17:27:55 CDT

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