VMD-L Mailing List

From: Ting Wang (twang_at_ucdavis.edu)
Date: Tue Sep 19 2006 - 13:28:40 CDT

Hi Akshay,

1.
set sel [atomselect top "resname POPC"]
set com [measure center $sel] # you will get the mass center of membrane x1,y1,z1

2. do the same the get the mass center of the protein-> x2, y2, z2

3. set sel [atomselect top protein]
    $sel move [transoffset {x1-x2,y1-y2,z2-z3} ]

Now, the protein should be at the mass center of the membrane

Ting
  ----- Original Message -----
  From: Akshay Patny
  To: vmd-l_at_ks.uiuc.edu
  Sent: Monday, September 18, 2006 12:28 PM
  Subject: vmd-l: Centering GPCR onto Lipid Bilayer

  Hi VMD users

   

  I am trying to embed my GPCR protein in the POPC bilayer made from the membrane plug-in of VMD.

   

  I have aligned the Z-axis of my GPCR along the longest principal axis of the TM domain.

   

  Now I want to translate my protein to the correct center of the bilayer. I know I can manually translate the protein to the center of the bilayer. However, I was curious if there is some way to calculate and then align them according to the center (of mass etc.) of the bilayer and the protein, which might be more accurate?

   

  I would appreciate suggestions.

   

  Thanks and Regards

  Akshay

   

  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