From: Akshay Patny (
Date: Tue Sep 19 2006 - 16:19:59 CDT

Thank you very much Ting. That worked.





From: Ting Wang []
Sent: Tuesday, September 19, 2006 1:29 PM
Subject: Re: vmd-l: Centering GPCR onto Lipid Bilayer


Hi Akshay,



set sel [atomselect top "resname POPC"]

set com [measure center $sel] # you will get the mass center of membrane


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



----- Original Message -----

From: Akshay Patny <>


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 Patny

Graduate Research Assistant
Faser Hall 417, Department of Medicinal Chemistry

Research Institute of Pharmaceutical Sciences
University of Mississippi
University, MS 38677
Tel: 662-915-1286 (office); Web: