From: Chris Harrison (
Date: Wed Feb 29 2012 - 21:35:28 CST

What do you mean the position is "not correct?" Please be more specific.
 The protein is too high/low in the membrane; the protein is at an
incorrect angle to the membrane's normal axis; there's a big gap of lipids
between protein and the membrane that floods with water; etc ....

On Wed, Feb 29, 2012 at 3:33 PM, Albert <> wrote:

> Hello:
> I've superimposed my homology models with related OPM protein. And now I
> would like to embed my protein to pre-equilibrated membrane POPE from
> But I found that the position is not correct for the membrane.... Does
> anybody have any idea how to do it? I am going to use CHARMM36 based POPE
> for my aligned protein.

Chris Harrison, Ph.D.
NIH Center for Macromolecular Modeling and Bioinformatics
Theoretical and Computational Biophysics Group
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801       Voice: 773-570-6078                          Fax: 217-244-6078