VMD-L Mailing List

From: Ting Wang (twang_at_ucdavis.edu)
Date: Tue Sep 12 2006 - 13:58:07 CDT

Hi,

My experience is :

1. Align the protein along VMD principal axes by using scrcipts
auto_path.txt and align_axies.txt.

2. Generate the membrane in VMD

3. Translate the protein to the center of the membrane

4. Combine the protein and the membrance and delete overlaped lipid and
water. To do this, you have to
    generate a psf for pure protein without ACE, HOH and et.al. If
combine.tcl cannot work, you can delete overlaped lipid manually (still
writing a script to specify the distance cutoff).

Ting

----- Original Message -----
From: <javier.vallejos_at_correo.usach.cl>
To: <vmd-l_at_ks.uiuc.edu>
Sent: Friday, September 08, 2006 3:35 PM
Subject: vmd-l: protein in membrane

>
> Can anyone tell me how can I embedding protein in any membrane??
>
>
>
>
> Saludos
> Javier Vallejos M
> Graduate Student
> University of Santiago of Chile
> (USACH)