From: Ting Wang (twang_at_ucdavis.edu)
Date: Tue Sep 12 2006 - 16:03:43 CDT

http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/orient/

best,

Ting
----- Original Message -----
From: "Akshay Patny" <akshay17_at_olemiss.edu>
To: "'Ting Wang'" <twang_at_ucdavis.edu>; <vmd-l_at_ks.uiuc.edu>
Sent: Tuesday, September 12, 2006 1:45 PM
Subject: RE: vmd-l: protein in membrane

> Hi Ting
>
> I have a similar problem to embed my GPCR protein into the membrane. Can
> you
> tell me where I can find the scripts you mentioned: auto_path.txt and
> align_axies.txt?
>
> That would be helpful to me.
>
> Thanks very much.
> 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
>
> |-----Original Message-----
> |From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf
> Of
> |Ting Wang
> |Sent: Tuesday, September 12, 2006 1:58 PM
> |To: javier.vallejos_at_correo.usach.cl; vmd-l_at_ks.uiuc.edu
> |Subject: Re: vmd-l: protein in membrane
> |
> |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)
>