VMD-L Mailing List

From: daniel aguayo (bioquimico_at_gmail.com)
Date: Wed Sep 13 2006 - 21:32:19 CDT

Here a script .

On 9/12/06, Akshay Patny <akshay17_at_olemiss.edu> wrote:
>
> Thanks, I appreciate that and I will give it a try.
> -Akshay
>
> |-----Original Message-----
> |From: Ting Wang [mailto:twang_at_ucdavis.edu]
> |Sent: Tuesday, September 12, 2006 4:04 PM
> |To: akshay17_at_olemiss.edu; vmd-l_at_ks.uiuc.edu
> |Subject: Re: vmd-l: protein in membrane
> |
> |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)
> |>
> |
>
>
> 

-- 
saludos desde el fin del mundo