VMD-L Mailing List

From: Akshay Patny (akshay17_at_olemiss.edu)
Date: Tue Sep 12 2006 - 16:05:04 CDT

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)
|>
|