VMD-L Mailing List

From: Akshay Patny (akshay17_at_olemiss.edu)
Date: Tue Sep 12 2006 - 15:45:31 CDT

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)