VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun May 06 2007 - 23:49:40 CDT

Hi,
  We need more information on what you're doing in order to help you.
What EMBO course are you working through? Can you at least post a URL
for us so we can see what you're attempting to do? Without such basic
information nobody will be able to come up with a guess as to
what your problem is. Are you actually using VMD for any of this process?
You've mentioned running some Gromacs tools, but I don't know what
steps, if any, you're doing with VMD. If this isn't a VMD question, then
I would suggest contacting the authors of the EMBO course as they would
be the most likely to have direct knowledge of the tasks you are trying
to perform.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, May 07, 2007 at 05:29:45AM +0100, nur avneet wrote:
> Dear all
> Please guide me how can we align a protein normal to the lipid bilayer and then merge the two to tart a simulation with gromacs.
> I have followed EMBO course, 2004 available online...it works well when i align the protein parallel to the bilayer but when i align the protein normal to the bilayer it fails.
> i place the protein normal to the bilayer (manually, by eye) and then save the coordinates of the protein. Next i copy the CRYST line from my lipid pdb file into the protein pdb file to place it in the lipid box. Then i give the genbox command of gromacs to combine the protein and lipid into one pdb. But the structure that is shown after i give this command does not show the protein in the location i placed it at.
> I v tried repeating it so many times, but the same happens when i place the protein normal to the bilayer but not when it is parallel.
>
> Can anyone guide me through..
>
> regards
> nur
>
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078