VMD-L Mailing List

From: nur avneet (nuravneet_at_yahoo.co.in)
Date: Sun May 06 2007 - 23:29:45 CDT

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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