VMD-L Mailing List

From: Stéphane Téletchéa (steletch_at_jouy.inra.fr)
Date: Mon May 07 2007 - 03:44:36 CDT

nur avneet a écrit :
> 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.
>
> Can anyone guide me through..
>
> regards
> nur

I assume you're using gromacs. You'll probably need to have a look at
the excellent paper written by P. Tieleman:

C. Kandt, W.L. Ash, D.P. Tieleman. 2007. Setting up and running membrane
protein simulations, Methods 41, pp. 475-488

He developped inflategro who will probably solve most of your problems
(conjugated with the above paper).

Cheers,
Stéphane 

-- 
Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901