[gmx-users] DPPC,Water,Protein?

[Martina Bertsch, PhD]

Dear Blaise,

To embed a protein into a membrane model, you could try the mdrun program modified by Drs. Tieleman and Smith, available at:

http://www.gromacs.org/contributions/index.php

(Look for mdrun_make_hole.tar.gz <http://www.gromacs.org/contributions/uploaded_contributions/mdrun_make_hole.tar.gz>). A tutorial will be included in share/tutor/make_hole upon installation.

You will also need to generate accessible molecular surface for your protein with GRASP or MSMS (see tutorial). 

Finally, in your share/top directory, you should include the newest ffgmx_lipids.tar.gz
available at:

http://gromacs.org/topologies/force_fields.php

that incorporates the parameters from the lipid.itp.

Kind regards,

Martina Bertsch, Ph.D.
Northwestern University
Feinberg School of Medicine
Molecular Pharmacology and Biological Chemistry
303 East Chicago Avenue
Chicago, IL 60611

Stud_Psychopharm wrote:

>Dear All,
>I could able to get 128 DPPC (lipid) with water molecules from tielemans 
>site, now I want place my protein (tetramer) into that by removing some 
>number of lipid and water molecules. Is there any program to do that job. 
>Please give soem idea. Many thanks in advance.
>Regards,
>Blaise M Costa.
>------------------------------------------------------------
>"The more we learn the more we realize how little we know." - 
>R.Buckminster Fuller 
>
>Blaise M.
>Graduate Student,
>Department of Psychopharmacology,
>National Institute of Mental Health And Neuro Sciences (NIMHANS),
>Bangalore-560029,
>India. Tel: 91 80 6995112.
>
>
>
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