[gmx-users] Fw: TM protein, lipids, force field

Itamar Kass ikass at cc.huji.ac.il
Wed Mar 22 18:52:34 CET 2006


In the lab I work in, we use DMPC and the GROMOS87 ff (see Tieleman site).

I saw that POPC is represented in the new ff (GROMOS96), so you might try it, or
build your top file using the atoms found at the ff files (as lego).


Quoting P <pyt1 at op.pl>:

> Dear Gromacs Users.
> I'm new gromacs user and I would be glad to get some advice from you.
> I wan to do MD of TM-protein in DPPC lipid bilayer and then I would
> like to investigate interactions between this protein and the ions present in
> the system.
> I've read the manual and checked mailing list but some things are still not
> clear to me.
> Which forcefield should I use for the protein and membrane simulation.
> I found parameters for DPPC lipids but  only for ffgmx forcefield
> (lipid.itp).
>  Is it correct to use those parameters with newer forcefield like GROMOS96
> 43a1.
>  Should I manually add new atom types for the DPPC molecules?
> Thank you for your help.
> All the best.

| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
| Department of Biological Chemistry
| The Hebrew University, Givat-Ram
| Jerusalem, 91904, Israel
| Tel: +972-(0)2-6585194
| Fax: +972-(0)2-6584329
| Email: ikass at cc.huji.ac.il
| Net: http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html

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