[gmx-users] POPC membrane simulations

[maite lopez]

Hi Chris:

I´ve created my own dppc.itp using the ffG53a5 force field. I did that
running  only a dppc lipid of the membrane that is available on
Tieleman's site and i included it on my topology file and of course
put in it the number of dppc molecules . i haven´t had any problem
with this simulation. I didn´t use the dppc.itp of the Tieleman's
site.

But the topology of the popc isn´t on the gromacs database, for this i
can´t do the same. How the difference between dppc and popc lipids are
few  atoms in the oleoyl chain i thougth i could to converter my own
only_a_lipid_dppc.itp file into popc.itp file. That´s why the popc.itp
file of the Tieleman's site was done with ffgmx force field.

I think that i can to use the lipid.itp of the Tieleman's site and to
converter it  into ffG53a5 force field how you explain me. But my
question is :
Can i to obtain  my own  only_a_lipid_popc.itp file from my dppc.itp
and do the same such as my dppc simulation?
How could i do this?

Cheers,
Maite



On 3/22/07, Chris Neale <chris.neale at utoronto.ca> wrote:
If I understand correctly you want to construct popc.itp from the
> dppc.itp that is available on Tieleman's site? And you have used PRODRG
> to do this? That sounds like a lot of extra work when popc.itp is
> directly available from Tieleman's site...
> http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
>
> The fact that you want to use ffG53a5 and not ffgmx is more of an issue.
> To do that you need to avoid lipid.itp and do something like this:
> http://www.gromacs.org/pipermail/gmx-users/2006-September/023639.html
> However, you will want to heed this warning (or at least understand it):
> http://www.gromacs.org/pipermail/gmx-users/2006-September/023640.html
>
> Chris.
>
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