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

[P]

Thank you for advice.
I looked over the *.rtp file and I couldn't find POPC there.   How can I 
rewrite DPPC
ffgmx topology file to newer GROMOS96 force field topology.  Is it all right 
to
change only the atom types to atom types present in GROMOS96
(please correct me if I am wrong).  Where can I get topology for
DPPC for GROMOS96 which I
could use for membrane-protein simulations.
All the best.

>
> Shalom,
>
> 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).
>
> Best,
> Itamar.
>
> 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.
>>