[gmx-users] Re: Fw: TM protein, lipids, force field
pyt1 at op.pl
Thu Mar 23 12:10:23 CET 2006
Thank you for advice.
I looked over the *.rtp file and I couldn't find POPC there. How can I
ffgmx topology file to newer GROMOS96 force field topology. Is it all right
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.
> 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
>> 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
>> Is it correct to use those parameters with newer forcefield like
>> Should I manually add new atom types for the DPPC molecules?
>> Thank you for your help.
>> All the best.
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