[gmx-users] Best Force Field for a Membrane Protein

[Anirban Ghosh]

Hi ALL,

Thanks a lot for the replies.
By long simulation I mean 500 ns to 1000 ns. Has anybody tried with the
ff43a1 with any membrane protein?

Thanks,

Anirban

On Fri, Apr 20, 2012 at 3:26 AM, Peter C. Lai <pcl at uab.edu> wrote:

> Define long simulations? CHARMM27/36 in the sub-100ns timescale works for
> us.
>
> The following paper:
> Vanni, S., Neri, M., Tavernelli, I., and Rothlisberger, U.: Predicting
> Novel Binding Modes of
> Agonists to Adrenergic Receptors Using All-Atom Molecular Dynamics
> Simulations. PLoS
> Comput Biol 7, e1001053 (2011)
>
> Uses Amber99SB over 500-800+ns for their beta2-adrenergic receptor system.
>
> On 2012-04-19 12:02:36PM +0530, Anirban Ghosh wrote:
> > Hi ALL,
> >
> > When running a membrane protein (say GPCR) in a lipid bilayer (say POPC
> or
> > DPPC etc.) which according to your experience is the most suited
> > force-field in GROMACS that best retains the 7TM / secondary structures
> of
> > the protein over long simulations? I have tried running with ff53a6 (as
> > suggested in Justin's tutorial), but find that the helices in the bilayer
> > tend to lose their helicity over time and turns into coils. ff43a2 seems
> to
> > do the job somewhat better by retaining the helicity. Will ff43a1 work
> even
> > better as the principle aim is to observe changes in the protein without
> > losing its secondary structures? Your experience please.
> > Thanks a lot in advance.
> >
> >
> > Regards,
> >
> > Anirban
>
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> --
> ==================================================================
> Peter C. Lai                    | University of Alabama-Birmingham
> Programmer/Analyst              | KAUL 752A
> Genetics, Div. of Research      | 705 South 20th Street
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