Yes, there is no reason why you can't do a simulation with a protein in a
membrane in AMBER. I'm not aware of any tutorials on this topic, but there
are some web services where you can get the coordinate files for
pre-equilibrated membranes, this might be a good place to start.
On Tue, Dec 20, 2011 at 7:03 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> I'm not sure it's that simple- in principle, Amber can do membrane
> simulations and examples have been published. If one is thinking of a
> particular simulation method that is wanted to enforce aspects of membrane
> structure and perhaps stop the inaccurate force fields from doing bad
> things, then it's a different question than just whether Amber can actually
> run membrane simulations...
>
> On Tue, Dec 20, 2011 at 6:54 PM, Albert <mailmd2011.gmail.com> wrote:
>
> > As far as I know, Amber doesn't support membrane protein simulation. It
> > is said that the next version of Amber may update this function.
> >
> >
> >
> > On 12/20/2011 04:56 PM, Rajesh Singh wrote:
> > > Dear All,
> > >
> > > I am facing problems in performing MD of membrane proteins (GPCRs). I
> > would
> > > highly appreciate if anybody can provide me a tutorial for performing
> > > membrane dynamics using AMBER.
> > >
> > > Thanks and regards
> >
> >
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Received on Tue Dec 20 2011 - 16:30:03 PST
