Thanks alot!
In my case using GB model I applied restraints on the membrane-embedded
part because I'd like to look at the loops (water-assesible regions) of the
protein to refine it. I'm not sure that It would be best solution but this
time I need for simplest protocol for loop sampling in NVT not focusing on
conformation dynamics of the rest of the protein and the membrane in these
models.
I'll be also thankful for any coments in the adjacent topic where I deal
with the aenhansed sampling methods + implicit solvent for such system.
James
2014-07-17 22:27 GMT+04:00 Ray Luo, Ph.D. <ray.luo.uci.edu>:
> I think the only IS model supporting membrane proteins up to amber14
> is the pb model with appropriate options set up. It doesn't work with
> MD, only for mmpbsa type of jobs.
>
> Ray
> --
> Ray Luo, Ph.D.
> Professor,
> Biochemistry, Molecular Biophysics, and
> Biomedical Engineering
> University of California, Irvine, CA 92697-3900
>
>
> On Thu, Jul 17, 2014 at 12:21 AM, James Starlight
> <jmsstarlight.gmail.com> wrote:
> > Dear Amber users!
> >
> > I'd like to use some IS amber model for the simulation of the membrane
> > protein. In particular I'd like to do NVT simulation with the applied
> > position restraints on all secondary structure elements of my protein (to
> > prevent conformation changes in its)
> >
> > restraint_wt=10.0,
> > restraintmask=':6-33,40-68,76-109,120-143,177-204,216-246,256-286',
> >
> > to refine only flexible loop parts of my model
> >
> > I'll be very thankful if someone have made simulation of any membrane
> > proteins using one of the gb models and could give me some suggestions
> > regarding most suitable gb model for this case.
> >
> >
> > James
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Received on Thu Jul 17 2014 - 13:00:02 PDT
