Hi Carlos,
I didnt find any reasonable suggestion about how to chose boost values for
amd for the implicit solvent simulation (the formuli presented in manual
are for explicit solvent). I guess it will be extremely hardly to tune this
parameters (expecially for double boost) for membrane protein simulation in
gb model and amd.
James
2014-07-17 21:55 GMT+02:00 Carlos Simmerling <carlos.simmerling.gmail.com>:
> since not everyone reads the Amber list carefully, a suggestion might be to
> look for people that have published work on the amd or other methods, and
> see if they can offer some suggestions. I haven't used it, and I know
> others here have, but might not be paying attention to these threads.
>
>
> On Thu, Jul 17, 2014 at 3:51 PM, James Starlight <jmsstarlight.gmail.com>
> wrote:
>
> > 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 Fri Jul 18 2014 - 02:30:03 PDT
