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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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
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> >
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Received on Thu Jul 17 2014 - 13:00:03 PDT
