In implicit solvent aMD simulations you boost only the dihedrals.
However, I would do what you want with Rosetta membrane module (loop
modeling with the core of the protein restrained), and then start MD from
one or more models that I like.
On 18 July 2014 12:06, James Starlight <jmsstarlight.gmail.com> wrote:
> 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
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jul 18 2014 - 02:30:04 PDT
