On 18 July 2014 13:05, James Starlight <jmsstarlight.gmail.com> wrote:
> Thanks alot!
>
> I'll try to check Rosetta. Does it like any software package or some
> options (e.g predictions and modeling) are available also as server ?
>
For the thing you want to do servers are useless. You have to look at the
tutorials in the Rosetta bundle as well as the Rosettacommons docs &
forums. This task requires a lot of reading a preparation.
BTW could someone tell me whether it possible to check in the ambler's amd
> log how much boost have been added to the system on each step ? (I've seen
> it on the NAMD logs)
>
>
>
## the amd.log file consists of the following lines:
Col1 col2 EPtot DIHED fwgt*EPtot fwgt*DIHED dV_EPtot dV_DIHED
# EPtot is the total potential energy (without the boost)
# DIHED is the total dihedral energy (without the boost)
# fwgt*EPtot factor by which total forces are scaled
# fwgt*DIHED factor by which dihedral forces are scaled
# dV_EPtot energy added by AMD to the total potential energy
# dV_DIHED energy added by AMD to the dihedral energies
>
> 2014-07-18 11:18 GMT+02:00 Thomas Evangelidis <tevang3.gmail.com>:
>
> > 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
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> >
> >
> >
> > --
> >
> > ======================================================================
> >
> > 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/
> > _______________________________________________
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> >
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--
======================================================================
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/
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Received on Fri Jul 18 2014 - 03:30:03 PDT
