Thanks a lot!
So here in the last column I can see boost per step in Kcal/mol? E.g for my
case
1000 15000 -3339.037810938433 3346.880069911480
1.000000000000 0.881741826846 0.000000000000
1.342196467672
1000 16000 -3301.976663347334 3339.000675370917
1.000000000000 0.820532227813 0.000000000000
3.316964357365
1000 17000 -3277.236140196212 3334.818359776400
1.000000000000 0.790599030330 0.000000000000
4.681968598956
1000 18000 -3295.561143518426 3319.090689167380
1.000000000000 0.691535397563 0.000000000000
11.556700614196
1000 19000 -3269.387649601325 3343.012569249608
1.000000000000 0.850872254539 0.000000000000
2.210395094728
just up to 11.5 kcal/mol have been added to ALL protein haven't it? Might
it be assumed that boost have been added to the loops only (if I add
restrains to the all rest atoms) or not? If not I think I should to
increase boost up to several times. It's intresting that with such low
boost I've seen in my md folding of the loops into the helix fragments on
several tens of nanoseconds. It seems not very physically-based for me :)
James
2014-07-18 12:22 GMT+02:00 Thomas Evangelidis <tevang3.gmail.com>:
> 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
> > > > > > > > _______________________________________________
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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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>
>
> --
>
> ======================================================================
>
> 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 - 04:00:02 PDT
