I see, then yes you'll want dihedral restraints.
On Jul 17, 2014 12:04 PM, "James Starlight" <jmsstarlight.gmail.com> wrote:
> yes,
>
> but in my case no posres are applied on loops so I could prevent the
> rotation along peptide bond during its refirement with amd or other energy
> boost added method.
>
> James
>
>
> 2014-07-17 14:00 GMT+02:00 Carlos Simmerling <carlos.simmerling.gmail.com
> >:
>
> > The amber gb models don't support membranes or dual dielectric regions.
> You
> > could look into work by others like wonpil im.
> >
> > - there is no box, so volume is infinite and pressure not really defined.
> > -if the positional restraints are strong, no dihedral restraints should
> be
> > needed. You can add them, or just check as the run proceeds to make sure
> > those atoms aren't moving.
> > On Jul 17, 2014 7:50 AM, "James Starlight" <jmsstarlight.gmail.com>
> > wrote:
> >
> > > I think I have no more problems with the gb radii which I've found it
> in
> > > the manual :) but the question with the
> > >
> > > 0) cut-offs is still exist because in case of in vacuum simulation I
> use
> > > infitinive cutoffs but not sure what should I do in case of gb.
> > >
> > > Some additional question:
> > > 1) Does the simulation with gb support NPT besides NVT (I guess that
> > with
> > > the infinitive cutoffs it could be quite impossiblebut who knows:) )
> > >
> > > 2) I need to add restraints which will prohibit isomerisation of
> peptide
> > > bond (it's needed in case of amd or sa simulations) in loops. In this
> > > simulation I've already frize all atoms of not-loops by means of
> addition
> > >
> > > restraint_wt=10.0, restraintmask=':6-33,40-68,76-
> > > 109,120-143,177-204,216-246,256-286',
> > >
> > > so what should be provided besides to prevent rotation around omega
> > > dihedral angle?
> > >
> > >
> > > 3) Is there some additional options to GB for membrane protein
> simulation
> > > w/o application of restrains to membrane-embedded part (assuming that
> > some
> > > part of protein should be in fact in water with di-electric 80 and
> > another
> > > in membrane with di-electirc= 2 )? How it could be taken into the
> account
> > > in the GB simulation?
> > >
> > > TFH to everyone,
> > >
> > > James
> > >
> > >
> > > 2014-07-17 11:27 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
> > >
> > > > Thanks for suggestion!
> > > >
> > > > Do you think that gb 8 model (in comparison to other gb models) might
> > be
> > > > best solution for membrane protein with frozen *membrane embedded*
> > > elements
> > > > of its secondary structure? Some technical questions:
> > > > 1)should I use infinitive cutoffs (999) during IS simulation ?
> > > > 2) I'm not sure If I assigned gb radii correctly - does it should be
> > done
> > > > explicitly during processing of my model by tleap ? Are there special
> > > > values for the membrane proteins might be?
> > > >
> > > >
> > > > TFH,
> > > >
> > > >
> > > > James
> > > >
> > > >
> > > > 2014-07-16 17:37 GMT+02:00 Carlos Simmerling <
> > > carlos.simmerling.gmail.com>
> > > > :
> > > >
> > > > I think that if you choose a reasonably accurate GB model then this
> > task
> > > is
> > > >> much easier than with explicit water. Explicit may be more accurate,
> > but
> > > >> sampling loop conformational changes can be too slow. You always
> have
> > to
> > > >> trade off accuracy and sampling. I would suggest giving our igb=8
> > model
> > > a
> > > >> try (read the manual for suggestions on radii, etc). As always,
> you'll
> > > >> want
> > > >> to make sure you have some data against which you can validate any
> > > >> predictions that you make about structure. Regarding the REMD part,
> > it's
> > > >> another good reason to give GB a try. REMD in explicit water is
> > > expensive
> > > >> (many replicas) and quite slow. Freezing part could be a problem-
> I'm
> > > not
> > > >> sure if you can do that in all of the Amber MD codes (using the GB
> > pmemd
> > > >> code is probably best). You could choose positional restraints on
> the
> > > >> non-loop region to keep it fixed. Having it be totaly frozen might
> not
> > > be
> > > >> good anyway, since there may be some adjustment needed for different
> > > loop
> > > >> options.
> > > >>
> > > >> Another possibility is to use loop modeling that doesn't involve MD
> -
> > > such
> > > >> as the analytical approaches. Then you might rescore the various
> > models
> > > >> with a good MM+GBSA approach.
> > > >> good luck
> > > >> CS
> > > >>
> > > >>
> > > >> On Thu, Jul 10, 2014 at 5:44 AM, James Starlight <
> > > jmsstarlight.gmail.com>
> > > >> wrote:
> > > >>
> > > >> > some suggestions.
> > > >> >
> > > >> > some people gave me evidence that for my task (see a full set of
> > loop
> > > >> > confirmations and chose most probable) it will not good to use
> > > implicit
> > > >> > solvent +amd because this will produce very unphysical
> > thermodynamics
> > > >> isn't
> > > >> > it?
> > > >> >
> > > >> > In fact I'm dealing with the membrane protein where
> membrane-embeded
> > > >> part
> > > >> > should be fixed (I would not refine something here) and loops
> which
> > > are
> > > >> > exposed to the solvent must be free to move. In this regards I've
> > > tried
> > > >> to
> > > >> > applied gb model of IS with the frozen of not refined part of my
> > > >> protein.
> > > >> > Will it be reasonable to use REMD with such implicit solvent model
> > for
> > > >> the
> > > >> > refinement? How It could be possible to really simplify REMD
> > protocol
> > > >> for
> > > >> > such loop prediction (e,g using small number of replicas or not).
> > > >> > Some another suggestion (e.g brut force md with gb models)?
> > > >> >
> > > >> > James
> > > >> >
> > > >> >
> > > >> >
> > > >> > 2014-07-09 12:01 GMT+02:00 James Starlight <
> jmsstarlight.gmail.com
> > >:
> > > >> >
> > > >> > > some updating of my issue
> > > >> > >
> > > >> > > I need to refine regions of my model consisted of water exposed
> > > 10-15
> > > >> > > residues loops in which I'm not certain after its homology
> > modeling.
> > > >> For
> > > >> > > this task I'd like to
> > > >> > > 1) Freeze all atoms of the protein consisted of the secondary
> > > >> structure
> > > >> > > elements in which I'm not interest.
> > > >> > > 2)Use some implicit solvent model for this simulation.
> > > >> > > 3) Use some enhancing sampling technique to sample all possible
> > > >> > > conformation of the loops at short timescale but keeping initial
> > > >> > > thermodynamics of the system => predict possible folding in the
> > > loops
> > > >> > > during the refinement.
> > > >> > >
> > > >> > > please suggest me possible GB implicit solvent model as well as
> > > >> enhanced
> > > >> > > sampling engine (I'm chosing between replica exchange and
> > > accelerated
> > > >> md
> > > >> > > with dihedral boost only). Any additional methods?
> > > >> > >
> > > >> > > I'll be very thankful to all,
> > > >> > >
> > > >> > >
> > > >> > > James
> > > >> > >
> > > >> > >
> > > >> > > 2014-06-14 22:21 GMT+02:00 James Starlight <
> > jmsstarlight.gmail.com
> > > >:
> > > >> > >
> > > >> > > Also I'll be thankful if someone check my example SA script with
> > > >> applied
> > > >> > >> multiple position restraints to some segment of my protein
> (here
> > > I'd
> > > >> > like
> > > >> > >> to freeze all atoms but not loop which I'd like to sample).
> > > >> > >>
> > > >> > >> SA with posres
> > > >> > >> &cntrl
> > > >> > >> imin=0,
> > > >> > >> ntx=1,
> > > >> > >> irest=0,
> > > >> > >> ntc=2,
> > > >> > >> ntf=2,
> > > >> > >> tol=0.0000001,
> > > >> > >> nstlim=50000,
> > > >> > >> ntt=3,
> > > >> > >> gamma_ln=1.0,
> > > >> > >> ntr=1,
> > > >> > >> ig=-1,
> > > >> > >> ntpr=100,
> > > >> > >> ntwr=10000,
> > > >> > >> ntwx=100,
> > > >> > >> dt=0.002,
> > > >> > >> nmropt=1,
> > > >> > >> ntb=0,
> > > >> > >> ntp=0,
> > > >> > >> cut=999.0,
> > > >> > >> ioutfm=1,
> > > >> > >> ntxo=2,
> > > >> > >> igb=1,
> > > >> > >> /
> > > >> > >> &wt
> > > >> > >> type='TEMP0',
> > > >> > >> istep1=0,
> > > >> > >> istep2=10000,
> > > >> > >> value1=0.0,
> > > >> > >> value2=103.0 /
> > > >> > >> &wt
> > > >> > >> type='TEMP0',
> > > >> > >> istep1=10001,
> > > >> > >> istep2=20000,
> > > >> > >> value1=103.0,
> > > >> > >> value2=203.0 /
> > > >> > >> &wt
> > > >> > >> type='TEMP0',
> > > >> > >> istep1=20001,
> > > >> > >> istep2=50000,
> > > >> > >> value1=203.0,
> > > >> > >> value2=303.0 /
> > > >> > >> &wt type='END' /
> > > >> > >> fixed
> > > >> > >> 1000.0
> > > >> > >> RES 1 67
> > > >> > >> END
> > > >> > >> fixed
> > > >> > >> 1000.0
> > > >> > >> RES 75 142
> > > >> > >> END
> > > >> > >> fixed
> > > >> > >> 1000.0
> > > >> > >> RES 169 241
> > > >> > >> END
> > > >> > >> fixed
> > > >> > >> 1000.0
> > > >> > >> RES 249 286
> > > >> > >> END
> > > >> > >> END
> > > >> > >>
> > > >> > >>
> > > >> > >> Here I try to heat my system in 3 subsequent steps performing
> > > >> simulation
> > > >> > >> using implicit solvent without PBC. Does it correct in
> general? I
> > > >> could
> > > >> > not
> > > >> > >> visualize my system in VMD using
> > > >> > >> vmd -parm7 b2ar_Amber.prmtop -netcdf sa.nc
> > > >> > >> what should I fix here?
> > > >> > >>
> > > >> > >>
> > > >> > >> James
> > > >> > >>
> > > >> > >>
> > > >> > >> 2014-06-13 23:50 GMT+04:00 James Starlight <
> > jmsstarlight.gmail.com
> > > >:
> > > >> > >>
> > > >> > >> Dear Vlad,
> > > >> > >>>
> > > >> > >>>
> > > >> > >>> many thanks for suggestions. I've already seen some papers
> > > >> describing
> > > >> > >>> some methodologies of structural refinement based of some
> > enhanced
> > > >> > sampling
> > > >> > >>> methods. However in case of loop refinement what could be
> > expected
> > > >> > from the
> > > >> > >>> brute-force md with aplied restraints on the rest of the
> protein
> > > >> > (excluding
> > > >> > >>> refined loops) using 1) implicit solvent 2) some
> > > >> > high-temperatutre-based
> > > >> > >>> method like simulating annealing.
> > > >> > >>>
> > > >> > >>> James
> > > >> > >>>
> > > >> > >>>
> > > >> > >>> 2014-05-28 11:53 GMT+04:00 Vlad Cojocaru <
> > > >> > >>> vlad.cojocaru.mpi-muenster.mpg.de>:
> > > >> > >>>
> > > >> > >>> Dear James,
> > > >> > >>>>
> > > >> > >>>> I am afraid you'd have to do some reading ... Its very hard
> to
> > > >> believe
> > > >> > >>>> that somebody on this list has the time to give you detailed
> > > >> > >>>> instructions. What you ask for is a summary of many different
> > > >> papers.
> > > >> > >>>> The Amber manual has an example of simulated annealing
> protocol
> > > for
> > > >> > NMR
> > > >> > >>>> refinement which used to be with distance dependent
> dielectric
> > > >> (maybe
> > > >> > it
> > > >> > >>>> has changed in the meantime). Anyhow, you'd have to adapt
> that
> > to
> > > >> the
> > > >> > >>>> implicit solvent model you wish to use. The implicit solvent
> > > models
> > > >> > are
> > > >> > >>>> all well documented in the corresponding publications which
> are
> > > >> > >>>> referenced in the Amber manual.
> > > >> > >>>>
> > > >> > >>>> Besides, take care how you interpret your results. The longer
> > the
> > > >> > loops,
> > > >> > >>>> the less you can rely on the loop refinement. You'd need to
> > run a
> > > >> > number
> > > >> > >>>> of different simulations, maybe even test different force
> > fields
> > > >> ...
> > > >> > >>>> Especially if loops are functionally important, you may
> easily
> > > draw
> > > >> > >>>> wrong conclusions from such refinements. Comparison with
> > > >> experiments
> > > >> > is
> > > >> > >>>> always good.
> > > >> > >>>>
> > > >> > >>>> Best,
> > > >> > >>>> Vlad
> > > >> > >>>>
> > > >> > >>>>
> > > >> > >>>> On 05/28/2014 09:29 AM, James Starlight wrote:
> > > >> > >>>> > I try to specify my question.
> > > >> > >>>> >
> > > >> > >>>> > I suppose that force field based simulated annealing with
> > > >> positions
> > > >> > >>>> > restraints applied to the all protein atoms but not for
> loops
> > > >> which
> > > >> > >>>> I'd
> > > >> > >>>> > like to refine might be exactly what I'm looking for. Could
> > > >> someone
> > > >> > >>>> suggest
> > > >> > >>>> > appropriate SA setups for such loop refirement: e.g I'm
> > > >> interesting
> > > >> > in
> > > >> > >>>> > number of SA windows, coupling constants in each windows,
> > > >> > appropriate
> > > >> > >>>> > implicit solvent models?
> > > >> > >>>> >
> > > >> > >>>> >
> > > >> > >>>> > James
> > > >> > >>>> >
> > > >> > >>>> >
> > > >> > >>>> > 2014-05-26 14:06 GMT+04:00 James Starlight <
> > > >> jmsstarlight.gmail.com
> > > >> > >:
> > > >> > >>>> >
> > > >> > >>>> >> Dear Amber's users!
> > > >> > >>>> >>
> > > >> > >>>> >>
> > > >> > >>>> >> I need to refine some flexible regions (mainly long loop
> and
> > > >> linker
> > > >> > >>>> >> regions) of my proteins prior to the production MD run
> using
> > > >> some
> > > >> > >>>> enhanced
> > > >> > >>>> >> sampling engines implemented in Amber like accelerated
> > > molecular
> > > >> > >>>> dynamics
> > > >> > >>>> >> or simulated annealing. Please provide me with some basic
> > > >> ideas of
> > > >> > >>>> the
> > > >> > >>>> >> easiliest realization of these methods in amber including
> > > >> suitable
> > > >> > >>>> implicit
> > > >> > >>>> >> solvent models for such task with the tutorials and
> further
> > > >> > reading.
> > > >> > >>>> >>
> > > >> > >>>> >>
> > > >> > >>>> >> TFH,
> > > >> > >>>> >>
> > > >> > >>>> >> James
> > > >> > >>>> >>
> > > >> > >>>> > _______________________________________________
> > > >> > >>>> > AMBER mailing list
> > > >> > >>>> > AMBER.ambermd.org
> > > >> > >>>> > http://lists.ambermd.org/mailman/listinfo/amber
> > > >> > >>>> >
> > > >> > >>>>
> > > >> > >>>> --
> > > >> > >>>> Dr. Vlad Cojocaru
> > > >> > >>>> Max Planck Institute for Molecular Biomedicine
> > > >> > >>>> Department of Cell and Developmental Biology
> > > >> > >>>> Röntgenstrasse 20, 48149 Münster, Germany
> > > >> > >>>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> > > >> > >>>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> > > >> > >>>>
> > > >> > >>>>
> > > >> > >>>> _______________________________________________
> > > >> > >>>> 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
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> > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>
> > > >
> > > >
> > > _______________________________________________
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Received on Thu Jul 17 2014 - 10:30:03 PDT
