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
> > >> 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 - 09:30:02 PDT
