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
>>
>
>
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Received on Sat Jun 14 2014 - 13:30:02 PDT
