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
>>
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--
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
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Received on Wed May 28 2014 - 01:00:02 PDT
