Thanks for reply.
Here stablity means I want to keep PROTEIN-DNA complex as such throughout the
REMD simulation.When I am heating this complex in MD simulation beyond 363.15K
complex getting dissociate.
Here I dont want to dissociate complex, I only want to see rondom coil to helix
transition.
Is it possible at 270 to 363.15K temperature range?
> in principle yes, but you need to watch it carefully. it's not clear whether
> you are quoting an experiment (hard to know if simulation model reproduces
> it, and furthermore what is meant by "stability"- the transition midpoint?
> if so, it may still dissociate below that T since it is an ensembler
> measurement) or if you quote simulation stability (unlikely that you know
> this yet)
>
>
> On Thu, Jan 13, 2011 at 1:30 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
>>
>> Hello all,
>>
>> I have a protein DNA complex, at the C terminus there is 13 residues random
>> coil, I want
>> to use here REMD to convert random coil into alpha helix.This complex is
>> stable
>> at 363.15K, so
>> can I use here this temperature 363.15K as maximum temperature to run REMD?
>>
>> With regard
>> Sangita Kachhap
>> JRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
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>
With regard
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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AMBER mailing list
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Received on Thu Jan 13 2011 - 20:30:03 PST
