OK Thanks for reply
> before determining the # of replicas, you need to first decide the
> temperature range you are going to use. the low end often corresponds to
> something where you want to compare to an experiment, and the high end is
> determined by what temperature you need to improve sampling. in your case,
> this will be an important consideration because you don't want to unfold
> your protein or dissociate the complex or denature the DNA. this will be one
> of the most important decisions in your project and will require testing adn
> careful reading of the literature.
>
> On Sat, Dec 25, 2010 at 2:07 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
>>
>> Thanks for reply,I will go through the literature.
>> yes I have protien-DNA complex of 2688 total atoms 87 amino acid protein
>> and 20
>> base pair
>> DNA.I modelled 87 a.a residues protein have 16 residues C-terminus random
>> coil
>> then I docked it
>> onto 20bp DNA. Now I want to see folding of this random coil,into alpha
>> helix by
>> REMD.
>>
>>
>> > I strongly recommend reading literature on REMD and following procedures
>> in
>> > similar work.
>> > The number of replicas scales with system size- it isn't the sq root
>> > directly. There are many ways to calculate number of replicas, most
>> > depending on the potential energy of the system and how is scales with
>> > temperature.
>> > It's not clear to me how a protein-DNA complex is only 2688 atoms. If you
>> > can be more specific about exactly what you are doing we may be able to
>> help
>> > more.
>> >
>> > On Sat, Dec 25, 2010 at 7:53 AM, Sangita Kachhap <sangita.imtech.res.in
>> >wrote:
>> >
>> >>
>> >> Hello all
>> >>
>> >> I have a modelled protein - DNA complex in protein C-terminus has 16
>> >> residues
>> >> radom coil.
>> >> It is hypothesized that this region folds into a alpha helix when bound
>> to
>> >> DNA.So here I
>> >> want to use REMD.It has total 2688 atoms as first step is to determine
>> >> number of
>> >> replicas.
>> >> As according to amber tutorial :-
>> >> http://ambermd.org/tutorials/advanced/tutorial7/
>> >> number of replica is determine according to square root of number of
>> total
>> >> atoms, as my
>> >> sytem have total 2688 atoms and its square root is ~51 so should I
>> consider
>> >> number of replica
>> >> 51?
>> >>
>> >> So kindly suggest me.
>> >>
>> >> With regard
>> >> Sangita Kachhap
>> >> JRF
>> >> BIC,IMTECH
>> >> CHANDIGARH
>> >>
>> >>
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>> >
>>
>>
>> Sangita Kachhap
>> JRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Mon Dec 27 2010 - 08:30:02 PST
