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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Sat Dec 25 2010 - 11:30:02 PST
