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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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
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> >
>
>
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Dec 26 2010 - 09:30:03 PST
