you may be better off applying some restraints to the part of the complex
that you wish to retain. one observation of dissociation in an MD run does
not mean it's the transition temperature.
On Thu, Jan 13, 2011 at 11:23 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
> 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
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> With regard
> 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 Mon Jan 17 2011 - 10:00:02 PST
