either follow examples in the literature, or use trial and error. there is
not a well determined protocol for what you propose.
On Mon, Jan 17, 2011 at 1:09 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
> Thanks for reply.
>
> But how then I decide maximum temperature range.Can I go for more then 400K
> because
> beyond this temperature complex get completely denatured.
>
> > 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
> >> >>
> >> >>
> >> >> _______________________________________________
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> >> >>
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
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> >> >
> >>
> >>
> >> 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
> >
>
>
> 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 - 10:30:06 PST
