Thanks allot, for your suggestions
On Tue, Jan 18, 2011 at 4:02 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > I have heated 10-mer DNA .I want to determine the melting point of
> > DNA. For this I want to plot a graph between No.of base pairs and
> > Temperature. How can I plot this graph using Amber10.
>
> I think you would need to do long runs at different temperatures,
> using ptraj to measure the average degree of base pairing at each
> temperature, plus the amount of deviation from the average. You'd
> have to decide whether a single H-bond counts as half a base pair.
> For each temperature, you would want to equilibrate for a while.
>
> Bill
>
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--
SHESH NATH
RESEARCH SCHOLAR,
THEORETICAL CONDENSED MATTER PHYSICS,
DEPARTMENT OF PHYSICS,
BANARAS HINDU UNIVERSITY,
VARANASI-221005
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Received on Mon Jan 17 2011 - 20:00:02 PST
