> 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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Received on Mon Jan 17 2011 - 15:00:04 PST
