I would strongly recommend you use PB 1, MM 1, MS 1 and NM 1 options for DNAs.
As for your questions,
1). GBtot is binding free energy between two strands, isn't it?
Delta GBtot= Delta Hgas + Delta Gsolvation
you need to add 1.79 to Delta GBtot to get Delta H of binding.
2). If no, how can I calculate the binding free energy?
If you use NM 1 option, then you should be able to see TSTOT (temp*Stot) in your mm-pbsa output. In that case,
DeltaG (of binding) = Delta H - (TSTOT)
hope this helps,
jenk
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Received on Sun Jul 02 2006 - 06:07:11 PDT
