AMBER Archive (2006)

Subject: Re: AMBER: How to calculate binding free energy using MM-PBSA

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Thu Jun 29 2006 - 05:38:11 CDT

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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