AMBER Archive (2004)

Subject: AMBER: More details about free energy

From: Xiao He (hx_at_itcc.nju.edu.cn)
Date: Sun Sep 19 2004 - 03:02:53 CDT

Dear Amber users,

  I'm a doctoral student in NJU,and now doing a project on binding free energy calculations for drug-protein interaction.
  I read your paper

J. Wang, P. Morin, W. Wang & P.A. Kollman. Use of MM-PBSA in Reproducing the
Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode
to HIV-1 RT of Efavirenz by Docking and MM-PBSA. J. Am. Chem. Soc.
123, 5221-5230 (2001).

I have several questions:
In equation
deltaG(binding)=deltaE(intra)+deltaE(electrostatic)+deltaE(vdW)-T*deltaS+deltadeltaG(PB)+deltadeltaG(SA)

Now I can use Amber to solve deltaE(electrostatic),deltaE(vdW).
How do you use the NMODE to get the deltaS,and MM-PBSA to get the deltadeltaG(PB) with deltadeltaG(SA)?

Thanks a lot!

Regards!
　　　　　　　　Xiao He
　　　　　　　　hx_at_itcc.nju.edu.cn
　　　　　　　　　　2004-09-19

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