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.itcc.nju.edu.cn
2004-09-19
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Received on Sun Sep 19 2004 - 09:53:00 PDT
