AMBER Archive (2006)

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

From: Xioling Chuang (xioling_c_at_hotmail.com)
Date: Thu Jun 29 2006 - 04:38:58 CDT

Dear All,

I just finished MD simulation of DNA duplex. Next I would like to calculate
a binding free energy between 2 strands of the duplex using mm-pbsa. In
mm-pbsa script, I set one strand as receptor and another as ligand and I can
generate snapshots of complex, receptor and ligand. Then, I canculated free
energy with parameter GB=1 and I got energies like GB, GBsol, GBtot, etc. My
questions are
1). GBtot is binding free energy between two strands, isn't it?
2). If no, how can I calculate the binding free energy?

Thank you very much in advance for your kindness.

Best Regards,
Xioling

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