AMBER Archive (2006)

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

From: Xioling Chuang (
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,

Express yourself instantly with MSN Messenger! Download today it's FREE!

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to