AMBER Archive (2005)

Subject: AMBER: large std error in entropy estimation

From: Ye Mei (ymei_at_itcc.nju.edu.cn)
Date: Tue Jun 21 2005 - 21:51:43 CDT

Dear amber users£¬

I am trying to calculate the binding free energy of a drug molecule to a certain peptide. I used the mm_pbsa module in amber8. But the vibrational contribution to entropy(times T) often has very large std error, like -3.00+/-13.00Kcal/mol. Even though I pick out 20 snapshots from last 5 picoseconds when the system already in equilibrium.
What is your idea about this large std error? Or is there any way to improve it?

¡¡¡¡¡¡¡¡¡¡¡¡
                                 
Best regards,

Ye Mei
ymei_at_itcc.nju.edu.cn
Institute of Theoretical and Computational Chemistry
Key Laboratory of Mesoscopic Chemistry
School of Chemistry and Chemical Engineering
Nanjing University
Nanjing 210093
P.R.China
2005-06-22

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