AMBER: large std error in entropy estimation

From: Ye Mei <ymei.itcc.nju.edu.cn>
Date: Wed, 22 Jun 2005 10:51:43 +0800

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.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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Received on Wed Jun 22 2005 - 04:53:00 PDT
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