[AMBER] can thermodynamics integration be used for calculating binding free energy of peptides and proteins?

From: <sunyeping.aliyun.com>
Date: Sun, 28 Jul 2013 00:24:35 +0800

Dear AMBER users?
I have read the amber tutorial  "small molecules binding to T4 lysozyme" and learned TI method to calculating the energy difference between benzene and phenol binding to  T4. I am considering whether the same method can be used to  calculate binding free energy of a peptide and a protein. If it can, should I make a certain mutation to the peptide, as done in the tutorial, mutating  benzene to phenol? Dose anyone has a more relevent tutorial to complete my task? Thanks in advance.
Yeping Sun
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Received on Sat Jul 27 2013 - 09:30:03 PDT
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